WO2014093655A2 - Engineering and optimization of systems, methods and compositions for sequence manipulation with functional domains - Google Patents

Abstract

The invention provides for engineering and optimization of systems, methods, and compositions for manipulation of sequences and/or activities of target sequences. Provided are vectors and vector systems, some of which encode one or more components of a CRISPR complex, as well as methods for the design and use of such vectors with additional functional domains. Also provided are methods of directing CRISPR complex formation in prokaryotic and eukaryotic cells to ensure enhanced specificity for target recognition and avoidance of toxicity.

Description

RELATED APPLICATIONS AND INCORPORATION BY REFERENCE

[001] This application claims priority to LIS provisional patent applicatio 61/835,936 entitled ENG INEERING AND OPTI MIZATION OF SYSTEMS, METHODS AND COMPOSITIONS FOR SEQUENCE MANIPULATION WITH FUNCTIONAL DOMAINS FILED ON JUNE 17, 2013. This application also claims priority to US provisional patent applications 61/758,468; 61/769,046; 61/802,174; 61/806,375; 61/814,263; 61/819,803 and 61/828,130 each entitled ENGINEERING AND OPTIMIZATION OF SYSTEMS, METHODS AND COMPOSITIONS FOR SEQUENCE MANIPULATION, filed on January 30, 2013; February 25, 2013; March 15, 2013; March 28, 2013; April 20, 2013; May 6, 2013 and May 28, 2013 respectively. Priority is also claimed to US provisional patent applications 61 /736,527 and 61/748,427, both e titled SYSTEMS METHODS AND COMPOSITIONS FOR SEQUENCE MANIPULATION filed on December 12, 2012 and January 2, 2013, respectively. Priority is also claimed to LIS provisional patent applications 61/791,409 and 61/835,931 both entitled BI- 2011/008/44790.02.2003 and BI-2011/008/44790.03.2003 filed on March 15, 2013 and June 17, 2013 respectively.

[002] Reference is also made to US provisional patent applications 61/836,127, 61/836,101 , 61 /836,080, 61/836, 123, and 61/835,973 each filed June 17, 2013.

[003] The foregoing applications, and all documents cited therein or during their prosecution ("appln cited documents") and all documents cited or referenced in the appln cited documents, and all documents cited or referenced herein ("herein cited documents"), and all documents cited or referenced in herein cited documents, together with any manufacturer's instructions, descriptions, product specifications, and product sheets for any products mentioned herein or in any document incorporated by reference herein, are hereby incorporated herein by reference, and may be employed in the practice of the invention. More specifically, all referenced documents are incorporated by reference to the same extent as if each individual document was specifically and individual Sy indicated to be incorporated by reference. FIELD OF THE INVENTION

[004] The present invention generally relates to the engineering and optimization of systems, methods and compositions used for the control of gene expression involving sequence targeting, such as genome perturbation or gene-editing, that relate to Clustered Regularly- Interspaced Short Palindromic Repeats (CRISPR) and components thereof.

STATEMENT AS TO FEDERALLY SPONSORED RESEARCH

[005] This invention was made with government support under the NIH Pioneer Award (1 DPI MB 100706) awarded by the National Institutes of Health. The government has certain rights in the invention.

BACKGROUND OF THE INVENTION

[006] Recent advances in genome sequencing techniques and analysis methods have significantly accelerated the ability to catalog and map genetic factors associated with a diverse range of biological functions and diseases. Precise genome targeting technologies are needed to enable systematic reverse engineering of causal genetic variations by allowing selective perturbation of individual genetic elements, as well as to advance synthetic biology, biotechnological, and medical applications. Although genome-editing techniques such as designer zinc fingers, transcription activator-like effectors (TALEs), or homing meganuelcascs are available for producing targeted genome perturbations, there remains a need for new genome engineering technologies that are affordable, easy to set up, scalable, and amenable to targeting multiple positions within the eukaryotic genome.

SUMMARY OF THE IN VENTION

[007] The CRISPR/Cas or the CRISPR-Cas system (both terms are used interchangeably throughout this application) does not require the generation of customized proteins to target specific sequences but rather a single Cas enzyme can be programmed by a short RNA molecule to recognize a specific DNA target, in other words the Cas enzyme can be recruited to a specific DNA target using said short RNA. molecule. Adding the CRISPR -Cas system to the repertoire of genome sequencing techniques and analysis methods may significantly simplify the methodology and accelerate the ability to catalog and map genetic factors associated with a diverse range of biological functions and diseases. To utilize the CR ISPR-Cas system effectively for genome editing without deleterious effects, it is critical to understand aspects of engineering and optimization of these genome engineering tools, which are aspects of the claimed invention.

[008] There exists a pressing need for alternative and robust systems and techniques for sequence targeting with a wide array of applications. Aspects of this invention address this need and provide related advantages. An exemplary CRISPR complex may comprise a CRISPR enzyme complexed with a guide sequence hybridized to a target sequence within the target polynucleotide. The guide sequence is linked to a tracr mate sequence, which in turn hybridizes to a tracr sequence.

[009] In one aspect, the invention relates to one or more elements of a CRISPR system having improved or modified functionality. The CRISPR complex of the invention provides an effective means for modifying a target polynucleotide. The CRISPR complex of the invention has a wide variety of utilities including modifying (e.g., deleting, inserting, translocating, inactivating, activating) a target polynucleotide in a multiplicity of cell types. As suc the CRISPR complex of the invention has a broad spectrum of applications in, e.g., gene or genome editing, gene therapy, drug discovery, drug screening, disease diagnosis, and prognosis. An exemplar}⁷ CRISPR complex may comprise a CRISPR enzyme complexed with a guide sequence hybridized to a target sequence within the target polynucleotide. The guide sequence is linked to a tracr mate sequence, which in turn hybridizes to a tracr sequence.

[0010] In some embodiments, a CRISPR/Cas system may comprise: (a) a first regulatory element operably linked to a tracr mate sequence and one or more insertion sites for inserting one or more guide sequences upstream of the tracr mate sequence, wherein when expressed, the guide sequence directs sequence-specific binding of a CRISPR complex to a target sequence in a eukaryotic cell, wherein the CRISPR complex may comprise a CRISPR enzyme complexed with (1) the guide sequence that is hybridized to the target sequence, and (2) the tracr mate sequence that is hybridized to the tracr sequence; and (b) a second regulator}' element operably linked to an enzyme-coding sequence encoding said CRISPR enzyme which may comprise a nuclear localization sequence; wherein components (a) and (b) are located on the same or different vectors of the system. In some embodiments, component (a) further may comprise the tracr sequence downstream of the tracr mate sequence under the control of the first regulatory element. In some embodiments, component (a) further may comprise two or more guide sequences operably linked to the first regulatory element, wherein when expressed, each of the two or more guide sequences direct sequence specific binding of a CRISPR comple to a different target sequence in a eukaryotie cell. In some embodiments, the system may comprise the tracr sequence under the control of a third regulatory element, such as a polymerase III promoter. In some embodiments, the tracr sequence exhibits at least 50%, 60%, 70%, 80%, 90%, 95%, or 99% of sequence complementarity along the length of the tracr mate sequence when optimally aligned. In some embodiments, the CRISPR enzyme may comprise one or more nuclear localization sequences of sufficient strength to drive accumulation of said CRISPR enzyme in a detectable amount in the nucleus of a eukaryotie cell. Without wishing to be bound by theory, it is believed that a nuclear localization sequence is not necessary for CRISPR activity in eukaryotes, but that including such sequences enhances activity of the system. In some embodiments, the CR ISPR enzyme is a type I I CRISPR system enzyme. In some embodiments, the CRISPR enzyme is a Cas9 enzyme. In some embodiments, the Cas9 enzyme is S. pyogenes or S. thermopkilus Cas9, and may include mutated Cas9 derived from either of these organisms. The enzyme may be a Cas9 homolog or ortholog. In some embodiments, the CRISPR enzyme is codon-optimized for expression in a eukaryotie cell. In some embodiments, the CRISPR enzyme directs cleavage of one or two strands at the location of the target sequence. In some embodiments, the CRISPR enzyme lacks DNA. strand cleavage activity. In some embodiments, the first regulatory element is a polymerase III promoter. In some embodiments, the second regulatory element is a polymerase II promoter. In some embodiments, the guide sequence is at least 15, 16, 17, 18, 19, 20, 25 nucleotides, or between 10-30, or between 15-25, or between 15- 20 nucleotides in length. In general, and throughout this specification, the term ''vector" refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. Vectors include, but are not limited to, nucleic acid molecules that are single-stranded, double- stranded, or partially double-stranded; nucleic acid molecules that comprise one or more free ends, no free ends (e.g. circular); nucleic acid molecules that comprise DNA, RNA, or both; and other varieties of polynucleotides known in the art. One type of vector is a "plasmid," which refers to a circular double stranded DNA loop into which additional DNA segments can be inserted, such as by standard molecular cloning techniques. Another type of vector is a viral vector, wherem virally-derived DNA or RNA sequences are present in the vector for packaging into a virus (e.g. retroviruses, replication defective retroviruses, adenoviruses, replication defective adenoviruses, and adeno-associated viruses). Viral vectors also include polynucleotides carried by a virus for iransfection into a host cell. Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g. bacterial vectors having a bacterial origin of replication and episomal mammalian vectors). Other vectors (e.g., non-episornal mammalian vectors) are integrated into the genome of a host cel l upon introduction into the host cell, and thereby are replicated along with the host genome. Moreover, certain vectors are capable of directing the expression of genes to which they are operatively- linked. Such vectors are referred to herein as "expression vectors." Common expression vectors of utility in recombinant DNA techniques are often in the form of plasmids.

[0011] Recombinant expression vectors can comprise a nucleic acid of the invention in a form suitable for expression of the nucleic acid in a host cell, which means thai the recombinant expression vectors include one or more regulatory elements, which may be selected on the basis of the host cells to be used for expression, that is operatively-linked to the nucleic acid sequence to be expressed. Within a recombinant expression vector, "operably linked" is intended to mean that the nucleotide sequence of interest is linked to the regulatory element(s) in a manner that allows for expression of the nucleotide sequence (e.g. in an in vitro transcription/translation system or in a host cel l when the vector is introduced into the host ceil).

[0012] The term "regulatory element" is intended to include promoters, enhancers, internal ribosomai entry sites (IRES), and other expression control elements (e.g. transcription termination signals, such as polyadenylation signals and poly-U sequences). Such regulatory- elements are described, for example, in Goeddel, GENE EXPRESSION TECHNOLOGY: METHODS IN ENZYMOLOGY 185, Academic Press, San Diego, Calif. (1990). Regulatory elements include those that direct constitutive expression of a nucleotide sequence in many types of host ceil and those that direct expression of the nucleotide sequence only in certain host cells (e.g., tissue-specific regulator}' sequences). A tissue-specific promoter may direct expression primarily in a desired tissue of interest, such as muscle, neuron, bone, skin, blood, specific organs (e.g. liver, pancreas), or particular cell types (e.g. lymphocytes). Regulatory elements may also direct expression in a temporal-dependent manner, such as in a cel l-cycle dependent or developmental stage-dependent manner, which may or may not also be tissue or cell-type specific. In some embodiments, a vector may comprise one or more pol III promoter (e.g. 1 , 2, 3, 4, 5, or more pol III promoters), one or more pol II promoters (e.g. 1, 2, 3, 4, 5, or more pol II promoters), one or more pol I promoters (e.g. I, 2, 3, 4, 5, or more pol I promoters), or combinations thereof. Examples of pol 111 promoters include, but are not limited to, U6 and HI promoters. Examples of pol II promoters include, but are not limited to, the retroviral Rous sarcoma virus (RSV) LTR promoter (optionally with the RSV enhancer), the cytomegalovirus (CMV ) promoter (optionally with the CMV enhancer) [see, e.g., Boshart et al, Cell, 41 :521-530 (1985)], the SV40 promoter, the dihydro folate reductase promoter, the β-actin promoter, the phosphoglycero! kinase (PGK) promoter, and the EFI a promoter. Also encompassed by the term "regulatory element" are enhancer elements, such as WPRE; CMV enhancers; the R-U5' segment in LTR of HTLV-I (Mol. Ceil. Biol, Vol. 8(1), p. 466-472, 1988); SV40 enhancer; and the intron sequence between exons 2 and 3 of rabbit β-globin (Proc. Natl. Acad. Sci. USA., Vol. 78(3), p. 1527-31 , 1981). It will be appreciated by those skilled in the art that the design of the expression vector can depend on such factors as the choice of the host cell to be transformed, the level of expression desired, etc. A vector can be introduced into host cells to thereby produce transcripts, proteins, or peptides, including fusion proteins or peptides, encoded by nucleic acids as described herein (e.g., clustered regularly interspersed short palindromic repeats (CRISPR) transcripts, proteins, enzymes, mutant forms thereof, fusion proteins thereof, etc.).

[0013] Aspects of the invention relate to methods of improving or modifying the target specificity of a CRISPR enzyme (preferably a Cas9 enzyme) which may comprise: a) selecting the CRISPR enzyme having a smaller size for easy packaging into delivery vectors; or b) generating chimeric CRISPR enzymes; or c) utilizing mutated CRISPR (preferably Cas9) enzymes. Further aspects of the invention also relate to methods and compositions for improving target specificity involving two CRISPR enzymes (double nickase), improving the sgRNA scaffold by making improvement, to other components aside from the guide R A.

[0014] The invention comprehends a non-naturally occurring or engineered composition comprising a vector system that may comprise one or more vectors comprising I. a first regulatory element operably linked to a CRISPR/Cas system chimeric RNA (chiRNA) polynucleotide sequence, wherein the polynucleotide sequence may comprise (a) a guide sequence capable of hybridizing to a target sequence in a cell, (b) a tracr mate sequence, and (c) a tracr sequence, and II. a second regulatory element operably linked to an enzyme-coding sequence encoding a CRISPR enzyme comprising at least one or more nuclear localization sequences, wherein (a), (b) and (c) are arranged in a 5' to 3' orientation, wherein components I and II are located on the same or different vectors of the system, wherein when transcribed, the tracr mate sequence hybridizes to the tracr sequence and the guide sequence directs sequence- specific binding of a CRJSPR complex to the target sequence, wherein the CRISPR complex comprises the CRISPR enzyme complexed with (1) the guide sequence that is hybridized to the target sequence, and (2) the tracr mate sequence that is hybridized to the tracr sequence, wherein the CRISPR enzyme may comprise two or more mutations, such that the enzyme has altered nuclease activity compared with the wild type enzyme, and wherein the enzyme-coding sequence further encodes one or more heterologous functional domains.

[0015] The invention further comprehends a multiplexed two component CRISPR enzyme system composition comprising a vector system that may comprise one or more vectors comprising I. a first regulatory element operably linked to a CRISP /Cas system chimeric RNA (chiRNA) polynucleotide sequence, wherein the polynucleotide sequence comprises (a) a guide sequence capable of hybridizing to a target sequence in a cell, (b) a tracr mate sequence, and (c) a tracr sequence, and II. a second regulator}' element operably linked to an enzyme-coding sequence encoding a CRISPR enzyme may comprise at least one or more nuclear localization sequences, wherein (a), (b) and (c) are arranged in a 5' to 3' orientation, wherein components I and II are located on the same or different vectors of the system, wherein when transcribed, the tracr mate sequence hybridizes to the tracr sequence and the guide sequence directs sequence- specific binding of a CRJSPR complex to the target sequence, wherein the CRISPR complex comprises the CRISPR enzyme complexed with (1) the guide sequence that is hybridized to the target sequence, and (2) the tracr mate sequence that is hybridized to the tracr sequence, wherein the CRISPR enzyme comprises two or more mutations, such that the enzyme has altered nuclease activity compared with the wild type enzyme, wherein the enzyme-coding sequence further encodes one or more heterologous functional domains, and wherein in the multiplexed system composition multiple chiRNA polynucleotide sequences are used.

] 0016] The invention further comprehends a non-naturally occurring or engineered composition comprising a vector system that may comprise one or more vectors comprising I. a first regulatory element operably linked to (a) a guide sequence capable of hybridizing to a target sequence in a cell, and (b) at least one or more tracr mate sequences, II. a second regulatory- element operably linked to an enzyme-coding sequence encoding a CRISPR enzyme, and III. a third regulatory element operably linked to a tracr sequence, wherein components I, II and III are located on the same or different vectors of the system, wherein when transcribed, the tracr mate sequence hybridizes to the tracr sequence and the guide sequence directs sequence-specific binding of a CRISPR complex to the target sequence, wherein the CRISPR complex comprises the CRISPR enzyme complexed with (1) the guide sequence that is hybridized to the target sequence, and (2) the tracr mate sequence that is hybridized to the tracr sequence, wherein the CRISPR enzyme may comprise two or more mutations, such that the enzyme has altered nuclease activity compared wit the wild type enzyme, and wherein the enzyme-coding sequence further encodes one or more heterologous functional domains.

[0017] The invention also comprehends a multiplexed three component CRISPR enzyme system composition comprising a vector system that may comprise one or more vectors comprising I. a first regulatory element operably linked to (a) a guide sequence capable of hybridizing to a target sequence in a cel l, and (b) at least one or more tracr mate sequences, I I. a second regulatory element operably linked to an enzyme-coding sequence encoding a CRISPR enzyme, and II I. a third regulatory element operably linked to a tracr sequence, wherem components I, II and III are located on the same or different vectors of the system, wherem when transcribed, the tracr mate sequence hybridizes to the tracr sequence and the guide sequence directs sequence-specific binding of a CRISPR complex to the target sequence, wherem the CRISPR. complex comprises the CRISPR. enzyme complexed with (!) the guide sequence that is hybridized to the target sequence, and (2) the tracr mate sequence that is hybridized to the tracr setjiience, wherein the CRISPR enzyme comprises two or more mutations, such that the enzyme has altered nuclease activity compared with the wild type enzyme, wherein the enzyme-coding sequence further encodes one or more heterologous functional domains, and wherem in the multiplexed system composition multiple guide sequences capable of hybridizing to multiple target sequences are used.

[00.1.8] In embodiments of the invention the CRISPR enzyme may comprise one or more mutations in two or more catalytically active domains. In another embodiment the CRISPR enzyme has reduced or abolished nuclease activity compared with the wild type enzyme. In another embodiment the two mutations are D10A SpCas9 in a first catalytically active domain and H840A SpCas9 in a second catalytically active domain or corresponding residues of other CRISPR enzymes, in another embodiment the CRISPR enzyme may comprise two or more mutations in a residue selected from the group consisting of DIO, E762, H840, N854, N863, or D986. In another embodiment the CRISPR enzyme may comprise two or more mutations selected from the group comprising DIOA, E762.A, H840A, N854.A, N863A or D986A. In a preferred embodiment the CRISPR enzyme is a DNA binding protein that does not direct cleavage of either strand at the location of the target sequence. In an embodiment, each of the two or more mutations is in a catalytica! fy active domain of the CRISPR enzyme selected from the group comprising RuvCL RuvCII, RuvCIII or HNH domain. It will be understood throughout this application that many references to specific amino acid residues are to those of the SpCas9 enzyme. The skilled person will understand that the invention is applicable to other Cas enzymes, including Cas9 enzymes from other sources, and that where reference is made to specific SpCas9 enzyme residues corresponding alterations and mutations may be made in those other Cas enzymes. For example, the skilled person will be able to compare sequences of the SpCas9 and other enzymes, and identify corresponding residues and domains, and hence to make appropriate modifications to those enzymes.

[001 ] in further embodiments, the compositions of the in vention may comprise at least two or more nuclear localization sequences. In an aspect of the invention the functional domain is a transcriptional activation domain, e. g. VP64. In another aspect the functional domain is a transcriptio ai repressor domain, e.g. a KRAB domain, a SID domain or a SID4X domain. In another embodiment, the enzyme coding sequence encodes one, two, three, four, five or more heterologous functional domains fused to the CRISPR enzyme. The invention also comprehends one or more linker sequences between any two domains. Embodiments of the invention include one or more functional domains having one or more of the following activities: methyl ase activity, demethylase activity, transcription activation activity, transcription repression activity, transcription release factor activity, histone modification activity, RNA cleavage activity and nucleic acid binding activity. In another embodiment, the functional domain binds DNA and/or affects transcription of the target nucleic acid. In aspects of the invention the cell is a prokaryotic or eukaryotic cell. In a preferred embodiment, the cell is a mammalian cell or a human ceil. In some embodiments, the mammalian ceil may be a rodent (for example, mouse or rat) cell, an ungulate cell, or a primate cell. In some embodiments, the eukaryotic cell may be an arthropod (eg, insect) or nematode cell. In other embodiments the ceil may be a plant ceil (including algae) or a fungal cell. In further embodiments of the invention the CRISPR enzyme is codon optimized for expression in a eukaryotic cell; the CRISPR enzyme is a type II CRISPR enzyme; the CRISPR enzyme is a Cas9 enzyme and the Cas9 enzyme is from an organism selected from the group comprising of genus Streptococcus, Campylobacter, Nitrati tractor, Staphylococcus, Parvibaculum, Roseburia, Neisseria, Gluconaeetobacter, Azospirillum, Sphaerochaeta, Lactobacillus, Eubacterium or Corynebacter. In a further aspect, the vectors of the system are viral vectors seclected from the group comprising of a lenti viral vector, an adenoviral vector or an AAV vector.

0020j The invention also comprehends methods of modulating, i.e. altering, activating, repressing, gene expression at a genomic locus of interest in a cell by contacting the cell with compositions of the invention.

[0021] An aspect of the invention relates to a composition which may comprise a vector system which .may comprise one or more vectors which may comprise

I. a first regulator}' element operably linked to a CRISPR/Cas system chimeric R A (chiRNA) polynucleotide sequence, wherein the polynucleotide sequence may comprise

(a) a guide sequence capable of hybridizing to a target sequence in a eukaryotic cel l,

(b) a tracr mate sequence, and

(c) a tracr sequence, and

II. a second regulatory element operably linked to an enzyme-coding sequence encoding a CRISPR enzyme which may comprise at least one or more nuclear localization sequences, wherein (a), (b) and (c) are arranged in a 5' to 3 ' orientation,

wherein components I and II are located on the same or different vectors of the system, wherein when transcribed, the tracr mate sequence hybridizes to the tracr sequence and the guide sequence directs sequence-specific binding of a CRISPR complex to the target sequence,

wherein the CRISPR complex may comprise the CRISPR enzyme complexed with (1) the guide sequence that is hybridized to the target sequence, and (2) the tracr mate sequence that is hybridized to the tracr sequence, and

wherein the enzyme coding sequence encoding the CRISPR enzyme further encodes a heterologous functional domain.

[0014] The coding sequence may encode one or more heterologous functional domains (e.g. about or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 1 0, or more domains in addition to the CRISPR enzyme). A CRISPR enzyme fusion protein may comprise any additional protein sequence, and optionally a linker sequence between any two domains. Examples of protein domains that may be fused to a CRISPR enzyme include, without limitation, epitope tags, reporter gene sequences, and protein domains having one or more of the following activities: methyl ase activity, demethylase activity, transcription activation activity, transcription repression activity, transcription release factor activity, histone modification activity, RJN A cleavage activity and nucleic acid binding activity. Non-limiting examples of epitope tags include histidine (His) tags, V5 tags, FLAG tags, influenza hemagglutinin (HA) tags, yc tags, VSV-G tags, and thioredoxin (Trx) tags. Examples of reporter genes include, but are not limited to, glutathione-S-transferase (GST), horseradish peroxidase (HRP), chloramphenicol acetyliransferase (CAT) beta- gaiactosidase, beta-giucuronidase, iuciferase, green fluorescent protein (GFP), HcRed, DsRed, cyan fluorescent protein (CFP), yellow fluorescent protein (YFP), and autofluorescent proteins including blue fluorescent protein (BFP). A CRISPR enzyme may be fused to a gene sequence encoding a protein or a fragment of a protein that bind DNA molecules or bind other cellular molecules, including but not limited to maltose binding protein (M BP), S-tag, Lex A DNA binding domain (DBD) fusions, GAL4 DNA binding domain fusions, and herpes simplex vims (HSV) BP 16 protein fusions. Additional domains that may form part of a fusion protein which may comprise a CRISPR enzyme are described in US201 10059502, incorporated herein by reference. In some embodiments, a lagged CRISPR enzyme is used to identify the location of a target sequence.

[0015] In an aspect of the invention, the functional domain affects transcription of the target nucleic acid.

[0016] Non-limiting examples of CRISPR enzymes include Casl , CaslB, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7, Cas8, Cas9 (also known as Csnl and Csx l2), CaslO, Csyl , Csy2, Csy3, Cse1 , Cse2, Cscl , Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmrl , Cmr3, Cmr4, Cmr5, Cmr6, Csbl , Csb2, Csb3, Csx l 7, Csxl 4, Csx lO, Csxl6, CsaX, Csx3, Csx i , Csxl 5, Csfi , Csf2, Csf3, Csf4, homologues thereof, or modified versions thereof. These enzymes are known; for example, the amino acid sequence of S. pyogenes Cas9 protein may be found in the SwissProt database (available at the website uniprot.org) under accession number Q99ZW2. In some embodiments, the CRISPR enzyme is a Cas9 enzyme. In some embodiments, the Cas9 enzyme is S. pneumoniae, S. pyogenes or S. ihermophihis Cas9, and may include mutated Cas9 derived from these organisms. In some embodiments, the CRISPR enzyme is codon-optimized for expression in a eukaryotic ceil. In some embodiments, the CRISPR enzyme directs cleavage of one or two strands at the location of the target sequence. In some embodiments, the CRISPR enzyme lacks DNA strand cleavage activity.

[0017] In some aspects of the invention, a CRISPR enzyme may comprise one or more mutations and may be used as a generic DNA binding protein with or without fusion to a functional domain. The mutations may include but are not limited to catalytic mutations, for instance mutations in one of the catalytic domains or mutation of catalytic residues. Preferred examples of suitable catalytic mutations are the catalytic rcsidue(s) in the N-term RuvC I domain of Cas9 or the catalytic residue(s) in the internal HNH domain. In some embodiments, the Cas9 is (or is derived from) SpCas9. In such embodiments, preferred mutations are at any or ail or positions 10, 762, 840, 854, 863 and/or 986 of SpCas9 or corresponding positions in other Cas9s (which may be ascertained for instance by standard sequence comparison tools). In particular, any or all of the following mutations are preferred in SpCas9: D10A, E762A, H840A, N854A, N863A and/or D986A; as well as conservative substitution for any of the replacement amino acids is also envisaged. The same (or conservative substitutions of these mutations) at corresponding positions in other Cas9s are also preferred. Particularly preferred are D10 and H840 in SpCas9 . However, in other Cas9s, residues corresponding to SpCas9 D10 and H840 are also preferred.

[0018] In a more advantageous aspect of the invention the mutated CR ISPR enzyme may be fused to a transcriptional activation domain. In one aspect of the invention, the transcriptional activation domain may be VP64. Other aspects of the invention relate to the mutated CRISPR enzyme being fused to domains which include but are not limited to a transcriptional repressor, a recombinase, a transposase, a hi stone remodel er, a DNA methyl transferase, a cryptochrotne, a light inducible/controilable domain or a chemically inducible/controllable domain.

[0019] In some aspects of the in vention, the CRISPR. enzyme is comprised of less than four thousand, and in some aspects less than one thousand, amino acids. Such enzymes may be provided fused to a heterologous functional domain, or not. Where the enzyme is fused to a heterologous functional domain, the size of the enzyme (less than four thousand, less than one thousand amino acids) refers to the CRISPR portion of the fusion protein. In certain embodiments described herein, the invention or method is practiced on an organism or subject. In certain embodiments, the organism or subject is a eukaryote or a non-human eukaryote. In certain embodiments, the organism or subject is a plant. In certain embodiments, the organism or subject is a mammal or a non-human mammal. In certain embodiments, the organism or subject is algae. In some embodiments, the organism or subject may be a rodent (for example, mouse or rat), an ungulate, or a primate. In some embodiments, the organism or subject may be an arthropod (eg, insect) or nematode, in other embodiments the organism or subject may be a plant or a fungus.

0020j Accordingly, it is an object of the invention to not encompass within the invention any previously known product, process of making the product, or method of using the product such that Applicants reserve the right and hereby disclose a disclaimer of any previously known product, process, or method. It is further noted that the invention does not intend to encompass within the scope of the invention any product, process, or making of the product or method of using the product, which does not meet the written description and enablement requirements of the USPTO (35 U.S.C. § 112, first paragraph) or the EPO (Article 83 of the EPC), such that Applicants reserve the right and hereby disclose a disclaimer of any previously described product, process of making the product, or method of using the product.

[0021] It is noted that in this disclosure and particularly in the claims and/or paragraphs, terms such as "comprises", "comprised", "comprising" and the like can have the meaning attributed to it in U.S. Patent law; e.g., they can mean "includes", "included", "including", and the like; and that terms such as "consisting essentially of and "consists essentially of" have the meaning ascribed to them in U.S. Patent law, e.g., they allow for elements not explicitly recited, but exclude elements that are found in the prior art or that affect a basic or novel characteristic of the invention.

[0022] These and other embodiments are disclosed or are obvious from and encompassed by, the following Detailed Description.

BRIEF DESCRIPTION OF THE DRAWINGS

[0023] The novel features of the invention are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present invention will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the invention are utilized, and the accompanying drawings of which: [0024] Figure 1 shows a schematic of RNA -guided Cas9 nuclease. The Cas9 nuclease from Streptococcus pyogenes (yellow) is targeted to genomic DNA by a synthetic guide RNA (sgRNA) consisting of a 20-nt guide sequence (blue) and a scaffold (red). The guide sequence base-pairs with the DNA target (blue), directly upstream of a requisite 5'-NGG protospacer adjacent motif (PAM; magenta), and Cas9 mediates a double-stranded break (DSB) ~3 bp upstream of the PAM (red triangle).

[0025] Figures 2A-2F show an exemplary CRISPR system, a possible mechanism of action, an example adaptation for expression in eukaryotic cells, and results of tests assessing nuclear localization and CRISPR activity

[0026] Figure 3A-D is a phylogenetic tree of Cas genes

[0027] Figures 4A-4F show the phylogenetic analysis revealing five families of Cas9s, including three groups of large Cas9s (-1400 amino acids) and two of small Cas9s (~1100 amino acids).

[0028] Figure 5 shows a schematic construct in which the transcriptional activation domain (VP64) is fused to Cas9 with two mutations in the catalytic domains (D10 and H840).

[0029] Figure 6 shows a graphical representation of transcriptional activation following co- transfection of the Cas9- VP64 with PGR. generated chimeric crispr RN A (chiRNA) in 293 cells. Assessment was carried out 72 hours after transfection using RT-qPCR.

[0030] Figure 7 shows a number of vectors incorporating mutant Cas9 genes with VP64,

NLS, and GFP markers.

[0031] Figure 8 shows the localization of Cas9-VP64-GFP constructs into 293 cells as assessed by a fluorescent microscope 12 hours post transfection.

[0032] Figure 9 shows the localization of 16 dCas9-GFP fusions with the same alpha importin NLS sequence on either the N- or C-term looking at zero to three tandem repeats. Each construct was transfected mto HEK 293FT cells using Lipofectame 2000 and imaged 24 hours post-transfection

[0033] Figure 10 shows six versions of a 6x is tag added to dCas9, transfected into 293 FT cells, and stained with an anti-6xHis antibody. Three were constructed for transcriptional activation (VP64 fusions), and the other three were for transcriptional repression (no functional domain). [0034] Figure 11 shows a titrated ratio of chiRNA (Sox2.1 and Sox2.5) to Cas9 (NLS- VP64-NLS-hSpCas9-NLS-VP64-NLS), transfected into 293 cells, and quantified using RT- qPCR.

[0035] Figure 12 shows the positioning of target sites in the human Sox2 locus with each target being 20bp long with a neighboring NGG protspacer adjacent motif (PAM),

[0036] Figure 13 shows co-transfectirsg of each dCas9 containing construct with pA6 plasmids into HEK 293FT ceils using Lipofectame 2000. 72 hours post-transfeetion total RNA was extracted from the cells. 1 g of RNA was reverse transcribed into cDNA (q Script Supermix) in a 40 ul reaction. 2 ul of reaction product was added into a single 20 ul TaqMan assay qPCR reaction. Each experiment was performed in biological and technical triplicates. No RT control and no template control reactions showed no amplification.

[0037] Figure 14 shows testing of constructs (pXRPOl l, pXRPOB, pXRPOlS) using the same Sox2 targets as Figure 13.

[0038] Figures 15A-15B shows a list of 31 constructs to explore different linkers, functional domains, and N~ and C-term fusions and critical elements.

[0039] Figure 16 shows co-transfecting of each dCas9 repressor p!asmid with two guide RNAs targeted to the coding strand of the beta-catenin gene. RNA was isolated 72 hours after transfection and gene expression was quantified by RT-qPCR. The endogenous control gene was GAPDH. Two validated shRNAs were used as positive controls. Negative controls were certain plasmids transfected without gRNA, these are denoted as "pXRP## control".

[0040] Figure 17 shows a graphical representation of transcriptional activation further to the ratio of chiRNA (Sox2.1 and Sox2.5) to Cas9 (NLS-VP64-NLS-hSpCas9-NLS-VP64-NLS) being titrated and transfected in 293 cells. Results were quantified using Rt-qPCR.

[0041] Figure 18 shows luciferase reporter data for Cas9 activator (top panel) and repressor (bottom panel). Compared to "No Cas9" controls over 3 fold activation was achieved when targeting the promoter of Sox2. When targeting the gene body of beta-catenin (CTNNB l), about 3 fold repression was achieved.

[0042] Figure 19 shows gene expression of beta-catenin in HEK 293FT cells 72 hours after transfection. Cas9 repressor constructs were targeted to the beta-catenin locus and compared to the gold standard shRNAs. Similar repression could be seen with Cas9 repressors and the shRNA. [0043] Figure 20 shows a graphical representation of the fold Neurog2 expression of the 20 bp sgRNA sequences were targeted to the Neurog2 locus in mouse Neuro 2A cells. Ncurog2 mRNA levels were measured using RT-qPCR.

[CI044] Figure 21 shows the basal gene expression modulation of dCas9-VP64 that was measured for the indicated gene targets. Italics represent mouse gene targets tested in Neuro 2 A cells, all capsrepresent human gene targets tested in 293FT ceils. In each case, expression of thegene in GFP transfected cells was compared to expression in cells transfected withdCas9-VP64.

[0045] Figure 22 shows the changes in expression level of the indicated genes when samples transfected with the dCas9-VP64 construct, but without an sgRNA.

[0046] Figure 23A-G shows a, The RNA-guided nuclease Cas9 from the type ΪΙ Streptococcus pyogenes CRISPR/Cas system can be converted into a nucleolytically inactive RNA-guided DNA binding protein (Cas9**) by introducing two alanine substitutions (D10A and H8 0A). Schematic showing that a synthetic guide RNA (sgRNA) can direct Cas9**-effector fusion to a specific iocus in the human genome. The sgRNA contains a 20-bp guide sequence at the 5' end which specifies the target sequence. On the target genomic DNA, the 20-bp target site needs to be followed by a 5 -NGG PAM motif, b, c, Schematics showing the sgRNA target sites in the human KLF4 and SOX2 loci, respectively. Each target site is indicated by the blue bar and the corresponding PAM sequence is indicated by the magenta bar. d, e, Schematics of the Cas9**-VP64 transcription activator and SID4X-Cas9** transcription repressor constructs, f, g, Cas9**-VP64- and SID4X-Cas9** -mediated activation of LF4 and repression of SQX2, respectively. All mRNA levels were measured relative to GFP mock-transfected 293 FT cells (mean ± s.e.m.; n = 3 biological replicates).

[0047] Figure 24 shows the Cas9 activator sequence.

[0048] Figure 25 shows the Cas9 repressor sequence.

[0049] Figure 26 shows the graphical representation of fold activation of different genes targeted by the Cas9 acti vator (pXRP57) and guide RN A.

[0050] Figure 27 shows the graphical representation of fold repression of the hSox2 gene targeted by the Cas9 activator (pXRP57) and guide RNA.

[0051] Figure 28 shows a pAAV-EFla-dCas9-GS-Cmi(mNLS d318-

334) WPRE hGI-I po 1 y A pi asmi d ma . [0052] Figure 29 shows a pAAV-EFla-dCas9-GS-NLS-cibl -WPRE-hGHpA plasmid map.

[0053] Figure 30 shows a pAAV-EFla-dCas9-GS-NLS-NLS-cibl-WPRE-hGHpA plasmid map.

[0054] Figure 31 shows a graphical representation of CasLITE constructs exhibiting varying levels of light-inducible transcriptional activation.

[0055] Figure 32 shows the validation of Rosa26 Cre-dependent Cas9 knocki mouse embryonic stem cells,

[0056] Figure 33 shows a gel image indicating the genotyping results for Cas9 mice.

[0057] Figure 34 shows CRISPR/Cmr mediated silencing of RNA. Cmr proteins form a complex with mature crRNA to site-specifically target and cleave RNA. Mature crRNAs from P. furiosus exist in two forms of different lengths, long (45 nt) and short (39 nt), consisting of a 5' handle and a guide sequence. The 5' handle is required for the crRNA to be included in the Cmr complex. The guide sequence programs the target site and can be either long (37 nt) or short (31 nt). RNA cleavage occurs 14 nucleotides from the 3^* end of the crRNA. This platform could be repurposed to target mammalian genes expressed from a genomic locus by only changing the guide sequence.

[0058] Figure 35A-B shows Cmr proteins are expressed within mammalian cells. Six Cmr genes (Cmr 1-6) and one Cas gene (Cas6) from P. furiosus were cloned into mammalian expression vectors and transfected into HE 293 FT cells. 72 hours post-transfection fluorescence images were taken and protein lysates were prepared. A) EGFP expression is strongly observed suggesting that the exogenous proteins are robustly expressed. B) Western blot images show protein bands located at the expected size. The second band within each lane is ~ 30 kDa larger in each case and is likely the result of uncleaved P2A sequence.

[0059] Figure 36 shows CRISPR Cmr expression vectors.

[0060} The figures herein are for illustrative purposes only and are not necessarily drawn to scale.

DETAILED DESCRIPTION OF THE INVENTION

[0061] The invention relates to the engineering and optimization of systems, methods and compositions used for the control of gene expression involving sequence targeting, such as genome perturbation or gene-editing, that relate to the CRISPR/Cas system and components thereof. In advantageous embodiments, the Cas enzyme is Cas9; for example, Cas9 from S .pyogenes or S. mermophilus.

[0062] The terms "polynucleotide", "nucleotide", "nucleotide sequence", "nucleic acid" and "oligonucleotide" are used interchangeably. They refer to a polymeric form of nucleotides of any length, either deoxyribonucleotides or ribonucleotides, or analogs thereof. Polynucleotides may have any three dimensional structure, and may perform any function, known or unknown. The following are non-limiting examples of polynucleotides: coding or non-coding regions of a gene or gene fragment, loci (locus) defined from linkage analysis, exons, mtrons, messenger RNA (mRNA), transfer RNA, ribosomal RNA, short interfering RNA (siRNA), short-hairpin RNA (shRNA), micro-RNA (miRNA), ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, and primers. The term also encompasses nucleic-acid-like structures with synthetic backbones, see, e.g., Eckstein, 1991: Baserga et ai., 1992; Miiligan, 1993; WO 97/03211 ; WO 96/39154; Mata, 1997; Strauss-Soukup, 1997; and Samstag, 1996. A polynucleotide may comprise one or more modified nucleotides, such as methylated nucleotides and nucleotide analogs. If present, modifications to the nucleotide structure may be imparted before or after assembly of the polymer. The sequence of nucleotides may be interrupted by iion-nucleotide components. A polynucleotide may be further modified after polymerization, such as by conjugation with, a labeling component.

[0063] In aspects of the invention the terms "chimeric RNA", "chimeric guide RNA", "guide RNA", "single guide RNA" and "synthetic guide RNA" are used interchangeably and refer to the polynucleotide sequence comprising the guide sequence, the tracr sequence and the tracr mate sequence. The term "guide sequence" refers to the about 20bp sequence within the guide RNA that specifies the target site and may be used interchangeably with the terms "guide" or "spacer". The term "tracr mate sequence" may also be used interchangeably with the term "direct repeat(s)".

[0064] As used herein the term "wild type" is a term of the art understood by skilled persons and means the typical form of an organism, strain, gene or characteristic as it occurs in nature as distinguished from mutant or variant forms. For example, "wild type StCas9" refers to wild type Cas9 from S thermophilus, the protein sequence of which is given in the SwissProt database under accession number G3ECRJ . Similarly, S pyogenes Cas9 is included in SwissProt under accession number Q99ZW2.

[0065] As used herein the term "variant" should be taken to mean the exhibition of qualities that have a pattern that deviates from what occurs in nature.

[0066] The terms "non-naturally occurring" or "engineered" are used interchangeably and indicate the involvement of the hand of man. The terms, when referring to nucleic acid molecules or polypeptides mean that the nucleic acid molecule or the polypeptide is at least substantially free from at least one other component with which they are naturally associated in nature and as found in nature.

[0067] "Complementarity" refers to the ability of a nucleic acid to form hydrogen bond(s) with another nucleic acid sequence by either traditional Watson -Crick base pairing or other non- traditional types. A percent complementarity indicates the percentage of residues in a nucleic acid molecule which can form hydrogen bonds (e.g., Watson-Crick base pairing) with a second nucleic acid sequence (e.g., 5, 6, 7, 8, 9, 10 out of 10 being 50%, 60%, 70%, 80%, 90%, and 100% complementary). "Perfectly complementary" means that all the contiguous residues of a nucleic acid sequence will hydrogen bond with the same number of contiguous residues in a second nucleic acid sequence. "Substantially complementary" as used herein refers to a degree of complementarity that is at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% over a region of 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, or more nucleotides, or refers to two nucleic acids that hybridize under stringent conditions.

[CI068] As used herein, "stringent conditions" for hybridization refer to conditions under which a nucleic acid having complementarity to a target sequence predominantly hybridizes with the target sequence, and substantially does not hybridize to non-target sequences. Stringent conditions are generally sequence-dependent, and vary depending on a number of factors. In general, the longer the sequence, the higher the temperature at which the sequence specifically hybridizes to its target sequence. Non-limiting examples of stringent conditions are described in detail in Tijssen (1993), Laboratory Techniques In Biochemistry And Molecular Biology- Hybridization With Nucleic Acid Probes Part I, Second Chapter "Overview of principles of hybridization and the strategy of nucleic acid probe assay", Elsevier, N.Y. [0069] "Hybridization" refers to a reaction in which one or more polynucleotides react to form a complex that is stabilized via hydrogen bonding between the bases of the nucleotide residues. The hydrogen bonding may occur by Watson Crick base pairing, Hoogstein binding, or in any other sequence specific manner. The complex may comprise two strands forming a duplex structure, three or more strands forming a multi stranded complex, a single self- hybridizing strand, or any combination of these. A hybridization reaction may constitute a step in a more extensive process, such as the initiation of PGR, or the cleavage of a polynucleotide by an enzyme. A sequence capable of hybridizing with a given sequence is referred to as the "complement" of the given sequence.

[0070] As used herein, the term "genomic locus" or "locus" (plural loci) is the specific location of a gene or D A sequence on a chromosome. A "gene" refers to stretches of DNA or RNA that encode a polypeptide or an RNA chain that has functional role to play in an organism and hence is the molecular unit of heredity in living organisms. For the purpose of this in vention it may be considered that genes include regions which regulate the productio of the gene product, whether or not such regulatory sequences are adjacent to coding and/or transcribed sequences. Accordingly, a gene includes, but is not necessarily limited to, promoter sequences, terminators, translational regulatory sequences such as ribosome binding sites and internal ribosome entry sites, enhancers, silencers, insulators, boundary elements, replication origins, matrix attachment sites and locus control regio s.

[0071] As used herein, "expression of a genomic locus" or "gene expression" is the process by which information from a gene is used in the synthesis of a functional gene product. The products of gene expression are often proteins, but in non-protein coding genes such as rRNA genes or tRNA genes, the product is functional RNA. The process of gene expression is used by all known life - eukaryotes (including multicellular organisms), prokaryotes (bacteria and archaea) and viruses to generate functional products to survive. As used herein "expression" of a gene or nucleic acid encompasses not only cellular gene expression, but also the transcription and translation of nucleic acid(s) in cloning systems and in any other context. As used herein, "expression" also refers to the process by which a polynucleotide is transcribed from a DNA template (such as into and mRNA or other RNA transcript) and/or the process by which a transcribed mRNA is subsequently translated into peptides, polypeptides, or proteins. Transcripts and encoded polypeptides may be col lectively referred to as "gene product." If the polynucleotide is derived from genomic DMA, expression may include splicing of the mRNA. in a eukaryotic cell.

[0072] The terms "polypeptide", "peptide" and "protein" are used interchangeably herein to refer to polymers of amino acids of any length. The polymer may be linear or branched, it may comprise modified amino acids, and it may be interrupted by non amino acids. The terms also encompass an amino acid polymer that has been modified; for example, disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation, such as conjugation with a labeling component. As used herein the term "amino acid" includes natural and/or unnatural or synthetic amino acids, including glycine and both the D or L optical isomers, and amino acid analogs and peptidomirneti.es.

10073 j As used herein, the term "domain" or "protein domain" refers to a part of a protein sequence that may exist and function independently of the rest of the protein chain.

[CI074] As described in aspects of the invention, sequence identity is related to sequence homology. Homology comparisons may be conducted by eye, or more usually, with the aid of readily available sequence comparison programs. These commercially available computer programs may calculate percent (%) homology between two or more sequences and may also calculate the sequence identity shared by two or more amino acid or nucleic acid sequences. Sequence homologies may be generated by any of a number of computer programs known in the art, for example BLAST or FAST A, etc. A suitable computer program for carrying out such an alignment is the GCG Wisconsin Bestfit package (University of Wisconsin, U.S.A; Devereux et ai., 1984, Nucleic Acids Research 12:387). Examples of other software than may perform sequence comparisons include, but are not limited to, the BLAST package (see Ausubel et al., 1999 ibid - Chapter 18), FASTA (Atschul et al., 1990, J. Mol. Biol, 403-410) and the GENEWOR S suite of comparison tools. Both BLAST and FASTA are available for offline and online searching (see Ausubel et al., 1999 ibid, pages 7-58 to 7-60). However it is preferred to use the GCG Bestfit program .

[CI075] % homology may be calculated over contiguous sequences, i.e., one sequence is aligned with the other sequence and each amino acid or nucleotide in one sequence is directly compared with the corresponding amino acid or nucleotide in the other sequence, one residue at a time. This is called an "ungapped" alignment. Typically, such ungapped alignments are performed only over a relatively short number of residues. [0076] Although this is a very simple and consistent method, it fails to take into consideration that, for example, in an othemise identical pair of sequences, one insertion or deletion may cause the following amino acid residues to be put out of alignment, thus potentially resulting in a large reduction in % homology when a global alignment is performed. Consequently, most sequence comparison methods are designed to produce optimal alignments that take into consideration possible insertions and deletions without unduly penalizing the overall homology or identity score. This is achieved by inserting "gaps" in the sequence alignment to try to maximize local homology or identity.

[0077] However, these more complex methods assign "gap penalties" to each gap that occurs in the alignment so that, for the same number of identical amino acids, a sequence alignment with as few gaps as possible - reflecting higher relatedness between the two compared sequences - may achieve a higher score than o e with ma y gaps, "Affinity gap costs" are typically used that charge a relatively high cost for the existence of a gap and a smaller penalty for each subsequent residue in the gap. This is the most commonly used gap scoring system. High gap penalties may, of course, produce optimized alignments with fewer gaps. Most alignment- programs allow the gap penalties to be modified. However, it is preferred to use the default values when using such software for sequence comparisons. For example, when using the GCG Wisconsin Bestfit package the default gap penalty for amino acid sequences is -12 for a gap and -4 for each extension,

[0078] Calculation of maximum % homology therefore first requires the production of an optimal alignment, taking into consideration gap penalties. A suitable computer program for earn ing out such an alignment is the GCG Wisconsin Bestfit package (Devereux et ah, 1984 Niic. Acids Research 12 p387). Examples of other software than may perform sequence comparisons include, but are not limited to, the BLAST package (see Ausubel et a!., 1999 Short Protocols in Molecular Biology, 4^th Ed. - Chapter 18), FA ST A (Aitschui et al, 1990 J. Mol. Biol. 403-410) and the GENEWGRKS suite of comparison tools. Both BLAST and FAST A are available for offline and online searching (see Ausubel et al., 1999, Short Protocols in Molecular Biology, pages 7-58 to 7-60), However, for some applications, it is preferred to use the GCG Bestfit program, A new tool, called BLAST 2 Sequences is also available for comparing protein and nucleotide sequences (see FEMS Microbiol Lett. 1999 174(2): 247-50; FEMS Microbiol Lett. 1999 177(1): 187-8 and the website of the National Center for Biotechnology information at the website of the National Institutes for Health).

[0079] Although the final % homology may be measured in terms of identity, the alignment process itself is typically not based on an all-or-nothing pair comparison. Instead, a scaled similarity score matrix is generally used that assigns scores to each pair-wise comparison based on chemical similarity or evolutionary distance. An example of such a matrix commonly used is the BLOSUM62 matrix - the default matrix for the BLAST suite of programs. GCG Wisconsin programs generally use either the public default values or a custom symbol comparison table, if supplied (see user manual for further details). For some applications, it is preferred to use the public default values for the GCG package, or in the case of other software, the default matrix, such as BLOSUM62.

[0080] Alternatively, percentage homologies may be calculated using the multiple alignment feature in DNASIS^, (Hitachi Software), based on an algorithm, analogous to CLUSTAL (Higgins DG & Sharp PM (1988), Gene 73(1), 237-244). Once the software has produced an optimal alignment, it is possible to calculate % homology, preferably % sequence identity. The software typically does this as part of the sequence comparison and generates a numerical result.

[0081] The sequences may also have deletions, insertions or substitutions of amino acid residues which produce a silent change and result in a functionally equivalent substance. Deliberate amino acid substitutions may be made on the basis of similarity in amino acid properties (such as polarity, charge, solubility, hydrophobicity, hydrophilicity, and/or the amphipathic nature of the residues) and it is therefore useful to group amino acids together in functional groups. Amino acids may be grouped together based on the properties of their side chains alone. However, it is more useful to include mutation data as well. The sets of amino acids thus derived are likely to be conserved for structural reasons. These sets may be described in the form of a Venn diagram (Livingstone CD. and Barton G.J. (1993) "Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation" Comput. Appl. Biosci. 9: 745-756) (Taylor W.R. ( 1986) "The classification of amino acid conservation" J. Theor, Biol. 119; 205-218). Conservative substitutions may be made, for example according to the table below which describes a generally accepted Venn diagram grouping of amino acids. Set Sub-set

Hydrophobic F W Y H M I L V A G C Aromatic F W Y H

Aliphatic I L V

Polar W Y I \ K R E D C S T N Q Charged H K R E D

Positively H K R

charged

Negatively E D

charged

Small V C A G S P T D Tiny A G S

[0082] Embodiments of the invention include sequences (both polynucleotide or polypeptide) which may comprise homologous substitution (substitution and replacement are both used herein to mean the interchange of an existing amino acid residue or nucleotide, with an alternative residue or nucleotide) that may occur i.e., like-for-like substitution in the case of amino acids such as basic for basic, acidic for acidic, polar for polar, etc. Non-homologous substitution may also occur i.e., from one class of residue to another or alternatively involving the inclusion of unnatural amino acids such as ornithine (hereinafter referred to as Z), diaminobutyric acid ornithine (hereinafter refen'ed to as B), norleueirse ornithine (hereinafter referred to as O), pyriyiaianine, thienylalanine, naphthylalanine and phenylglycine.

[0083] Variant amino acid sequences may include suitable spacer groups that may be inserted between any two amino acid residues of the sequence including alkyl groups such as methyl, ethyl or propyl groups in addition to amino acid spacers such as glycine or β-alanine residues. A further form of variation, which involves the presence of one or more amino acid residues in peptoid form, may be well understood by those skilled in the art. For the avoidance of doubt, "the peptoid form" is used to refer to variant amino acid residues wherein the a-carbon substituent group is on the residue's nitrogen atom rather than the a-carbon. Processes for preparing peptides in the peptoid form are known in the art, for example Simon RJ ei al., PNAS (1992) 89(20), 9367-9371 and Horwell DC, Trends Biotechnol. (1995) 13(4), 132-134. [0084] The practice of the present invention employs, unless otherwise indicated, conventional techniques of immunology, biochemistry, chemistry, molecular biology, microbiology, cell biology, genomics and recombinant DNA, which are within the skill of the art. See Sambrook, Fritsch and Maniatis, MOLECULAR C LON ING: A LABORATORY MANUAL, 2nd edition (1989); CURRENT PROTOCOLS IN MOLECULAR BIOLOGY (F. M. Ausubel, et al. eds., (1987)); the series METHODS IN ENZYMOLOGY (Academic Press, Inc.): PCR 2: A PRACTICAL APPROACH (M.J. MacPherson, B.D. ! lames and G.R. Taylor eds. (1995)), Harlow and Lane, eds. (1988) ANTIBODIES, A LABORATORY MANUAL, and ANIMAL CELL CULTURE (R.I. Freshney, ed. (1987)).

[0085] In one aspect, the invention provides for vectors that are used in the engineering and optimization of CRISPR/Cas systems.

[0086] A used herein, a "vector" is a tool that allows or facilitates the transfer of an entity from one environment to another. It is a repSicon, such as a pSasmid, phage, or cosmid, into which another DNA segment may be inserted so as to bring about the replication of the inserted segment. Generally, a vector is capable of replication when associated with the proper control elements. In general, the term "vector" refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. Vectors include, but are not limited to, nucleic acid molecules that are single-stranded, double-stranded, or partially double-stranded; nucleic acid molecules that comprise one or more free ends, no free ends (e.g. circular); nucleic acid molecules that comprise DNA, RNA, or both; and other varieties of polynucleotides known in the art. One type of vector is a "plasmid," which refers to a circular double stranded DNA loop into which additional DNA segments can be inserted, such as by standard molecular cloning techniques. Another type of vector is a viral vector, wherein viraily-derived DNA or RNA sequences are present in the vector for packaging into a virus (e.g. retroviruses, replication defective retroviruses, adenoviruses, replication defective adenoviruses, and adeno-associated viruses). Viral vectors also include polynucleotides carried by a virus for transfection into a host cel l. Certain vectors are capable of autonomous replication in a host cel l into which they are introduced (e.g. bacterial vectors having a bacterial origin of replication and episomal mammalian vectors). Other vectors (e.g., non-episomal mammalian vectors) are integrated into the genome of a host ceil upon introduction into the host cell, and thereby are replicated along with the host genome. Moreover, certain vectors are capable of directing the expression of genes to which they are operatively-linked . Such vectors are referred to herein as "expression vectors." Common expression vectors of utility in recombinant DNA techniques are often in the form of plasmids.

[0087] Recombinant expression vectors can comprise a nucleic acid of the invention in a form suitable for expression of the nucleic acid in a host cell, which means that the recombinant expression vectors include one or more regulatory elements, which may be selected on the basis of the host cells to be used for expression, that is operatively-linked to the nucleic acid sequence to be expressed. Within a recombinant expression vector, "operably linked" is intended to mean that the nucleotide sequence of interest is linked to the regulatory element(s) in a manner that allows for expression of the nucleotide sequence (e.g. in an in vitro transcription/translation system or in a host cell when the vector is introduced into the host cell). With regards to recombination and cloning methods, mention is made of U.S. patent application 10/815,730, the contents of which are herein incorporated by reference in their entirety.

[0088] Aspects of the invention relate to bieistronic vectors for chimeric RNA and Cas9. Bicistronic expression vectors for chimeric RNA and Cas9 are preferred, in general and particularly in this embodiment Cas9 is preferably driven by the CBh promoter. The chimeric RNA may preferably be driven by a U6 promoter. Ideally the two are combined. The chimeric guide RNA typically consists of a 20bp guide sequence (Ns) and this may be joined to the tracr sequence (running from the first "U" of the lower strand to the end of the transcript). The tracr sequence may be truncated at various positions as indicated. The guide and tracr sequences are separated by the tracr-mate sequence, which may be GUUUUAGAGCUA. This may be followed by the loop sequence GAAA as shown. Both of these are preferred examples. Applicants have demonstrated Cas9-mediated indels at the human EMXl and PVALB loci by SURVEYOR assays. ChiRNAs are indicated by their "-fit" designation, and crRNA refers to a hybrid RNA where guide and tracr sequences are expressed as separate transcripts. Throughout this application, chimeric RNA. may also be called single guide, or synthetic guide RNA (sgRNA). The loop is preferably GAAA, but it is not limited to this sequence or indeed to being only 4bp in length. Indeed, preferred loop forming sequences for use in hairpin structures are four nucleotides in length, and most preferably have the sequence GAAA. However, longer or shorter loop sequences may be used, as may alternative sequences. The sequences preferably include a nucleotide triplet (for example, AAA), and an additional nucleotide (for example C or

G). Examples of loop forming sequences include CAAA and AAAG.

[0089]

[0090] The term "^'regulatory element" is intended to include promoters, enhancers, internal ribosomal entry sites (IRES), and other expression control elements (e.g. transcription termination signals, such as polyadenylation signals and poly-U sequences). Such regulatory elements are described, for example, in Goeddel, GENE EXPRESSION TECHNOLOGY: METHODS IN ENZYMOLOGY 185, Academic Press, San Diego, Calif. (1990). Regulatory elements include those that direct constitutive expression of a nucleotide sequence in many types of host cell and those that direct expression of the nucleotide sequence only in certain host cells (e.g., tissue-specific regulator}' sequences). A tissue-specific promoter may direct expression primarily in a desired tissue of interest, such as muscle, neuron, bone, skin, blood, specific organs (e.g. liver, pancreas), or particular cell types (e.g. lymphocytes). Regulatory elements may also direct expression in a temporal-dependent manner, such as in a cell-cycle dependent or developmental stage-dependent manner, which may or may not also be tissue or cell-type specific. In some embodiments, a vector may comprise one or more pol III promoter (e.g. 1, 2, 3, 4, 5, or more pol I II promoters), one or more pol II promoters (e.g. 1, 2, 3, 4, 5, or more pol II promoters), one or more pol I promoters (e.g. 1, 2, 3, 4, 5, or more pol I promoters), or combinations thereof. Examples of pol III promoters include, but are not limited to, U6 and HI promoters. Examples of pol II promoters include, but are not limited to, the retroviral Rous sarcoma virus (RSV) LTR promoter (optionally with the RSV enhancer), the cytomegalovirus (CMV) promoter (optionally with the CMV enhancer) [see, e.g., Boshart et al, Cell, 41 :521 -530 (1985)], the SV40 promoter, the dihydro folate reductase promoter, the β-actin promoter, the phosphoglycerol kinase (PGK) promoter, and the EFl promoter. Also encompassed by the term "regulatory element" are enhancer elements, such as WPRE; CMV enhancers; the R-U5' segment in LTR of HTLV-I (Mol. Ceil. Biol, Vol. 8(1), p. 466-472, 1988); SV40 enhancer; and the intron sequence between exons 2 and 3 of rabbit β-globin (Proc. Natl, Acad. Sci. US A., Vol, 78(3), p. 1527-31, 1981). It will be appreciated by those skilled in the art that the design of the expression vector can depend on such factors as the choice of the host cell to be transformed, the level of expression desired, etc. A vector can be introduced into host ceils to thereby produce transcripts, proteins, or peptides, including fusion proteins or peptides, encoded by nucleic acids as described herein (e.g., clustered regularly interspersed short paiindromic repeats (CRISPR) transcripts, proteins, enzymes, mutant forms thereof, fusion proteins thereof, etc.). With regards to regulatory sequences, mention is made of U.S. patent application 10/491,026, the contents of which are incorporated by reference herein in their entirety. With regards to promoters, mention is made of PCT publication WO 2011/028929 and U.S. application 12/511,940, the contents of which are incorporated by reference herein in their entirety.

[0091] Vectors can be designed for expression of CRISPR transcripts (e.g. nucleic acid transcripts, proteins, or enzymes) in prokaryotic or eukaryotic cells. For example, CRISPR transcripts can be expressed in bacterial cells such as Escherichia coli, insect ceils (using baculovirus expression vectors), yeast cells, or mammalian cells. Suitable host cells are discussed further in Goeddel, GENE EXPRESSION TECHNOLOGY: METHODS IN ENZYMOLOGY 185, Academic Press, San Diego, Calif. (1990). Alternatively, the recombinant expression vector can be transcribed and translated in vitro, for example using T7 promoter regulatory sequences and T7 polymerase.

[0092] Vectors may be mtroduced and propagated in a prokaryote or prokaryotic cell. In some embodiments, a prokaryote is used to amplify copies of a vector to be introduced into a eukaryotic cell or as an intermediate vector in the production of a vector to be introduced into a eukaryotic ceil (e.g. amplifying a plasmid as part of a viral vector packaging system). In some embodiments, a prokaryote is used to amplify copies of a vector and express one or more nucleic acids, such as to provide a source of one or more proteins for deliver}' to a host, cell or host, organism. Expression of protems in prokaryotes is most often carried out in Escherichia coli with vectors containing constitutive or inducible promoters directing the expression of either fusion or non-fusion proteins. Fusion vectors add a number of amino acids to a protein encoded therein, such as to the amino temiinus of the recombinant protein. Such fusion vectors may serve one or more purposes, such as: (i) to increase expression of recombinant protein; (ii) to increase the solubility of the recombinant protein; and (iii) to aid in the purification of the recombinant, protein by acting as a ligand in affinity purification. Often, in fusion expression vectors, a proteolytic cleavage site is introduced at the junction of the fusion moiety and the recombinant protein to enable separation of the recombinant protein from the fusion moiety subsequent to purification of the fusion protein. Such enzymes, and their cognate recognition sequences, include Factor Xa, thrombin and enterokinase. Example fusion expression vectors include pGEX (Phannacia Biotech Inc; Smith and Johnson, 1988. Gene 67: 31-40), pMAL (New England Biolabs, Beverly, Mass.) and pRJT 5 (Pharmacia, Piscataway, N.J.) that fuse glutathione S-transferase (GST), maltose E binding protein, or protein A, respectively, to the target recombinant protein.

[0093] Examples of suitable inducible non-fusion E. coli expression vectors include pTrc (Arm-ami et af, (1988) Gene 69:301 -315) and pET l i d (Studier et a!.. GENE EXPRESSION TECHNOLOGY: METHODS IN ENZYMOLOGY 185, Academic Press, San Diego, Calif. (1990) 60-89).

[0094] In some embodiments, a vector is a yeast expression vector. Examples of vectors for expression in yeast Saccharomyces cerivisae include pYepSecl (Baldari, et a!., 1987. EMBO J. 6: 229-234), p Fa (Kuijan and Herskowitz, 1982. Cell 30: 933-943), pJRY88 (Sebultz et al., 1987. Gene 54: 113-123), pYES2 (Invitrogen Corporation, San Diego, Calif), and picZ (inVitrogen Corp, San Diego, Calif.),

[0095] In some embodiments, a vector drives protein expression in insect cells using baculovirus expression vectors. Baculovirus vectors available for expression of proteins in cultured insect cells (e.g., SF9 cells) include the pAc series (Smith, et al., 1983. Mol. Cell. Biol. 3: 2156-2165) and the pVL series (Lucklow and Summers, 1989. Virology 170: 31-39).

[0096] In some embodiments, a vector is capable of driving expression of one or more sequences in mammalian cells using a mammalian expression vector. Examples of mammalian expression vectors include pCDMS (Seed, 1987. Nature 329: 840) and pMT2PC (Kaufman, et al., 1987. EMBO J. 6: 187-195). When used in mammalian cells, the expression vector's control functions are typically provided by one or more regulatory elements. For example, commonly used promoters are derived from polyoma, adenovirus 2, cytomegalovirus, simian virus 40, and others disclosed herein and known in the art. For other suitable expression systems for both prokaryotie and eukaryotic cells see, e.g., Chapters 16 and 17 of Sambrook, et al., MOLECULAR CLONING: A LABORATORY MANUAL. 2nd ed„ Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N. Y., 1989.

[0097] In some embodiments, the recombinant mammalian expression vector is capable of directing expression of the nucleic acid preferentiall in a particular cell type (e.g., tissue- specific regulatory elements are used to express the nucleic acid). Tissue-specific regulatory elements are known in the art. Non-limiting examples of suitable tissue-specific promoters include the albumin promoter (liver-specific; Pmkert, et ai, 1987, Genes Dev. 1 ; 268-277), lymphoid-specific promoters (Calame and Eaton, 1988. Adv. Immunol. 43: 235-275), in particular promoters of T cell receptors (Winoto and Baltimore, 1989. EMBO J. 8: 729-733) and immunoglobulins (Baneiji, et af., 1983. Ceil 33: 729-740; Queen and Baltimore, 1983. Cell 33: 741-748), neuron-specific promoters (e.g., the neurofilament promoter; Byrne and Ruddle, 1989. Proc. Nail. Acad. Sci. USA 86: 5473-5477), pancreas-specific promoters (Edhmd, et al, 1985. Science 230: 912-916), and mammary gland-specific promoters (e.g., milk whey promoter; U.S. Pat. No. 4,873,3.16 and European Application Publication No. 264,166). Developmental!}'- regulated promoters are also encompassed, e.g., the murine hox promoters (Kessel and Grass, 1990. Science 249: 374-379) and the a-fetoprotein promoter (Campes and Tilghman, 1989. Genes Dev. 3: 537-546). With regards to these prokaryotie and eukaryotic vectors, mention is made of U.S. Patent 6,750,059, the contents of which are incorporated by reference herein in their entirety. Other embodiments of the invention may relate to the use of viral vectors, with regards to which mention is made of U.S. Patent application 13/092,085, the contents of which are incorporated by reference herein in their entirety. Tissue-specific regulatory elements are known in the art and in this regard, mention is made of U.S. Patent 7,776,321 , the contents of which are incorporated by reference herein in their entirety.

[0098] In some embodiments, a regulatory element is operably linked to one or more elements of a CRISPR system so as to drive expression of the one or more elements of the CRISPR system, in general, C ISPRs (Clustered Regularly Interspaced Short Palindromic Repeats), also known as SPIDRs (SPacer Interspersed Direct Repeats), constitute a family of D^'NA loci that are usually specific to a particular bacterial species. The CRISPR locus may comprise a distinct class of interspersed short sequence repeats (SSRs) that were recognized in E. coli (Ishino et al., J. Bacterid., 169:5429-5433 [1987]; and Nakata et al., J. Bacterid., 171 :3553- 3556 [ 1989]), and associated genes. Similar interspersed SSRs have been identified in Haloferax mediterranei, Streptococcus pyogenes, Anabaena, and Mycobacterium tuberculosis (See, Groenen et al., Mol. Microbiol, 10: 1057-1065 [1993]; Hoe et al, Emerg. Infect. Dis., 5:254-263 [1999]; Masepohl et al, Bioehim. Biophys. Acta 1307:26-30 [1996]; and Mojica et al, Mol. Microbiol, 17:85-93 [1995]). The CRISPR loci typically differ from other SSRs by the stmcture of the repeats, which have been termed short regularly spaced repeats (SRSRs) (Janssen et al, OMICS J. Integ. Biol, 6:23-33 [2002]; and Mojica et al, Mol. Microbiol, 36:244-246 [2000]). In general, the repeats are short elements that occur in clusters that are regularly spaced by unique intervening sequences with a substantially constant length (Mojica et al, [2000], supra). Although the repeat sequences are highly conserved between strains, the number of interspersed repeats and the sequences of the spacer regions typically differ from strain to strain (van Embden et al., J. BacterioL, 182:2393-2.401 [2000]). CRISPR loci have been identified in more than 40 prokaryotes (See e.g., Jansen et al., Mol. Microbiol., 43: 1565-1575 [2002]; and Mojica et al., [2005]) including, but not limited to Aeropyrum, Pyrobaculum, Sulfolobus, Arehaeoglobus, Halocarcuia, Methanobacterium, Metlianococcus, Methanosarcina, Methanopyrus, Pyrococcus, Picrophiius, Thermoplasma, Corynebacterium, Mycobacterium, Streptomyces, Aquifex, Porphyromonas, Chlorobium, Thermus, Bacillus, Listeria, Staphylococcus, Clostridium, Thermoanaerobacter, Mycoplasma, Fusobaeterium, Azarcus, Chromobacterium, Neisseria, Nitrosomonas, Desulfovibrio, Geobacter, Myxococcus, Campylobacter, Wolinella, Aeinetobacter, Erwinia, Escherichia, Legionella, Methylococcus, Pasteurella, Photobacterium, Salmonella, Xanthomonas, Yersinia, Treponema, and Thermotoga.

[0099] In general, "CRISPR system" refers collectively to transcripts and other elements involved in the expression of or directing the activity of CRISPR-associated ("Cas") genes, including sequences encoding a Cas gene, a tracr (tran -activating CRISPR) sequence (e.g. tracrRJMA or an active partial tracrR A), a tracr-mate sequence (encompassing a "direct repeat" and a tracrRNA-processed partial direct repeat in the context of an endogenous CRISPR system), a guide sequence (also referred to as a "spacer" in the context of an endogenous CRISPR system), or other sequences and transcripts from a CRISPR locus. In embodiments of the invention the terms guide sequence and guide RNA are used interchangeably. In some embodiments, one or more elements of a CRISPR system is derived from a type I, type II, or type II I CRISPR system. In some embodiments, one or more elements of a CRISPR. system is derived from a particular organism which may comprise an endogenous CRISPR system, such as Streptococcus pyogenes. In general, a CRISPR system is characterized by elements that promote the formation of a CRISPR complex at the site of a target sequence (also referred to as a protospacer in the context of an endogenous CRISPR system). In the context of formation of a CRISPR complex, "target sequence" refers to a sequence to which a guide sequence is designed to have complementarity, where hybridization between a target sequence and a guide sequence promotes the formation of a CRISPR complex. A target sequence may comprise any polynucleotide, such as DNA. or RNA polynucleotides. In some embodiments, a target sequence is located in the nucleus or cytoplasm of a cell .

[00100] In preferred embodiments of the invention, the CRISPR system is a type II CRISPR system and the Cas enzyme is Cas9, which catalyzes DNA cleavage. Enzymatic action by Cas9 derived from Streptococcus pyogenes or any closely related Cas9 generates double stranded breaks at target site sequences whic hybridize to 20 nucleotides of the guide sequence and that have a protospacer-adjacent motif (PAM) sequence NGG following the 20 nucleotides of the target sequence. CRISPR activity through Cas9 for site-specific DNA recognition and cleavage is defined by the guide sequence, the tracr sequence that hybridizes in part to the guide sequence and the PAM sequence. More aspects of the CRISPR system are described in Karginov and Hannon, The CRISPR system: small RNA-guided defense in bacteria and archaea, Mole Cell 2010, January 15; 37(1): 7,

[00101] The type II CRISPR locus from Streptococcus pyogenes SF370 contains a cluster of four genes Cas9, Casl, Cas2, and Csnl, as well as two non-coding RNA elements, tracrRNA and a characteristic array of repetitive sequences (direct repeats) interspaced by short stretches of non-repetitive sequences (spacers, about 30bp each). In this system, targeted DNA double- strand break (DSB) is generated in four sequential steps (Figure 2A). First, two non-coding RNAs, the pre-crRNA array and tracrRNA, are transcribed from the CRISPR locus. Second, tracrRNA hybridizes to the direct repeats of pre-crRNA, which is then processed into mature crRNAs containing individual spacer sequences. Third, the mature crRNA :tracrRN A comple directs Cas9 to the DNA target consisting of the protospacer and the corresponding PAM via heterodupiex formation between the spacer region of the crRNA and the protospacer DNA. Finally, Cas9 mediates cleavage of target DNA upstream of PAM to create a DSB within the protospacer (Figure 2 A). Figure 2B demonstrates the nuclear localization of the codon optimized Cas9. To promote precise transcriptional initiation, the RNA polymerase Ill-based U6 promoter was selected to drive the expression of tracrRNA (Figure 2C). Similarly, a U6 promoter-based construct was developed to express a pre-crRNA array consisting of a single spacer flanked by two direct repeats (DRs, also encompassed by the term "tracr-mate sequences"; Figure 2C). The initial spacer was designed to target a 33-base-pair (bp) target site (30-bp protospacer plus a 3 -bp CRISPR motif (PAM) sequence satisfying the NGG recognition motif of Cas9) in the human EMX1 locus (Figure 2C), a key gene in the development of the cerebral cortex. [00102] Typically, in the context of an endogenous CRISPR system, formation of a CRISPR complex (which may comprise a guide sequence hybridized to a target sequence and complexed with one or more Cas proteins) results in cleavage of one or both strands in or near (e.g. within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, or more base pairs from) the target sequence. Without wishing to be bound by theory, the tracr sequence, which may comprise or consist of all or a portion of a wild-type tracr sequence (e.g. about or more than about 20, 26, 32, 45, 48, 54, 63, 67, 85, or more nucleotides of a wild-type tracr sequence), may also form part of a CRISPR complex, such as by hybridization along at least a portion of the tracr sequence to all or a portion of a tracr mate sequence that is operably linked to the guide sequence. In some embodiments, one or more vectors driving expression of one or more elements of a CRISPR system are introduced into a host cell such that expression of the elements of the CRISPR system direct formation of a CRISPR complex at one or more target sites. For example, a Cas enzyme, a guide sequence linked to a tracr-mate sequence, and a tracr sequence could each be operably linked to separate regulatory elements on separate vectors. Alternatively, two or more of the elements expressed from the same or different regulatory elements, may be combined in a single vector, with one or more additional vectors providing any components of the CRISPR system not included in the first vector. CRISPR system elements that are combined in a single vector .may be arranged in any suitable orientation, such as one element located 5' with respect to ("upstream" of) or 3' with respect to ("downstream" of) a second element. The coding sequence of one element may be located on the same or opposite strand of the coding sequence of a second element, and oriented in the same or opposite direction. In some embodiments, a single promoter drives expression of a transcript encoding a CRISPR enzyme and one or more of the guide sequence, tracr mate sequence (optionally operably linked to the guide sequence), and a tracr sequence embedded within one or more intron sequences (e.g. each in a different intron, two or more in at least one intron, or all in a single intron). In some embodiments, the CRISPR enzyme, guide sequence, tracr mate sequence, and tracr sequence are operably linked to and expressed from the same promoter.

[00103] In some embodiments, a vector may comprise one or more insertion sites, such as a restriction endonuclease recognition sequence (also referred to as a "cloning site"). In some embodiments, one or more insertion sites (e.g. about or more than about I, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more insertion sites) are located upstream and/or downstream of one or more sequence elements of one or .more vectors. In some embodiments, a vector may comprise an insertion site upstream of a tracr mate sequence, and optionally downstream of a regulatory element operably linked to the tracr mate sequence, such that following insertion of a guide sequence into the insertion site and upon expression the guide sequence directs sequence-specific binding of a CRISPR complex to a target sequence in a eukaryotic cell. In some embodiments, a vector may comprise two or more insertion sites, each insertion site being located between two tracr mate sequences so as to allow insertion of a guide sequence at each site. In such an arrangement, the two or more guide sequences may comprise two or more copies of a single guide sequence, two or more different guide sequences, or combinations of these. When multiple different guide sequences are used, a single expression construct may be used to target CRISPR activity to multiple different, corresponding target sequences within a cell. For example, a single vector may comprise about or more than about I, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or more guide sequences. In some embodiments, about or more than about 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, or more such guide-sequence-containing vectors may be provided, and optio ally delivered to a cell.

[00104] In some embodiments, a vector may comprise a regulatory element operably linked to an enzyme-coding sequence encoding a CRISPR enzyme, such as a Cas protein. Non-limiting examples of Cas proteins include Casl, Casl B, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7, Cas8, Cas9 (also known as Csnl and Csxl2), Cas 10, Csyl, Csy2, Csy3, Csel, Cse2, Csc l , Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmrl, Cmr3, Cmr4, Cmr5, Cmr6, Csbl, Csb2, Csb3, Csxl7, Cs l4, CsxlO, Csx16, CsaX, Csx3, Csxl, Csx15, Csfl , Csf2, CsO, Csf4, homologies thereof, or modified versions thereof. In some embodiments, the unmodified CRISPR enzyme has DNA cleavage activity, such as Cas9. In some embodiments, the CRISPR enzyme directs cleavage of one or both strands at the location of a target sequence, such as within the target sequence and/or within the complement of the target sequence. In some embodiments, the CRISPR enzyme directs cleavage of one or both strands within about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 50, 100, 200, 500, or more base pairs from the first or last nucleotide of a target sequence. In some embodiments, a vector encodes a CRISPR enzyme that is mutated to with respect to a corresponding wild-type enzyme such that the mutated CRISPR enzyme lacks the ability to cleave one or both strands of a target polynucleotide containing a target sequence. For example, an aspartate-to-alanine substitution (D10A) in the RuvC I catalytic domain of Cas9 from S. pyogenes converts Cas9 from a nuclease that cleaves both strands to a nickase (cleaves a single strand). Other examples of mutations that render Cas9 a nickase include, without limitation, H840A, N854A, and N863A. As a further example, two or more catalytic domains of Cas9 (RuvC I, RuvC II, and RuvC III or the HNH domain) may be mutated to produce a mutated Cas9 substantially lacking all DNA cleavage activity, in some embodiments, a D1 QA mutation is combmed with one or more of H840A, N854A, or N863A mutations to produce a Cas9 enzyme substantially lacking all DNA cleavage activity. In some embodiments, a CR iSPR enzyme is considered to substantially lack all DNA cleavage activity when the DNA cleavage activity of the mutated enzyme is less than about 25%, 10%, 5%, 1 %, 0.1 %, 0.01 %, or lower with respect to its non-mutated form. Where the enzyme is not SpCas9, mutations may be made at any or al l residues corresponding to positions 10, 762, 840, 854, 863 and/or 986 of SpCas9 (which may be ascertained for instance by standard sequence comparison tools . In particular, any or all of the following mutations are preferred in SpCas9: D10A, E762A, H840A, N854A, N863A and/or D986A; as well as conservative substitution for any of the replacement amino acids is also envisaged. The same (or conservative substitutions of these mutations) at corresponding positions in other Cas9s are also preferred. Particularly preferred are D10 and H840 in SpCas9 . However, in other Cas9s, residues corresponding to SpCas9 D10 and H840 are also preferred.

[00105] An aspartate-to-alanine substitution (D10A) in the RuvC I catalytic domain of SpCas9 was engineered to convert the nuclease into a nickase (SpCas9n) (see e.g. Sapranauskas et a!., 2011 , Nucleic Acis Research, 39: 9275; Gasiunas et a!,, 2012, Proc. Natl. Acad. Sci. USA, 109:E2579), such that nicked genomic DNA undergoes the high-fidelity homoiogy-directed repair (HDR). Surveyor assay confirmed that SpCas9rs does not generate indels at the EMX1 protospacer target. Co-expression of EMX 1 -targeting chimeric crRNA (having the tracrRNA component as well) with SpCas9 produced indels in the target site, whereas co-expression with SpCas9n did not (n=3). Moreover, sequencing of 327 amplicons did not detect any indels induced by SpCas9n. The same locus was selected to test CRISPR -mediated HR by co- transfecting HE 293FT cells with the chimeric RNA targeting EMX1 , hSpCas9 or hSpCas9n, as well as a HR template to introduce a pair of restriction sites (Hindlll and Nhel) near the protospacer.

[00106] Preferred orthologs are described herein. A Cas enzyme may be identified Cas9 as this can refer to the general class of enzymes that share homology to the biggest nuclease with multiple nuclease domains from the type II CRISPR system. Most preferably, the Cas9 enzyme is from, or is derived from, spCas9 or saCas9. By derived, Applicants mean that the derived enzyme is largely based, in the sense of having a high degree of sequence homology with, a wifdtype enzyme, but that it has been mutated (modified) in some way as described herein.

[00107] In some embodiments, an enzyme coding sequence encoding a CRISPR enzyme is codon optimized for expression in particular cells, such as eukaryotic cells. The eukaryotic cells may be those of or derived from a particular organism, such as a mammal, including but not limited to human, mouse, rat, rabbit, dog, or non-human primate. In general, codon optimization refers to a process of modifying a nucleic acid sequence for enhanced expression in the host cells of interest by replacing at least one codon (e.g. about or more than about 1, 2, 3, 4, 5, 10, 15, 20, 25, 50, or more codons) of the native sequence with codons that are more frequently or most frequently used in the genes of that host cell while maintaining the native amino acid sequence. Various species exhibit particular bias for certain codons of a particular amino acid. Codon bias (differences in codon usage between organisms) often correlates with the efficiency of translation of messenger RNA (mRNA), which is in turn believed to be dependent on, among other things, the properties of the codons being translated and the availability of particular transfer RNA (t NA) molecules. The predominance of selected tRNAs in a cell is generally a reflection of the codons used most frequently in peptide synthesis. Accordingly, genes can be tailored for optimal gene expression in a given organism based on codon optimization. Codon usage tables are readily available, for example, at the "Codon Usage Database" available at www.kazusa.orjp/codon/ (visited Jul. 9, 2002), and these tables can be adapted in a number of ways. See Nakamura, Y., et al. "Codon usage tabulated from the international DNA sequence databases: status for the year 2000" Nucl. Acids Res. 28:292 (2000). Computer algorithms for codon optimizing a particular sequence for expression in a particular host cell are also available, such as Gene Forge (Aptagen; Jacobus, PA), are also available. In some embodiments, one or more codons (e.g. 1 , 2, 3, 4, 5, 10, 15, 20, 25, 50, or more, or al l codons) in a sequence encoding a CRISPR enzyme correspond to the most frequently used codon for a particular amino acid.

[00108] In some embodiments, a vector encodes a CRISPR enzyme which may comprise one or more nuclear localization sequences (NLSs), such as about or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10. or more NLSs. In some embodiments, the CRISPR enzyme may comprise about or more than about 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, or more NLSs at or near the amino-terminus, about or more than about 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, or more NLSs at or near the carboxy-terminus, or a combination of these (e.g. one or more NLS at the amino-terminus and one or more NLS at the carboxy terminus). When more than one NLS is present, each may be selected independently of the others, such that a single NLS may be present in more than one copy and/or in combination with one or more other NLSs present in one or more copies. In a preferred embodiment of the invention, the CRISPR enzyme may comprise at most 6 N LSs. In some embodiments, an NLS is considered near the N- or C-terminus when the nearest amino acid of the NLS is within about 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 40, 50, or more amino acids along the polypeptide chain from the N- or C-terminus. Non-limiting examples of NLSs include an NLS sequence derived from; the NLS of the SV40 virus large T-antigen, having the amino acid sequence PK KR V; the NLS from nucleoplasm^ (e.g. the nucieoplasmin bipartite NLS with the sequence KRPAATKKAGQA K ); the c-myc NLS having the amino acid sequence PAA RV LD or RQRRNELKRSP; the hRNPAl M9 NLS having the sequence NQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGY; the sequence

RMRIZFKNKGKDl^'AELRRRRVEVSVELRKAKKDEQILKRRNV of the IBB domain from importin-alpha; the sequences VSR K RPRP and PPKKARED of the myoma T protein; the sequence POPKKKPL of human p53; the sequence SAl .1 ΜΛΡ of mouse c-abi IV; the sequences DRLRR and P QKKR of the influenza vims NS 1 ; the sequence RKLKKKJKKL of the Hepatitis virus delta antigen; the sequence REKKKFL RR of the mouse Mxl protein; the sequence KRKGDEVDGVDEVAKKKSKK of the human poiy(ADP-ribose) polymerase; and the sequence RKCLQAG NLEiAR TK of the steroid hormone receptors (human) glucocorticoid.

[00109] In general, the one or more NLSs are of sufficient strength to drive accumulation of the CRISPR enzyme in a detectable amount in the nucleus of a eukaryotic cell. In general, strength of nuclear localization activity may derive from the number of NLSs in the CRISPR enzyme, the particular NLS(s) used, or a combination of these factors. Detection of accumulation in the nucleus may be performed by any suitable technique. For example, a detectable marker may be fused to the CRISPR enzyme, such that location within a cell may be visualized, such as in combination with a means for detecting the location of the nucleus (e.g. a stain specific for the nucleus such as DAP I). Cell nuclei may also be isolated from cells, the contents of which may then be analyzed by any suitable process for detecting protein, such as immiinohistochemistry, Western blot, or enzyme activity assay. Accumulation in the nucleus may also be determined indirectly, such as by an assay for the effect of CRISPR complex formation (e.g. assay for DNA cleavage or mutation at the target sequence, or assay for altered gene expression activity affected by CRISPR complex formation and/or CRISPR enzyme activity), as compared to a control no exposed to the CRISPR enzyme or complex, or exposed to a CRISPR enzyme lacking the one or more NLSs.

[00110] In general, a guide sequence is any polynucleotide sequence having sufficient complementarity with a target polynucleotide sequence to hybridize with the target sequence and direct sequence-specific binding of a CRISPR complex to the target sequence. In some embodiments, the degree of complementari y between a guide sequence and its corresponding target sequence, when optimally aligned using a suitable alignment algorithm, is about or more than about 50%, 60%, 75%, 80%, 85%, 90%, 95%, 97.5%, 99%, or more. Optimal alignment may be determined with the use of any suitable algorithm for aligning sequences, non-limiting example of which include the Smith- Waterman algorithm, the N eedleman-Wunsch algorithm, algorithms based on the Burrows-Wheeler Transform (e.g. the Burrows Wheeler Aligner), ClustalW, Clustal X, BLAT, Novoalign (Novocraft Technologies; available at www.novocraft.com), ELAND (illumina, San Diego, CA), SOAP (available at soap.genomics.org.cn), and Maq (available at maq.sourceforge.net). In some embodiments, a guide sequence is about or more than about 5, 10, 1 1 , 12, 13, 14, 15, 16, 1 7, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 75, or more nucleotides in length. In some embodiments, a guide sequence is less than about 75, 50, 45, 40, 35, 30, 25, 20, 15, 12, or fewer nucleotides in length. The ability of a guide sequence to direct sequence-specific binding of a CRISPR comple to a target sequence may be assessed by any suitable assay. For example, the components of a CRISPR system sufficient to form a CRISPR complex, including the guide sequence to be tested, may be provided to a host cell having the corresponding target sequence, such as by transfection with vectors encoding the components of the CRIS PR sequence, fol lowed by an assessment of preferential cleavage within the target sequence, such as by Surveyor assay as described herein. Similarly, cleavage of a target polynucleotide sequence may be evaluated i a test tube by providing the target sequence, components of a CRISPR complex, including the guide sequence to be tested and a control guide sequence different from the test guide sequence, and comparing binding or rate of cleavage at the target sequence between the test and control guide sequence reactions. Other assays are possible, and will occur to those skilled in the art.

[00111] A guide sequence may be selected to target any target sequence. In some embodiments, the target sequence is a sequence within a genome of a cell. Exemplary target sequences i clude those that are unique i the target genome. For example, for the S, pyogenes Cas9, a unique target sequence in a genome may include a Cas9 target site of the form MMMMMMMMNNNNNNNNNNNNXGG where NNNNNNNNNNNNXGG (N is A, G, T, or C; and X can be anything) has a single occurrence in the genome. A. unique target sequence in a genome may include an 5. pyogenes Cas9 target site of the form MMMMMMMMMNNNNNNNNNNNXGG where NNNNNNNNNNNXGG (N is A, G, T, or C; and X can be anything) has a single occurrence in the genome. For the S. thermophihis CRISPR1 Cas9, a unique target sequence in a genome may include a Cas9 target site of the form MMMMMMMMNNNNNNNNNNNNXXAGAAW where NNNNNNNNNNNNXXAGAAW (N is A. G, T, or C; X can be anything; and W is A or T) has a single occurrence in the genome. A unique target sequence in a genome .may include an S, thermophiius CRJSPR1 Cas9 target site of the form MMMMMMMMMNNNNNNNNNNNXXAGAAW^" where

NNNNNNNNNNNXXAGAAW (N is A, G, T, or C; X can be anything; and W is A or T) has a single occurrence in the genome. For the S. pyogenes Cas9, a unique target sequence in a genome may include a Cas9 target site of the form M MM MM MM MNNNNNNNNNNNNXG GX G where NNNNNNNNNNNNXGGXG (N is A, G, T, or C; and X can be anything) has a single occurrence in the genome. A unique target sequence in a genome may include an S. pyogenes Cas9 target site of the form MMMM MM MMMNNNNNNNNNNNXGGXG where NNNNNNNNNNNXGGXG i^'N is Λ. G, T, or C; and X can be anything) has a single occurrence in the genome. In each of these sequences "M" may be A, G, T, or C, and need not be considered in identifying a sequence as unique.

[00 12] hi some embodiments, a guide sequence is selected to reduce the degree of secondary structure within the guide sequence. In some embodiments, about or less than about 75%, 50%, 40%, 30%, 25%>, 20%, 15%, 10%, 5%, 1%, or fewer of the nucleotides of the guide sequence participate in self-complementary base pairing when optimally folded. Optimal folding may be determined by any suitable polynucleotide folding algorithm. Some programs are based on calculating the minimal Gibbs free energy. An example of one such algorithm is mFold, as described by Zuker and Stiegler (Nucleic Acids Res. 9 (1981), 133-148). Another example folding algorithm is the online webserver RNAfold, developed at Institute for Theoretical Chemistry at the University of Vienna, using the centroid structure prediction algorithm (see e.g. A.R. Gruber et aL, 2008, Cell 106(1): 23-24; and PA Carr and GM Church, 2009, Nature Biotechnology 21 ^'(12): 1151 -62).

[001131 In general, a tracr mate sequence includes any sequence that has sufficient complementarity with a tracr sequence to promote one or more of: (I) excision of a guide sequence flanked by tracr mate sequences in a ceil containing the corresponding tracr sequence; and (2) formation of a CRISPR complex at a target sequence, wherein the CRISP R complex may comprise the tracr mate sequence hybridized to the tracr sequence. In general, degree of complementarity is with reference to the optimal alignment of the tracr mate sequence and tracr sequence, along the length of the shorter of the two sequences. Optimal alignment may be determined by any suitable alignment algorithm, and may further account for secondary structures, such as self-complementarity within either the tracr sequence or tracr mate sequence. In some embodiments, the degree of complementarity between the tracr sequence and tracr mate sequence along the length of the shorter of the two when optimally aligned is about or more than about 25%, 30%, 40%, 50%, 60%, 70%», 80%, 90%, 95%, 97.5%, 99%, or higher. In some embodiments, the tracr sequence is about or more than about 5, 6, 7, 8, 9, 10, I I, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 50, or more nucleotides in length. In some embodiments, the tracr sequence and tracr mate sequence are contained within a single transcript, such that hybridization between the two produces a transcript having a secondary structure, such as a hairpin. In an embodiment of the invention, the transcript or transcribed polynucleotide sequence has at least two or more hairpins. In preferred embodiments, the transcript has two, three, four or five hairpins. In a further embodiment of the invention, the transcript has at most five hairpins. In a hairpin structure the portion of the sequence 5' of the final "N" and upstream of the loop corresponds to the tracr mate sequence, and the portion of the sequence 3' of the loop corresponds to the tracr sequence. Further non-limiting examples of single polynucleotides which may comprise a guide sequence, a tracr mate sequence, and a tracr sequence are as fol lows (listed 5' to 3'), where "N" represents a base of a guide sequence, the first block of lower case letters represent the tracr mate sequence, and the second block of lower case letters represent the tracr sequence, and the final poly-T sequence represents the transcription terminator: (1) N N N N N N NNNNNNNNgtttitgtactctcaagatitaG^ Ataaatcitgcagaagctacaaagataaggctt catgccgaaatcaacaccctgtcatrttatggcagggtgttttcgttatttaaTTT TT; (2) NNNNNNNNNNN gtttttgtactctcaGAAAtgcagaagctacaaagataaggcttcatgccgaaatca acaccctgtcattttatggcagggtgttttcgttatttaaTTTTTT; (3) NNNNNN NNNNNNNgtttttgtactctcaGAAAtgcagaagctacaaagataaggcttcatgccgaaatca acaccctgtcattttatggcagggtgtTTTTTT; (4) NNNNNNNNNNNNNNNNNNNNgttttagagctaGAAAtagcaa

agtggcaccgagtcggtgcTTTTTT; (5) NNNNNNNNNNNNNNNNNNNNgtlttagagc aGAAATAGc^

aaagigTTTTTTT; and (6)

\\\\\\\\\\\\\\\ N\ N\ NuU!!agagciauAA A ! AGc^^

TTT. In some embodiments, sequences (1 ) to (3) are used in combination with Cas9 from S. thermophilics CRISPRl. In some embodiments, sequences (4) to (6) are used in combination with Cas9 from S. pyogenes. In some embodiments, the tracr sequence is a separate transcript from a transcript which may comprise the tracr mate sequence.

[00114] In some embodiments, a recombination template is also provided, A. recombination template may be a component of another vector as described herein, contained in a separate vector, or provided as a separate polynucleotide. In some embodiments, a recombination template is designed to serve as a template in homologous recombination, such as within or near a target sequence nicked or cleaved by a CRISPR enzyme as a part of a CRISPR complex. A template polynucleotide may be of any suitable length, such as about or more than about 10, 15, 20, 25, 50, 75, 100, 150, 200, 500, 1000, or more nucleotides in length. In some embodiments, the template polynucleotide is complementary to a portion of a polynucleotide which may comprise the target sequence. When optimally aligned, a template polynucleotide might overlap with one or more nucleotides of a target sequences (e.g. about or more than about 1 , 5, 10, 15, 20, or more nucleotides). In some embodiments, when a template sequence and a polynucleotide which may comprise a target sequence are optimally aligned, the nearest nucleotide of the template polynucleotide is within about 1, 5, 10, 15, 20, 25, 50, 75, 100, 200, 300, 400, 500, 1000, 5000, 10000, or more nucleotides from the target sequence. [00115] In some embodiments, the CRISPR enzyme is part of a fusion protein which may comprise one or more heterologous protein domains (e.g. about or more than about 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, or more domains in addition to the CRISPR enzyme). A CRISPR enzyme fusion protein may comprise any additional protein sequence, and optionally a linker sequence between any two domains. Examples of protein domains that may be fused to a CRISPR enzyme include, without limitation, epitope tags, reporter gene sequences, and protein domains having one or more of the following activities: methylase activity, demethylase activity, transcription activation activity, transcription repression activity, transcription release factor activity, histone modification activity, RNA cleavage activity and nucleic acid binding activity. Non-limiting examples of epitope tags include histidine (His) tags, V5 tags, FLAG tags, influenza hemagglutinin (HA) tags, Myc tags, VSV-G tags, and thioredoxin (Trx) tags. Examples of reporter genes include, but are not limited to, glutathione-S-transferase (GST), horseradish peroxidase (HRP), chloramphenicol acetyltransfera.se (CAT) beta-galactosidase, beta- glucuroiiidase, luciferase, green fluorescent protein (GFP), HcRed, DsRed, cyan fluorescent protein (CFP), yellow fluorescent protein (YFP), and autofluorescent proteins including blue fluorescent protein (BFP). A CRISPR enzyme may be fused to a gene sequence encoding a protein or a fragment of a protein thai bind DNA molecules or bind other cellular molecules, including but not limited to maltose binding protein (MBP), S-tag, Lex A DNA binding domain (DBD) fusions, GAL4 DNA binding domain fusions, and herpes simplex vims (HSV) BP 16 protein fusions. Additional domains that may form part of a fusion protein which may comprise a CRISPR enzyme are described in US20110059502, incorporated herein by reference. In some embodiments, a tagged CRISPR enzyme is used to identify the location of a target sequence.

[00116] In some aspects, the invention provides methods which may comprise delivering one or more polynucleotides, such as or one or more vectors as described herein, one or more transcripts thereof, and/or one or proteins transcribed therefrom, to a host cell. In some aspects, the invention further provides cells produced by such methods, and animals which may comprise or produced from such cells. In some embodiments, a CRISPR enzyme in combinatio with (and optionally compiexed with) a guide sequence is delivered to a cell. Conventional viral and non-viral based gene transfer methods can be used to introduce nucleic acids in mammalian cells or target tissues. Such methods can be used to administer nucleic acids encoding components of a CRISPR system to cells in culture, or in a host organism. Non-viral vector delivery systems include DNA plasmids, RNA (e.g. a transcript of a vector described herein), naked nucleic acid, and nucleic acid compiexed with a delivery vehicle, such as a liposome. Viral vector delivery systems include DNA and RNA viruses, which have either episomal or integrated genomes after delivery to the cell. For a review of gene therapy procedures, see Anderson, Science 256:808- 813 (1992); Nabel & Feigner, TIBTECH 11 :211-217 (1993); Mitani & Caskey, TIBTECH 1 1 ; 162-166 (1993); Dillon, TIBTECH 1 1 : 167-175 (1993); Miller, Nature 357:455-460 (1992); Van Brunt, Biotechnology 6( 10): 1 149-1154 (1988); Vigne, Restorative Neurology and Neuroscience 8:35-36 (1995); Kremer & Perricaudet. British Medical Bulletin 51(l):31-44 (1995); Haddada et al., in Current Topics in Microbiology and Immunology Doerfler and Bohm (eds) (1995); and Yu et al, Gene Therapy 1 : 13-26 (1994).

|00117| Methods of non-viral delivery of nucleic acids include lipofection, microinjection, biolistics, virosomes, liposomes, imraunoliposomes, polycation or lipid :nucleic acid conjugates, naked DNA, artificial virions, and agent-enhanced uptake of DNA. Lipofection is described in e.g., U.S. Pat. Nos. 5,049,386, 4,946,787; and 4,897,355) and lipofection reagents are sold commercially (e.g., Transfectam™ and Lipofectin™). Cationic and neutral lipids that are suitable for efficient receptor-recognition lipofection of polynucleotides include those of Feigner, WO 91/17424; WO 91/16024. Delivery can be to cells (e.g. in vitro or ex vivo administration) or target tissues (e.g. in vivo administration).

[00118] The preparation of lipid:nucleic acid complexes, including targeted liposomes such as immunolipid complexes, is well known to one of skill in the art (see, e.g., Crystal, Science 270:404-410 (1995); Blaese et al, Cancer Gene Ther, 2:291-297 (1995); Behr et al, Bioconjugate Chem. 5:382-389 (1994); Remy et al, Bioconjugate Chem. 5:647-654 (1994); Gao et al., Gene Therapy 2:710-722 (1995); Ahmad et ai., Cancer Res. 52:4817-4820 (1992); U.S. Pat. Nos. 4,186,183, 4,237,344, 4,235,871, 4,261,975, 4,485,054, 4,501,728, 4,774,085, 4,837,028, and 4,946,787).

[0011 ] The use of RNA or DNA viral based systems for the delivery of nucleic acids take advantage of highly evolved processes for targeting a virus to specific cells in the body and trafficking the viral payload to the nucleus. Viral vectors can be administered directly to patients (in vivo) or they can be used to treat cells in vitro, and the modified cells may optionally be administered to patients (ex vivo). Conventional viral based systems could include retroviral, lenti virus, adenoviral, adeno-associated and herpes simplex virus vectors for gene transfer. Integration in the host genome is possible with the retrovirus, lentivirus, and adeno-assoeiated virus gene transfer methods, often resulting in long term expression of the inserted transgene. Additionally, high tra sduction efficiencies have been observed in many different ceil types and target tissues.

[00120] The tropism of a retrovirus can be altered by incorporating foreign envelope proteins, expanding the potential target population of target cells. Lentiviral vectors are retroviral vectors that are able to transduce or infect non-dividing ceils and typically produce high viral titers. Selectio of a retroviral gene transfer system would therefore depend on the target tissue. Retroviral vectors are comprised of cis-acting long terminal repeats with packaging capacity for up to 6-10 kb of foreign sequence. The minimum cis-acting LT s are sufficient for replication and packaging of the vectors, which are then used to integrate the therapeutic gene into the target ceil to provide permanent transgene expression. Widely used retroviral vectors include those based upon murine leukemia virus (MuLV), gibbon ape leukemia virus (GaLV), Simian Imrmmo deficiency vims (SIV), human immuno deficiency vims (HIV), and combinations thereof (see, e.g., Buchscher et al., J. Virol. 66:2731 -2739 (1992); Johann et al, J. Virol. 66: 1635-1640 ( 1992); Sommnerfelt et al., Virol. 176:58-59 (1990); Wilson et al., J. Virol. 63:2374-2378 (1989); Miller et al, J. Virol. 65:2220-2224 (1991); PCT/US94/05700).

[00121] In applications where transient expression is preferred, adenoviral based systems may be used. Adenoviral based vectors are capable of very high transduction efficiency in many cell types and do not require cell division. With such vectors, high titer and levels of expression have been obtained. This vector can be produced in large quantities in a relatively simple system. Adeno-associated virus ("AAV") vectors may also be used to transduce cells with target nucleic acids, e.g., in the in vitro production of nucleic acids and peptides, and for in vivo and ex vivo gene therapy procedures (see, e.g., West et al., Virology 160:38-47 (1987); U.S. Pat. No. 4,797,368; WO 93/24641 ; otin, Human Gene Therapy 5:793-801 (1994); Muzyczka, J. Clin. Invest. 94:13 1 (1994). Construction of recombinant AAV vectors are described in a number of publications, including U.S. Pat. No. 5,173,41.4; Tratschin et al., ol. Cell. Biol. 5:3251-3260 (1985); Tratschin, et al, Mol. Cell. Biol. 4:2072-2081 (1984); Hermonat & Muzyczka, PNAS 81 :6466-6470 (1984); and Samuiski et. al., .1. Virol. 63:03822-3828 (1989).

[001221 Packaging cells are typically used to form vims particles that are capable of infecting a host cell. Such cells include 293 cells, which package adenovirus, and ψ2 cells or PA317 cells, which package retrovirus. Viral vectors used in gene therapy are usually generated by producer a cell line that packages a nucleic acid vector into a viral particle. The vectors typically contain the minimal viral sequences required for packaging and subsequent integration into a host, other viral sequences being replaced by an expression cassette for the polynucleotide(s) to be expressed. The missing viral functions are typically supplied in trans by the packaging cell line. For example, AAV vectors used in gene therapy typically only possess FIR sequences from the AAV genome which are required for packaging and integration into the host genome. Viral DNA is packaged in a cell line, which contains a helper plasmid encoding the other AAV genes, namely rep and cap, but lacking Fill sequences. The cell line may also infected with adenovirus as a helper. The helper virus promotes replication of the AAV vector and expression of AAV genes from the helper plasmid. The helper plasmid is not packaged in significant amounts due to a lack of ITR sequences. Contamination with adenovirus can be reduced by, e.g., heat treatment to which adenovirus is more sensitive than AAV. Additional methods for the delivery of nucleic acids to cells are known to those skilled in the art. See, for example, US20030087817, incorporated herein by reference.

[00123] In some embodiments, a host cell is transiently or non-transiently transfected with one or more vectors described herein. I some embodiments, a cell is transfected as it naturally occurs in a subject. In some embodiments, a cell that is transfected is taken from a subject. In some embodiments, the cell is derived from cells taken from a subject, such as a cell line. A wide variety of cell lines for tissue culture are known in the art. Examples of cell lines include, but are not limited to, C816L CCRF-CEM, MOLT, mIMCD-3, NHDF, HeLa-S3, Huhl, Huh4, Huh7, HUVEC, HASMC, HEKn, HE a, MiaPaCe!i, Panel , PC-3, TF1, CTLL-2, OR, Rat6, CV1, RPTE, A10, T24, J82, A375, ARH-77, Calul, SW48Q, SW620, SKOV3, SK-UT, CaCo2, P388D1, SEM-K2, WEHI-231, HB56, TIB55, Jurkat, J45.01, LRMB, Bcl-1, BC-3, IC21, DLD2, Raw264.7, NRK, NRK-52E, MRC5, MEF, Hep G2, HcLa B, HcLa T4, COS, COS-1 , COS-6, COS-M6A, BS-C-1 monkey kidney epithelial, BALB/ 3T3 mouse embryo fibroblast, 3T3 Swiss, 3T3-L1, 132-d5 human fetal fibroblasts; 10.1. mouse fibroblasts, 293-T, 3T3, 721 , 9L, A2780, A2780ADR, A2780cis, A172, A20, A253, A431, A-549, ALC, B16, B35, BCP-1 cells, BEAS- 2B, bEnd.3, BHK-21, BR 293, BxPC3, C3H-10T1/2, C6/36, Cal-27, CHO, CHO-7, CHO-IR, CHO-K1, CHO-K2, CHQ-T, CHO Dhfr -/-, COR-L23, COR-L23/CPR, COR-L23/5010, CGR- L23/R23, COS-7, COV-434, CML Ti, CMT, CT26, D17, DH82, DU145, DuCaP, EL4, EM2, EM3, EMT6/AR1 , EMT6/AR10.0, FM3, H1299, H69, HB54, HB55, HCA2, HEK-293, HeLa, Hepal cl c7, HL-60, HMEC, HT-29, Jurkat, JY cells, K562 cells, u812, CL22, KGl , Y01 , LNCap, Ma-Mel 1-48, MC-38, MCF-7, MCF-IOA, MDA-MB-231, MDA-MB-468, MDA-MB- 435, MDCK II, MDCK. 11, MOR/0.2R, MONO-MAC 6, MTD-1 A, My End, NCI-H69/CPR, NCI-H69 LX10, NCI-H69/LX20, NCI-H69/LX4, NIH-3T3, NALM-1, NW-145, OPC / OPCT cell lines, Peer, PNT-1A / P^'NT 2, RenCa, RIN-5F, RMA RMAS, Saos-2 cells, Sf-9, SkBr3, T2, T-47D, T84, ΊΉΡ1 cell line, U373, U87, U937, VCaP, Vero cells, WM39, WT-49, X63, YAC-1, YAR, and transgenic varieties thereof. Cell lines are available from a variety of sources known to those with skill in the art (see, e.g., the American Type Culture Collection (ATCC) (Manassus, Va.)). In some embodiments, a cell transfected with one or more vectors described herein is used to establish a new cell line which may comprise one or more vector-derived sequences, in some embodiments, a cell transiently transfected with the components of a CRISPR system as described herein (such as by transient transfection of one or more vectors, or transfection with RNA), and modified through the activity of a CRISPR complex, is used to establish a new cell line which may comprise ceils containing the modification but lacking any other exogenous sequence. In some embodiments, cells transiently or non-transiently transfected with one or more vectors described herein, or cell lines derived from such cells are used in assessing one or more test compounds.

[00124] In some embodiments, one or more vectors described herein are used to produce a non-human transgenic animal or transgenic plant. In some embodiments, the transgenic animal is a mammal, such as a mouse, rat, or rabbit. Methods for producing transgenic plants and animals are known in the art, and generally begin with a method of cell transfection, such as described herein.

[00125] With recent advances in crop genomics, the ability to use CRISPR-Cas systems to perform efficient and cost effective gene editing and manipulation will allow the rapid selection and comparison of single and and multiplexed genetic manipulations to transform such genomes for improved production and enhanced traits. In this regard reference is made to US patents and publications: US Patent No. 6,603,061 - Agrobacterium-Mediated Plant Transformation Method; US Patent No. 7,868,149 - Plant Genome Sequences and Uses Thereof and US 2009/0100536 - Transgenic Plants with Enhanced Agronomic Traits, all the contents and disclosure of each of which are herein incorporated by reference in their entirely. In the practice of the invention, the contents and disclosure of Morreli et al "Crop genomics :advanees and applications" Nat Rev Genet. 2011 Dec 29;13(2):85-96 are also herein incorporated by reference in their entirety. In an advantageous embodiment of the invention, the CRISPR/Cas9 system is used to engineer microalgae. Accordingly, reference herein to animal cells may also apply, mutatis mutandis, to plant cells unless otherwise apparent.

[00126] In plants, pathogens are often host-specific. For example, Fusarium oxysporum f. sp. lycopersici causes tomato wilt but attacks only tomato, and F. oxysporum f. dianthii Puccinia graminis f. sp. tritici attacks only wheat. Plants have existing and induced defenses to resist most pathogens. Mutations and recombination events across plant generations lead to genetic variability that gives rise to susceptibility, especially as pathogens reproduce with more frequency than plants. In plants there can be non-host resistance, e.g., the host and pathogen are incompatible. There can also be Horizontal Resistance, e.g., partial resistance against all races of a pathogen, typically controlled by many genes and Vertical Resistance, e.g., complete resistance to some races of a pathogen but not to other races, typically controlled by a few genes. In a Gene-for-Gene level, plants and pathogens evolve together, and the genetic changes in one balance changes in other. Accordingly, using Natural Variability, breeders combine most useful genes for Yield, Quality, Uniformity, Hardiness, Resistance. The sources of resistance genes include native or foreign Varieties, Heirloom Varieties, Wild Plant Relatives, and Induced Mutations, e.g., treating plant material with mutagenic agents. Using the present invention, plant breeders are provided with a new tool to induce mutations. Accordingly, one skilled in the art can analyze the genome of sources of resistance genes, and in Varieties having desired characteristics or traits employ the present invention to induce the rise of resistance genes, with more precision than previous mutagenic agents and hence accelerate and improve plant breeding programs.

[00127] In one aspect, the invention provides for methods of modifying a target polynucleotide in a eukaryotic cell, which may be in vivo, ex vivo or in vitro. In some embodiments, the method comprises sampling a cell or population of cells from a human or non- human animal or plant (including micro-algae), and modifying the cell or cells. Culturing may occur at any stage ex vivo. The cell or cells may even be re-introduced into the non-human animal or plant (including micro-algae). For re-introduced cells it is particularly preferred that the cells are stem cells. [00128] In one aspect, the invention provides for methods of modifying a target polynucleotide in a eukaryotic ceil. In some embodiments, the method may comprise allowing a CRISPR complex to bind to the target polynucleotide to effect cleavage of said target polynucleotide thereby modifying the target polynucleotide, wherein the CRISPR complex may comprise a CRISPR enzyme complexed with a guide sequence hybridized to a target sequence within said target polynucleotide, wherein said guide sequence is linked to a tracr mate sequence which in turn hybridizes to a tracr sequence.

[00129] In one aspect, the invention provides a method of modifying expression of a polynucleotide in a eukaryotic cell. In some embodiments, the method may comprise allowing a CRISPR complex to bind to the polynucleotide such that said binding results i increased or decreased expression of said polynucleotide; wherein the CRISPR complex may comprise a CRISPR enzyme complexed with a guide sequence hybridized to a target sequence within said polynucleotide, wherein said guide sequence is linked to a tracr mate sequence which in turn hybridizes to a tracr sequence.

[00130] In one aspect, the inventio provides kits containing any one or more of the elements disclosed in the above methods and compositions. Elements may be provided individually or in combinations, and may be provided in any suitable container, such as a vial, a bottle, or a tube. In some embodiments, the kit includes instructions in one or more languages, for example in more than one language.

[00131] In some embodiments, a kit may comprise one or more reagents for use in a process utilizing one or more of the elements described herein. Reagents may be provided in any suitable container. For example, a kit may provide one or more reaction or storage buffers. Reagents may be provided in a form that is usable in a particular assay, or in a form that requires addition of one or more other components before use (e.g. in concentrate or lyophilized form). A buffer can be any buffer, including but not limited to a sodium carbonate buffer, a sodium bicarbonate buffer, a borate buffer, a Tris buffer, a MOPS buffer, a HEPES buffer, and combinations thereof. In some embodiments, the buffer is alkaline. In some embodiments, the buffer has a pH from about 7 to about 10. In some embodiments, the kit may comprise one or more oligonucleotides corresponding to a guide sequence for insertion into a vector so as to operably link the guide sequence and a regulatory element. In some embodiments, the kit may comprise a homologous recombination template polynucleotide. [00132] In one aspect, the invention provides methods for using one or more elements of a CR!SPR system. The CRISPR complex of the invention provides an effective means for modifying a target polynucleotide. The CRISPR complex of the invention has a wide variety of utility including modifying (e.g., deleting, inserting, translocating, inactivating, activating) a target polynucleotide In a multiplicity of cell types. As such the CRISPR complex of the invention has a broad spectrum of applications in, e.g., gene therapy, drug screening, disease diagnosis, and prognosis. An exemplary CRISPR complex may comprise a CRISPR enzyme complexed with a guide sequence hybridized to a target sequence within the target polynucleotide. The guide sequence is linked to a tracr mate sequence, which in turn hybridizes to a tracr sequence.

[00133] In one embodiment, this invention provides a method of cleaving a target polynucleotide. The method may comprise modifying a target polynucleotide using a CRISPR complex that binds to the target polynucleotide and effect cleavage of said target polynucleotide. Typically, the CRISPR complex of the invention, when introduced into a cell, creates a break (e.g., a single or a double strand break) in the genome sequence. For example, the method can be used to cleave a disease gene in a cell.

[00134] The break created by the CRISPR. complex can be repaired by a repair processes such as the error prone non-homologous end joining (NHEJ) pathway or the high fidelity homology- directed repair (HDR). During these repair process, an exogenous polynucleotide template can be introduced into the genome sequence. In some methods, the HDR process is used modify genome sequence. For example, an exogenous polynucleotide template which may comprise a sequence to be integrated flanked by an upstream sequence and a downstream sequence is introduced into a cell. The upstream and downstream sequences share sequence similarity with either side of the site of integration in the chromosome.

[001351 Where desired, a donor polynucleotide can be DNA, e.g., a DNA plasmid, a bacterial artificial chromosome (BAG), a yeast artificial chromosome (YAC), a viral vector, a linear piece of DNA, a PGR. fragment, a naked nucleic acid, or a nucleic acid complexed with a deliver)? vehicle such as a liposome or poloxamer.

[00136] The exogenous polynucleotide template may comprise a sequence to be integrated (e.g, a mutated gene). The sequence for integration may be a sequence endogenous or exogenous to the cell. Examples of a sequence to be integrated include polynucleotides encoding a protein or a non-coding RNA (e.g., a micro RN A). Thus, the sequence for integration may be operabiy linked to an appropriate control sequence or sequences. Alternatively, the sequence to be integrated may provide a regulatory function.

[00137] The upstream and downstream sequences in the exogenous polynucleotide template are selected to promote recombination between the chromosomal sequence of interest and the donor polynucleotide. The upstream sequence is a nucleic acid sequence that shares sequence similarity with the genome sequence upstream of the targeted site for integration. Similarly, the downstream sequence is a nucleic acid sequence that shares sequence similarity with the chromosomal sequence downstream of the targeted site of integration. The upstream and downstream sequences in the exogenous polynucleotide template can have 75%, 80%, 85%, 90%, 95%, or 100% sequence identity with the targeted genome sequence. Preferably, the upstream and downstream sequences in the exogenous polynucleotide template have about 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with the targeted genome sequence. In some methods, the upstream and downstream sequences in the exogenous polynucleotide template have about 99% or 100% sequence identity with the targeted genome sequence.

[00138] An upstream or downstream sequence may comprise from about 20 bp to about 2500 bp, for example, about 50, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, 2100, 2200, 2300, 2400, or 2500 bp. In some methods, the exemplary upstream or downstream sequence have about 200 bp to about 2000 bp, about 600 bp to about 1000 bp, or more particularly about 700 bp to about 1000 bp.

[00139] In some methods, the exogenous polynucleotide template may further comprise a marker. Such a marker may make it easy to screen for targeted integrations. Examples of suitable markers include restriction sites, fluorescent proteins, or selectable markers. The exogenous polynucleotide template of the invention can be constructed using recombinant techniques (see, for example, Sambrook et ai., 2001 and Ausubel et al., 1996).

[00140] In an exemplary method, for modifying a target polynucleotide by integrating an exogenous polynucleotide template, a double stranded break is introduced into the genome sequence by the CRISPR complex, the break is repaired via homologous recombination an exogenous polynucleotide template such that, the template is integrated into the genome. The presence of a double-stranded break facilitates integration of the template. [00141] In other embodiments, this invention provides a method of modifying expression of a polynucleotide in a eukaryotie cell. The method may comprise increasing or decreasing expression of a target polynucleotide by using a CRISPR complex that binds to the polynucleotide,

[00142] In some methods, a target polynucleotide can be inactivated to effect the modification of the expression in a cell. For example, upon the binding of a CR ISPR complex to a target sequence in a ceil, the target polynucleotide is inactivated such that the sequence is not transcribed, the coded protein is not produced, or the sequence does not function as the wild -type sequence does. For example, a protein or microRNA coding sequence may be inactivated such thai the protein is not produced.

[00143] In some methods, a control sequence can be inactivated such that it no longer functions as a control sequence. As used herein, "control sequence" refers to any nucleic acid sequence that effects the transcription, translation, or accessibility of a nucleic acid sequence. Examples of a control sequence include, a promoter, a transcription terminator, and an enhancer are control sequences.

[0Θ144] The inactivated target sequence may include a deletion mutation (i.e., deletion of one or more nucleotides), an insertion mutation (i.e., insertion of one or more nucleotides), or a nonsense mutation (i.e., substitution of a single nucleotide for another nucleotide such that a stop codon is introduced). In some methods, the inactivation of a target sequence results in "knockout" of the target sequence.

[00145] A method of the invention may be used to create a plant, an animal or cell that may be used as a disease model. As used herein, "disease" refers to a disease, disorder, or indication in a subject. For example, a method of the invention may be used to create an animal or ceil that may comprise a modification in one or more nucleic acid sequences associated with a disease, or an animal or cell in which the expression of one or more nucleic acid sequences associated with a disease are altered. Such a nucleic acid sequence may encode a disease associated protein sequence or may be a disease associated control sequence.

[00146] In some methods, the disease model can be used to study the effects of mutations on the animal or cel l and development and/or progression of the disease using measures commonly used in the study of the disease. Alternatively, such a disease model is useful for studying the effect of a pharmaceutically active compound on the disease. [00147] In some methods, the disease model can be used to assess the efficacy of a potential gene therapy strategy. That is, a disease-associated gene or polynucleotide can be modified such that the disease development and/or progression is inhibited or reduced. In particular, the method may comprise modifying a disease-associated gene or polynucleotide such that an altered protein is produced and, as a result, the animal or cell has an altered response. Accordingly, in some methods, a genetically modified animal may be compared with an animal predisposed to development of the disease such that the effect of the gene therapy event may be assessed.

[00148] In another embodiment, this in vention provides a method of developing a biologically active agent that modulates a cell signaling event associated with a disease gene. The method may comprise contacting a test compound with a cell which may comprise one or more vectors that drive expression of one or more of a CRISPR enzyme, a guide sequence linked to a tracr mate sequence, and a tracr sequence; and detecting a change in a readout that is indicative of a reduction or an augmentation of a cell signaling event associated with, e.g., a mutation in a disease gene contained in the ceil.

[00149] A cell model or animal model can be constructed in combination with the method of the invention for screening a cellular function change. Such a model may be used to study the effects of a genome sequence modified by the CRISPR comple of the invention on a cellular function of interest. For example, a cellular function model may be used to study the effect of a modified genome sequence on intracellular signaling or extracellular signaling. Alternatively, a cellular function model may be used to study the effects of a modified genome sequence on sensory perception. In some such models, one or more genome sequences associated with a signaling biochemical pathway in the model are modified.

[00150] An altered expression of one or more genome sequences associated with a signaling biochemical pathway can be determined by assaying for a difference in the mRNA levels of the corresponding genes between the test model cell and a control ceil, when they are contacted with a candidate agent. Alternatively, the differential expression of the sequences associated with a signaling biochemical pathway is determined by detecting a difference in the level of the encoded polypeptide or gene product.

[00151] To assay for an agent-induced alteration in the level of mRNA transcripts or corresponding polynucleotides, nucleic acid contained in a sample is first extracted according to standard methods in the art. For instance, mRNA can be isolated using various lytic enzymes or chemical solutions according to the procedures set forth in Sambrook et al. (1989), or extracted by nucle c-acid-binding resins following the accompanying instructions provided by the manufacturers. The mRNA contained in the extracted nucleic acid sample is then detected by amplification procedures or conventional hybridization assays (e.g. Northern blot analysis) according to methods widely known in the art or based on the methods exemplified herein.

[00152] For purpose of this invention, amplification means any method employing a primer and a polymerase capable of replicating a target sequence with reasonable fidelity. Amplification may be earned out by natural or recombinant DNA. polymerases such as TaqGold™, T7 DNA polymerase, Klenow fragment of E.coli DNA polymerase, and reverse tra scriptase. A preferred amplification method is PGR. In particular, the isolated RNA can be subjected to a reverse transcription assay that is coupled with a quantitative polymerase chain reaction (RT-PCR) in order to quantify the expression level of a sequence associated with a signaling biochemical pathway.

[00153] Detection of the gene expression level can be conducted in real time in an amplification assay. In one aspect, the amplified products can be directly visualized with fluorescent DNA-binding agents including but not limited to DNA intercalators and DNA groove binders. Because the amount of the intercalators incorporated into the double-stranded DNA molecules is typically proportional to the amount of the amplified DNA products, one can conveniently determine the amount of the amplified products by quantifying the fluorescence of the intercalated dye using conventional optical systems in the art. DNA-binding dye suitable for this application include SYBR green, SYBR blue, DAPL propidium iodine, Hoeste, SYBR gold, ethidium bromide, acridities, proflavine, acridine orange, aerifiavine, fluorcoumanin, ellipticine, daunomycin, chloroquine, distamycin D, chromomycin, homidium, mithramycin, ruthenium polypyridyls, anthramycin, and the like.

[00154] In another aspect, other fluorescent labels such as sequence specific probes can be employed in the amplificatio reaction to facilitate the detection and quantificatio of the amplified products. Probe-based quantitative amplification relies on the sequence-specific detection of a desired amplified product. It utilizes fluorescent, target-specific probes (e.g., TaqMan® probes) resulting in increased specificity and sensitivity. Methods for performing probe-based quantitative amplification are well established in the art and are taught in U.S. Patent No. 5,210,015. [00155] In yet another aspect, conventional hybridization assays using hybridization probes that share sequence homology with sequences associated with a signaling biochemical pathway can be performed. Typically, probes are allowed to form stable complexes with the sequences associated with a signaling biochemical pathway contained within the biological sample derived from the test subject in a hybridization reaction. It will be appreciated by one of skill in the art that where antisense is used as the probe nucleic acid, the target polynucleotides provided in the sample are chosen to be complementary to sequences of the antisense nucleic acids. Conversely, where the nucleotide probe is a sense nucleic acid, the target polynucleotide is selected to be complementary to sequences of the sense nucleic acid.

[00156] Hybridization can be performed under conditions of various stringency. Suitable hybridization conditions for the practice of the present invention are such that the recognition interaction between the probe and sequences associated with a signaling biochemical pathway is both sufficiently specific and sufficiently stable. Conditions that increase the stringency of a hybridization reaction are widely known and published in the art. See, for example, Sambrook, et a!., (1989); Nonradioactive In Situ Hybridization Application Manual, Boehringer Mannheim, second edition. The hybridization assay can be formed using probes immobilized on any solid support, including but are not limited to nitrocellulose, glass, silicon, and a variety of gene arrays. A preferred hybridization assay is conducted on high-density gene chips as described in U.S. Patent No. 5,445,934.

[00157] For a convenient detection of the probe-target complexes formed during the hybridization assay, the nucleotide probes are conjugated to a detectable label. Detectable labels suitable for use in the present invention include any composition detectable by photochemical, biochemical, spectroscopic, immunochemical, electrical, optical or chemical means. A wide variety of appropriate detectable labels are known in the art, which include fluorescent or ehemilumineseent labels, radioactive isotope labels, enzymatic or other ligands. In preferred embodiments, one will likely desire to employ a fluorescent label or an enzyme tag, such as digoxigenin, β-galactosidase, urease, alkaline phosphatase or peroxidase, avidin/biotin complex .

[00158] The detection methods used to detect or quantify the hybridization intensity will typically depend upon the label selected above. For example, radiolabels may be detected using photographic film or a phospholmager. Fluorescent markers may be detected and quantified using a photodetector to detect emitted light. Enzymatic labels are typically detected by providing the enzyme with a substrate and measuring the reaction product produced by the action of the enzyme on the substrate; and finally colorimetric labels are detected by simply visualizing the colored label.

[00159] An agent-induced change in expression of sequences associated with a signaling biochemical pathway can also be determined by examining the corresponding gene products. Determining the protein level typically involves a) contacting the protein contained in a biological sample with an agent that specifically bind to a protein associated with a signaling biochemical pathway; and (b) identifying any agentprotein complex so formed. In one aspect of this embodiment, the agent that specifically binds a protein associated with a signaling biochemical pathway is an antibody, preferably a monoclonal antibody.

[00160] The reaction is performed by contacting the agent with a sample of the proteins associated with a signaling biochemical pathway derived from the test samples under conditions that will allow a complex to form between the agent and the proteins associated with a signaling biochemical pathway. The formation of the complex can be detected directly or indirectly according to standard procedures in the art. In the direct detection method, the agents are supplied with a detectable label and unreacted agents may be removed from the complex; the amount of remaining label thereby indicating the amount of complex formed. For such method, it is preferable to select labels that remain attached to the agents even during stringent washing conditions. It is preferable that the label does not interfere with the binding reaction. In the alternative, an indirect detection procedure may use an agent that contains a label introduced either chemically or eiizymaticaily, A desirable label generally does not interfere with binding or the stability of the resulting agentpolypeptide complex, i low e er, the label is typically designed to be accessible to an antibody for an effective binding and hence generating a detectable signal .

[00161] A wide variety of labels suitable for detecting protein levels are known in the art. Non-limiting examples include radioisotopes, enzymes, colloidal metals, fluorescent compounds, bioiuminescent compounds, and chemiluminescent compounds.

[00162] The amount of agentpolypeptide complexes formed during the binding reaction can be quantified by standard quantitative assays. As illustrated above, the formation of agentpolypeptide complex can be measured directly by the amount of label remained at the site of binding. In an alternative, the protein associated with a signaling biochemical pathway is tested for its ability to compete with a labeled analog for binding sites on the specific agent. In this competitive assay, the amount of label captured is inversely proportional to the amount of protein sequences associated with a signaling biochemical pathway present in a test sample.

[00163] A number of techniques for protein analysis based on the general principles outlined above are available in the art. They include but are not limited to radioimmu oassays, ELISA (enzyme linked immunoradiometric assays), "sandwich" immunoassays, immunoradiometric assays, in situ immunoassays (using e.g., colloidal gold, enzyme or radioisotope labels), western blot analysis, immunoprecipitation assays, immunofluorescent assays, and SDS-PAGE.

[00164] Antibodies that specifically recognize or bind to proteins associated with a signaling biochemical pathway are preferable for conducting the aforementioned protein analyses. Where desired, antibodies that recognize a specific type of post-translational modifications (e.g., signaling biochemical pathway inducible modifications) can be used. Post-translational modifications include but are not limited to glyeosylation, lipidation, acetylation, and phosphorylation. These a tibodies may be purchased from commercial vendors. For example, anti-phosphotyrosine antibodies that specifically recognize tyrosine-phosphorylated proteins are available from a number of vendors including Invitrogen and Perkin Elmer. Anti- phosphotyrosine antibodies are particularly useful in detecting proteins thai are differentially phosphorylated on their tyrosine residues in response to an ER stress. Such proteins include but are not limited to eukaryotic translation i itiation factor 2 alpha (eIF-2a). Alternatively, these antibodies can be generated using conventional polyclonal or monoclonal antibody technologies by immunizing a host animal or an antibody-produci g cell with a target protein that exhibits the desired post-translational modification.

[00165] In practicing the subject method, it may be desirable to discern the expression pattern of an protein associated with a signaling biochemical pathway in different bodily tissue, in different ceil types, and/or in different subcellular structures. These studies can be performed with the use of tissue-specific, cell-specific or subcellular structure specific antibodies capable of binding to protein markers that are preferentjally expressed in certain tissues, cel l types, or subcellular structures.

[00166] An altered expression of a gene associated with a signaling biochemical pathway can also be determined by examining a change in activity of the gene product relative to a control cell. The assay for an agent-induced change in the activity of a protein associated with a signaling biochemical pathway will dependent on the biological activity and/or the signal transduction pathway that is under investigation. For example, where the protein is a kinase, a change in its ability to phosphorylate the downstream substrate(s) can be determined by a variety of assays known in the art. Representative assays include but are not limited to immunoblotting and imniunoprecipitation with antibodies such as anti-phosphotyrosine antibodies that recognize phosphorylated proteins, In addition, kinase activity can be detected by high throughput ehemiluminescent assays such as AlphaScreen™ (available from Perkin Elmer) and eTag™ assay (Chan-Bui, et al. (2003) Clinical Immunology 111 : 162-174).

[00167] Where the protein associated with a signaling biochemical pathway is part of a signaling cascade leading to a fluctuation of intracellular pH condition, pH sensitive molecules such as fluorescent pH dyes can be used as the reporter molecules. In another example where the protein associated with a signaling biochemical pathway is an ion channel, fluctuations in membrane potential and/or intracellular ion concentration can be monitored. A number of commercial kits and high-throughput devices are particularly suited for a rapid and robust screening for modulators of ion channels. Representative instruments include FLIPRTM (Molecular Devices, Inc.) and V1PR (Aurora Biosciences). These instruments are capable of detecting reactions in over 1000 sample wells of a microplate simultaneously, and providing real-time measurement and functional data within a second or even a millisecond.

[00168] In practicing any of the methods disclosed herein, a suitable vector can be introduced to a cell or an embryo via one or more methods known in the art, including without limitation, microinjection, eiectroporation, sonoporation, biolistics, calcium phosphate-mediated transfection, eationie transfection, liposome transfection, dendrimer transfection, heat shock transfection, nucleofection transfection, magnetofection, lipofection, impalefection, optical transfection, proprietary agent-enhanced uptake of nucleic acids, and delivery via liposomes, immunoliposomes, virosomes, or artificial virions, in some methods, the vector is introduced into an embryo by microinjection. The vector or vectors may be microinjected into the nucleus or the cytoplasm of the embryo. In some methods, the vector or vectors may be introduced into a cell by nucleofection.

[00169] The target polynucleotide of a CRJSPR complex can be any polynucleotide endogenous or exogenous to the eukaryotic cell. For example, the target polynucleotide can be a polynucleotide residing in the nucleus of the eukaryotic cel l. The target polynucleotide can be a sequence coding a gene product (e.g., a protein) or a non-coding sequence (e.g., a regulatory polynucleotide or a junk DNA).

[00170] Examples of target polynucleotides include a sequence associated with a signaling biochemical pathway, e.g., a signaling biochemical pathway-associated gene or polynucleotide. Examples of target polynucleotides include a disease associated gene or polynucleotide. A "disease-associated" gene or polynucleotide refers to any gene or polynucleotide which is yielding transcription or translation products at an abnormal level or in an abnormal form in cells derived from a disease-affected tissues compared with tissues or cells of a non disease control. It may be a gene that becomes expressed at an abnormally high level; it may be a gene that becomes expressed at an abnormally low level, where the altered expression correlates with the occurrence and/or progression of the disease. A disease-associated gene also refers to a gene possessing mutation(s) or genetic variation that is directly responsible or is in linkage disequilibrium with a gene(s) that is responsible for the etiology of a disease. The transcribed or translated products may be known or unknown, and may be at a normal or abnormal level.

[00171] The target polynucleotide of a CRISPR complex can be any polynucleotide endogenous or exogenous to the eukaryotic cell. For example, the target polynucleotide can be a polynucleotide residing in the nucleus of the eukaryotic cel l. The target polynucleotide can be a sequence coding a gene product (e.g., a protein) or a non-coding sequence (e.g., a regulatory polynucleotide or a junk DNA). Without wishing to be bound by theory, it is believed that the target sequence should be associated with a PAM (protospacer adjacent motif); that is, a short sequence recognized by the CRISPR complex. The precise sequence and length requirements for the PAM differ depending on the CRISPR enzyme used, but PAMs are typically 2-5 base pair sequences adjacent the protospacer (that is, the target sequence) Examples of PAM sequences are given in the examples section below, and the skilled person wil l be able to identify further PAM sequences for use with a given CRISPR enzyme.

[00172] Examples of target polynucleotides include a sequence associated with a signaling biochemical pathway, e.g., a signaling biochemical pathway-associated gene or polynucleotide. Examples of target polynucleotides include a disease associated gene or polynucleotide. A "disease-associated" gene or polynucleotide refers to any gene or polynucleotide which is yielding transcription or translation products at an abnormal level or in an abnormal form in cells derived from a disease-affected tissues compared with tissues or cells of a non disease control. It may be a gene that becomes expressed at an abnormally high level; it may be a gene that becomes expressed at an abnormally low level, where the altered expression correlates with the occurrence and/or progression of the disease, A disease-associated gene also refers to a gene possessing mutation (s) or genetic variation that is directly responsible or is in linkage disequilibrium with a gene(s) that is respo sible for the etiology of a disease. The transcribed or translated products may be known or unknown, and may be at a normal or abnormal level.

0Θ173] The target polynucleotide of a CPJSPR complex may include a number of disease- associated genes and polynucleotides as well as signaling biochemical pathway-associated genes and polynucleotides as listed in US provisional patent applications 61/736,527 and 61/748,427 having Broad reference BI-2011/008/WSGR Docket No, 44063-701.101 and BI~ 201 1/008/WSGR Docket No. 44063-701 .102 respectively, both entitled SYSTEMS METHODS AND COMPOSITIONS FOR SEQUENCE MANIPULATION filed on December 12, 2012 and January 2, 2013, respectively, the contents of all of which are herein incorporated by reference in their entirety.

[00174] Examples of target polynucleotides include a sequence associated with a signaling biochemical pathway, e.g., a signaling biochemical pathway-associated gene or polynucleotide. Examples of target polynucleotides include a disease associated gene or polynucleotide. A "disease-associated" gene or polynucleotide refers to any gene or polynucleotide which is yielding transcription or translation products at an abnormal level or in a abnormal form in cells derived from a disease-affected tissues compared with tissues or cel ls of a non disease control. It may be a gene that becomes expressed at an abnormally high level; it may be a ge e that becomes expressed at an abnormally low level, where the altered expression correlates with the occurrence and/or progression of the disease. A disease-associated gene also refers to a gene possessing mutation(s) or genetic variation that is directly responsible or is in linkage disequilibrium with a ge e(s) that is responsible for the etiology of a disease. The transcribed or translated products may be known or unknown, and may be at a normal or abnormal level.

[00175] Examples of disease-associated genes and polynucleotides are available from Mc usick-Nathans Institute of Genetic Medicine, Johns Hopkins U iversity (Baltimore, Md.) and National Center for Biotechnology Information, National Library of Medicine (Bethesda, Md.), available on the World Wide Web. [00176] Examples of disease-associated genes and polynucleotides are listed in Tables A and B. Disease specific information is available from McKiisiek-Nathans Institute of Genetic Medicine, Johns Hopkins University (Baltimore, Md.) and National Center for Biotechnology Information, National Library of Medicine (Bethesda, Md.), available on the World Wide Web. Examples of signali g biochemical pathway-associated genes and polynucleotides are listed in Table C.

[00177] Mutations in these genes and pathways can result in production of improper proteins or protems in improper amounts which affect function. Further examples of genes, diseases and proteins are hereby incorporated by reference from US Provisional applications 61/736,527 filed December 12, 2012 and 61/748,427 filed January 2, 2013. Such genes, proteins and pathways may be the target pol nucleotide of a CRISPR complex.

Table A

Parkinson's Disease x-SymicSein; DJ-1; LRR 2; Parkin; PIN 1

Table B:

GMPS, AFIO, ARHGEF12, LARG, KJAA0382, CALM, CLTPL

CEBPA, CEBP, CFJIC2, BTL, FLT3, KIT, PBT, LPP, NPM1, NUP214, D9S46E, CAN, CALN, RUNX1, CBFA2, AML1, WHSC1L1, NSD3, l i.13. AF1Q, NPM1 , UMA1, ZNF145, PLZF, PML, MYL, STAT5B, AFIO, CALM, CLT , ARL11, ARLTS1, P2RX7, P2X7, BCR, CML, PHL, ALL, GRAF, NFL VRNF, WSS, NFNS, PTPN11, PTP2C, SHP2, NS1, BCL2, CCND1, PRAD1, BCL1, TCRA, GATA1, GFl, ERYF1, NFE1, ABLI, NQOl, DIA4, NMQRl, NUP214, D9S46E, CAN, CAIN).

Inflammation and AIDS (K1R3DL1, N AT3, NKB1, AMB11 , KIR3DS1 , IFNG, CXCL12, immune related SDF1); Autoimmune lymphoproiiferative syndrome (TNFRSF6, APTl, diseases and disorders FAS, CD95, ALPS 1 A); Combined immunodeficiency, (IL2RG,

SCIDXl, SCIDX, IMD4); HIV-l (CCL5, SCYA5, D17S136E, TCP228), HIV susceptibility or infection (ILIO, CSIF, CMKBR2, CCR2,

C KBR.5, CCCKR5 (CCR5)); Immunodeficiencies (CD3E, CD3G, AICDA, AID, FJ1GM2, TNFRSF5, CD40, UNG, DGU, HIGM4, TNFSF5, CD40LG, HIGM1, IGM, FOXP3, IPEX, AIID, XP1D, PIDX, TNFRSF14B, TACi); Inflammation (JL- 10, IL-1 ilL-la, IL-lb), IL-13, IL-17 (IL-17a (CTLA8), IL-17b, IL-17c, IL-17d, Π.-Γ7Π.11-23, Cx3crl, ptpn22, TNFa, NOD2/CARD15 for IBD, II. -6. IL-12 (11,·! 2a. IL-12b), CTLA4, Cx3cii); Severe combined imnmnodeficiencies (SCIDs)(JAK3, JAKL, DCLRE.1C, ARTEMIS, SCIDA, RAGl, RAG2, ADA, PTPRC, CD45, LCA, IL7R, CD3D, T3D, IL2RG, SCIDXl , SCIDX, IMD4).

Metabolic, liver, Amyloid neuropathy (TTR, PALB); Amyloidosis (APOA1, APP, AAA, kidney and protein CVAP, ADL GSN,^' FGA, LYZ, TTR, PALB); Cirrhosis (KRT18, KRT8, diseases and disorders CIRHIA, NAIC, TEX292, KIAA1988); Cystic fibrosis (CFTR, ABCC7,

CF, MRP7); Glycogen storage diseases (SLC2A2, GLUT2, G6PC, G6PT, G6PT1, GAA, LAMP2, LAMPB, AGL, GDE, GBE1, GYS2, PYGL, PFKM); Hepatic adenoma, 142330 (TCF1, HNF1A, MODY3), Hepatic failure, early onset, and neurologic disorder (SCODl, SCOl), Hepatic lipase deficiency (LIPC), Hepatoblastoma, cancer and carcinomas (CTN B1, PDGFRL, PDGRL, PRLTS, AXIN1, AXIN, CT NB1 , TP53, P53, LFS1, IGF2R, MPRJ, MET, CASP8, MCI 15: Medullary cystic kidney disease (UMOD, HNFJ, FJHN, MCKD2, ADMCKD2); Phenylketonuria (PAH, P U1, QDPR, DHPR, PTS); Polycystic kidney and hepatic disease (FCYT, PKHDl, ARPKD, PKDi, PKD2, PKD4, PKDTS, PRKCSH, G19P1, PCLD, SEC63).

Muscular / Skeletal Becker muscular dystrophy (DMD, BMD, MYF6), Ducheniie Muscular diseases and disorders Dystrophy (DMD, BMD); Emery-Dreifuss muscular dystrophy (LMNA,

LMNl, EMD2, FPLD, CMD1A, HGPS, LGMD1B, LMNA, LMNl, EMD2, FPLD, CMD1A); Facioscapulohumeral muscular dystrophy (FSHMD1 A, FSHD1 A); Muscular dystrophy (FKRP, MDC1C,

LGMD2I, LAMA2, LAMM, LARGE, KIAA0609, MDCID, l i MIX Ί 111). MYOT, CAPN3, CANP3, DYSF, LGMD2B, SGCG, LGMD2C, DMDAl, SCG3, SGCA, ADL, DAG2, LGMD2D, DMDA2, SGCB,

LGMD2E, SGCD, SGD, LGMD2F, CMD1L, TCAP, LGMD2G, CMDIN, TRIM32, HT2A, LGMD2H, FKRP, MDCIC, LGMD2I, TTN, CMDIG, TMD, LGMD2J, POMTl, CAV3, LGMDIC, SEPNl, SEEN, R.SMD1, PLEC1, PLTN, EBS1); Osteopetrosis (LRP5, BMND1, LRP7, LR3, OPPG, VBCH2, CLCN7, CLC7, OPTA2, OSTM1, GL, TCIRG1, '! !! ( 7. OC116, OPTB1 ^'); Muscular atrophy (VAPB, VAPC, ALS8, SMN1, SMA1, SMA2, SMA3, SMA.4, BSCL2, SPG 17, GARS, SMAD1, CMT2D, HEXB, IGHMBP2, SMUBP2, CATF1, SMARD1).

Neurological and ALS (SODl, ALS2, STEX, FUS, TARDBP, VEGF (VEGF-a, VEGF-b, neuronal diseases and VEGF-c); Alzheimer disease (APP, AAA, CVAP, AD1, APOE, AD2, disorders PSEN2, AD4, STM2, APBB2, FE65L1, NOS3, PLAU, URK, ACE,

DCP1, ACEl, MPO, PACIP1, PAXIP1L, PTIP, A2M, BLMH, BMH, PSEN1, AD3); Autism (Mecp2, BZRAP1, MDGA2, Sema5A, Neurexin 1, GLOl, MECP2, RTT, PPMX, MRX16, MRX79, NLGN3, NLGN4, Κ1ΛΛ1260. AUTSX2); Fragile X Syndrome (FMR2, FXR1, FXR2, mGLURS); Huntington's disease and disease like disorders (1 ID. ΠΜ5, PRNP, PRIP, JPH3, JP3, HDL2, TBP, SCA17): Parkinson disease (NR4A2, NURRL NOT, TINUR, SNCAIP, TBP, SCA17, SNCA, NACP, PAR i . PARKA DJ1, PARK 7, LRRK2, PARKS, PINK1, PARK6, UCHL1, PARK5, SNCA, NACP, PARK1 , PARK4, PRKN, PARK2, PDJ, DBH, NDUFV2); Rett syndrome (MECP2, RTT, PPMX, MRX16, MRX79, CDKL5, STK.9, MECP2, RTT, PPMX, MRX16, Mi¾X79, x-Synueiein, !>.!·- \ ): Schizophrenia (Neureguiml (Nrgl), Erb4 (receptor for Neuregulin), CompSexinl (Cplxl), Tp l Tr pu.phaii hydroxylase, Tph2, Tryptophan hydroxylase 2, Neurexin 1, GSK3, GSK3a^* GSK3b, 5-HTT (Sic6a4).^" COMT, DRD (Drdla), SLC6A3, DAOA, DTNBP1 , Dao (Daol)); Secretase Related Disorders (APH-1 (alpha and beta), Preseniiin (Psenl), nicastrin, (Ncst ), PEN-2, Nosl, Parpl, Natl, Nat2); Trinucleotide Repeat Disorders (HTT (Huntington^'s Dx), SBMA/SMAX 1/AR (Kennedy's Dx), FXN/X25 (Friedrich's Ataxia), ATX3 (Machado- Joseph's Dx), ATXN1 and ATXN2

(spinocerebellar ataxias), DMPK (myotonic dystrophy), Atrophin-l and Atnl (DRPLA Dx), CBP (Creb-BP - global instability), VLDLR

(Alzheimer's), Atxn7, AtxnlO).

Occular diseases and Age-related macular degeneration (Abcr, Cci2, Cc2, cp (ceruloplasmin), disorders Timp3, cathepsinD, Vid^'ir, Ccr2); Cataract (CRYAA, CR YAl , CRYBB2,

CRYB2, ΡΓΓΧ3, BFSP2, CP49, CP47, CRYAA, CRYAl, PAX6, AN 2, MGDA, CRYBA1, CRYB l , CRYGC, CRYG3, CCL, LIM2, MP19, CRYGD, CRYG4, BFSP2, CP49, CP47, HSF4, CTM, HSF4, CTM, MIP, AQPO, CRYAB, CRYA2, CTPP2, CRYBB1, CRYGD, CRYG4, CRYBB2, CRYB2, CRYGC, CRYG3, CCL, CRYAA, CRYAl, GJA8, CX50, CAE1, GJA3, CX46, CZP3, CAES, CCMl, CAM, KRIT1);

Corneal clouding and dystrophy (APOA1, TGFBI, CSD2, CDGG1, CSD, BIGH3, CDG2, TACSTD2, TROP2, 1S1, VSXI. RINX. PPCD,

PPD, KTCN, COL8A2, FECD, PPCD2, PIP5K3, CFD); Cornea plana congenital (KERA, CNA2); Glaucoma (MYOC, TIGR, GLC1A, JO AG, GPOA, (WIS. GLC1E, FIP2, HYPL, NRP, CYPIBI, GLC3A, OPAL NTG, NPG, CYPIBI, GLC3A); Leber congenital amaurosis (CRBl, RP12, CRX, CORD2, CRD, RPGRIPl, LCA6, CORD9, RPE65, RP20, AIPLl, LCA.4, GUCY2D, GUC2D, LCA1, CORD6, RDH12, LC A3 ); Macular dystrophy (ELOVL4, ADMD, STGD2, STGD3, RDS, RP7, PR!³! 12. PRPH, AVMD, AOFMD, VMD2).

TRAF2; TLR4; TNF; INSR; IKB G; RELB; MAP3K7; 1L8;

CHUK; NR1H2; TJP2; NFKB1; ESR1; SRE Fl; FGFR4;

JU ; ILIRI; PRKCA; IL6

IGF- 1 Signaling IGF 1 ; PRKCZ; ELK1 ; MAPKl ; PTP 11 ; NEDD ; AKT2;

PIK3CA; PRKCI; PTK2; FOS; PIK3CB; PIK3C3; MAPK8;

IGF1R; IRSi; MAPK3; 1GFBP7; KRAS; PIK3C2A;

YWHAZ; PXN; RAF1; CASP9; MAP2K2; AKT1; PIK3R1;

PDPK1; MAP2K1 ; IGFBP2; SFN; JUN; CY 61; AKT3;

FOXOl; SRF; CTGF; RPS6KB1

NRF2-mediated PRKCE; EP300; SOD2; PRKCZ; MAP l; SQSTM1;

Oxidative

Stress Response NQOl; PIK3CA; PRKCI; FOS; PIK3CB; PIK3C3; MAPK8;

PRKDl; MAPK3; KRAS; PRKCD; GSTPl; MAPK9; FTL;

NFE2L2; P1K3C2A; MAPK14; RAFl ; MAP3K7; CREBBP;

MAP2K2; ΑΚΊΊ; PIK3R1; MAP2K1; PPIB; JUN; KEAPl;

GSK3B; ATF4; PRKCA; EIF2AK3; HSP90AA1

Hepatic Fibrosis/Hepatic EDN1; IGF1; KDR; FLT1; SMAD2; FGFR1; MET; PGF;

Stellate Cell Activation SMAD3; EGFR; FAS; CSF1 ; NFKB2; BCL2; MYH9;

IGF1R; IL6R; RELA; TLR4; PDGFRB; TNF; RELB; 11 H;

PDGFRA; NFKBl; TGFBR i; SMAD4; VEGFA; BAX;

IL1R1; CCL2; FIGF; MMP1; STAT1; IL6; CTGF; MMP9

PPAR Signaling EP300; INS; TRAF6; PPARA; RXRA; MAPKl; 1KBKB;

NCOR2; FOS; NFKB2; MAP3K14; STAT5B; MAPK3;

NR!I ; KRAS; PPARG; RELA; STATS A; TRAF2;

PPARGC1A; PDGFRB; TNF; INSR; RAFl; IKBKG;

RELB; MAP3K7; CREBBP; MAP2K2; CHUK; PDGFRA;

MAP2K1; NFKBl; JUN; IL1R1; HSP90AA1

Fc Epsiion RI Signaling PRKCE; RAC1; PRKCZ; LYN; MAPKl; RAC2; PTPN11;

AKT2; PIK3CA; SYK; PRKCI; PIK3CB; PIK3C3; MAPK8;

PRKDl; MAPK3; MAPKIO; KRAS; MAPKl 3; PRKCD;

MAPK9; PIK3C2A; BTK; MAPKl 4; TNF; RAFl; FYN;

MAP2K2; AKT1; PIK3R1 ; PDPK1; MAP2K1 ; AKT3;

VAV3; PRKCA

G-Protein Coupled PRKCE; RAIMA: RGS16; MAPKl; GNAS; AKT2; IKBKB;

Receptor Signaling PIK3CA; CREB1; GNAQ; NFKB2; CAMK2A; PIK3CB;

PIK3C3; MAPK3; KRAS; RELA; SRC; PIK3C2A; RAFl;

IKBKG; RELB; FYN; MAP2K2; AKTI; PIK3R1; CHUK;

PDPK1; STAT3; MAP2K1; NFKBl; BRAF; ATF4; AKT3;

PRKCA.

Inositol Phosphate PRKCE; IRAKI ; PR AA2; EIF2AK2; PTEN; GRK6;

Metabolism MAPKl; PLK1; AK.T2; PIK3CA; CDK8; PIK3CB; PIK3C3;

MAPK8; MAPK3; PRKCD; PRKAA1; MAPK9; CDK2;

P1M1; PIK3C2A; DYRKIA; MAP2K2; P1P5K1A; PIK3R1;

MAP2K1; PAK3; ATM; TTK; CSN 1A1; BRAF; SGK

Sclerosis Signaling PIK3CA; BCL2; PI 3CB; PI 3C3; BCL2L1; CAPNl;

Cell Cvcle: G2/M DNA EP300; PCAF; BRCA1; GADD45A; PLK1; BTRC;

Metabolism Orcadian Rhythm CSNK1E; CREB1; ATF4; NR1 D1

Signaling

Coagulation System BD RB1; F2R ; SERP1NE1; F3

Dopamine Receptor PPP2R 1 A; PPP2CA; PPP i CC; PPP2R5C

Signaling

Glutathione Metabo lism ID! 12: GST l ; ANPEP; IDHl

Glycerolipid Metabolism ALDHlAl ; GPAM; SPHKl ; SPHK2

Linoleic Acid PRDX6; GRN; YWHAZ; CYPIBI

Metabolism

Methionine Metabolism DNMTl; DNMT3B; AHCY; DNMT3A

Pyruvate Metabolism GLOl; ALDHlAl; PKM2; LDHA

Arginine and Proline ALDHlAl; NOS3; NOS2A

Metabolism

Eicosanoid Signaling PRDX6; GRN; YWHAZ

Fructose and Marmose I IK 2: GCK; HK1

Metabolism

Galactose Metabolism 1 IK2; GCK; l !K !

Stiibene, Coumarine and PRDX6; PRDX l ; TYR

Lignin Biosynthesis

Antigen Presentation CALR; B2M

Pathway

Biosynthesis of Steroids ^■NQOl; DHCR7

Butanoate Metabolism ALDHl Al; NLGN1

Citrate Cycle IDH2; IDHl

Fatty Acid Metabolism ALDHl Al; CYTPI B!

Glycerophospholipid PRDX6; CH A

Metabolism

Histidine Metabolism PRMT5; ALDHlA l

Inositol Metabolism EROI L; APEX 1

Metabolism of GSTPl; CYPIBI

Xenobioties

by Cytochrome p450

Methane Metabolism PRDX6; PRDXl

Phenylalanine PRDX6; PRDX l

Metabolism

Proparsoate Metabo lism ALDHlAl ; LDHA

Selenoamino Acid PRMT5; AHCY

Metabolism

Sphingolipid Metabolism SPHKl; SPHK2

Aminophosphoiiate PRMT5

Metabolism

Androgen and Estrogen PRMT5

Metabolism

Ascorbate and Aldarate ALDHl Al

Metabolism Bile Acid Biosynthesis ALDH1A 1

Cysteine Metabolism LDHA

Fatty Acid Biosynthesis FASN

Giutamate Receptor G B2L1

Signaling

N RF2-med iated. PRDX1

Oxidative

Stress Response

Pentose Phosphate GPI

Pathway

Pentose and Glucuronate UCFIL1

mtereonversions

Retinol Metabolism ALDH1 A1

Riboflavin Metabolism TYR

Tyrosine Metabolism PR T5, TYR

Ubiquinone Biosynthesis PRMT5

Valine, Leucine and ALDH1A1

Isoleucine Degradation

Glycine, Serine and CHKA

Threonine Metabolism

Lysine Degradation ALDHIA!

Pain/Taste TRPM5; TRPA.1

Pain TRPM7; TRPC5; TRPC6; TRPC1 ; Cnrl ; cnr2; Grk2;

Trpal ; Pome; Cgrp; Crf; Pka; Era; Nr2b; TRPM5; Prkaca;

Prkacb; Prkar l a; Prkar2a

Mitochondrial Function AIF; CytC; SMAC (Diablo); Aifm-1; Aifin-2

Developmental BMP-4; Chordin (Chrd); Noggin (Nog); WNT (Wnt2;

Neurology

Wnt2b; Wnt3a; Wnt4; Wnt5a; Wnt6; Wnt7b; Wnt8b;

Wnt9a; Wiit9b; WntlOa; WntlOb; Wntl6); beta-catenin;

Dkk-1; Frizzled related proteins; Otx-2; Gbx2; FGF-8;

Reelin; Dabl; unc-86 (Pou4fl or Brn3a); Numb; Rein

[00178] Embodiments of the invention also relate to methods and compositions related to knocking out genes, amplifying genes and repairing particular mutations associated with DNA repeat instability and neurological disorders (Robert D. Wells, Tetsuo Ash.iz.awa, Genetic Instabilities and Neurological Diseases, Second Edition, Academic Press, Oct 13, 2011 - Medical). Specific aspects of tandem repeat sequences have been found to be responsible for more than twenty human diseases (New insights into repeat instability: role of RNA^sDNA hybrids. .Vic! s or EI, Polak U, Napierala M. RNA Biol 2010 Sep-Oct;7(5):551-8). The CRISPR- Cas system may be harnessed to correct these defects of genomic instability. [00179] A further aspect of the invention relates to utilizing the CRISPR-Cas system for correcting defects in the EMP2A and EMP2B genes that have been identified to be associated with Lafora disease. Lafora disease is an autosomal recessive condition which is characterized by progressive myoclonus epilepsy which may start as epileptic seizures in adolescence. A few cases of the disease may be caused by mutations in genes yet to be identified. The disease causes seizures, muscle spasms, difficulty walking, dementia, and eventual ly death. There is currently no therapy that has proven effective against disease progression. Other genetic abnormalities associated with epilepsy may also be targeted by the CRISPR-Cas sytem and the underlying genetics is further described in Genetics of Epilepsy and Genetic Epilepsies, edited by Gmliano Avanzini, Jeffrey L. Noebels, Mariani Foundation Paediatric Neuro!ogy:20; 2009).

[00180] In yet another aspect of the invention, the CRISPR-Cas system may be used to correct ocular defects that arise from several genetic mutatio s further described in Genetic Diseases of the Eye, Second Edition, edited by Elias L Traboulsi, Oxford University Press, 2012.

[00181] Several further aspects of the invention relate to correcting defects associated with a wide range of genetic diseases which are further described on the website of the National Institutes of Health under the topic subsection Genetic Disorders (website at health.nih.gov/topic/GeneticDisorders). The genetic brain diseases may include but are not limited to Adrenoleukodystrophy, Agenesis of the Corpus Callosum, Aicardi Syndrome, Alpers' Disease, Alzheimer's Disease, Barth Syndrome, Batten Disease, CADASIL, Cerebellar Degeneration, Fabry's Disease, Gerstmann-Straussier-Scheinker Disease, Huntington's Disease and other Triplet Repeat Disorders, Leigh's Disease, Lesch-Nyhan Syndrome, Menkes Disease, Mitochondrial Myopathies and NINDS Colpoeephary. These diseases are further described on the website of the National Institutes of Health under the subsection Genetic Brain Disorders.

[00182] In some embodiments, the condition may be neoplasia. In some embodiments, where the condition is neoplasia, the genes to be targeted are any of those listed in Table A (in this case PTEN asn so forth). In some embodiments, the condition may be Age-related Macular Degeneration. In some embodiments, the condition may be a Schizophrenic Disorder. In some embodiments, the condition may be a Trinucleotide Repeat Disorder. In some embodiments, the condition may be Fragile X Syndrome. In some embodiments, the condition may be a Secretase Related Disorder. I some embodiments, the conditio may be a Prion - related disorder. In some embodiments, the condition may be ALS. In some embodiments, the condition may be a drug addiction. In some embodiments, the condition may be Autism. In some embodiments, the condition may be Alzheimer's Disease. In some embodiments, the condition may be inflammation. In some embodiments, the condition may be Parkinson's Disease.

[00183] Examples of proteins associated with Parkinson's disease include but are not limited to a-symiclein, DJ-1, LRRK2, PINKL Parkin, UCHLl, Synphilin-1, and NURRl .

[00184] Examples of addiction-related proteins may include ABAT for example.

[00185] Examples of inflammation-related proteins may include the monocyte chemoattractant protein- 1 (MCP1) encoded by the Ccr2 gene, the C-C chemokine receptor type 5

(CCR5) encoded by the Ccr5 gene, the IgG receptor IIB (FCGR2b, also termed CD32) encoded by the Fcgr2b gene, or the Fc epsilon Rig (FCER lg) protein encoded by the Fcerlg gene, for example.

[00186] Examples of cardiovascular diseases associated proteins may include IL1B (interleukirs 1, beta), XDH (xanthine dehydrogenase), TP53 (tumor protein p53), PTG iS (prostaglandin 12 (prostacyclin) synthase), MB (myoglobin), IL4 (interieukin 4), ANGPTl (angiopoietin 1 ), ABCG8 (ATP-binding cassette, sub-family G (WHITE), member 8), or CTSK (cathcpsin ), for example.

[00187] Examples of Alzheimer's disease associated proteins may include the very low density lipoprotein receptor protein (VLDLR) encoded by the VLDLR gene, the ubiquitin-like modifier activating enzyme 1 (UBA1) encoded by the UBA1 gene, or the NEDD 8 -activating enzyme El catalytic subunit protein (UBE1 C) encoded by the UBA3 gene, for example.

[00188] Examples of proteins associated Autism Spectrum Disorder may include the benzodiazepine receptor (peripheral ) associated protein 1 (BZRAPl ) encoded by the BZRAP! gene, the AF4/FMR2 family member 2 protein (AFF2) encoded by the AFF2 gene (also termed MFR2), the fragile X mental retardation autosomal homolog 1 protein (FXRl) encoded by the FXR 1 gene, or the fragile X mental retardation autosomal homolog 2 protein (FXR2) encoded by the FXR2 gene, for example.

[00 89] Examples of proteins associated Macular Degeneration may include the ATP-binding cassette, sub-family A (ABCl) member 4 protein (ABCA4) encoded by the ABCR gene, the apo lipoprotein E protein (APOE) encoded by the APOE gene, or the chemokine (C-C motif) Ligand 2 protein (CCL2) encoded by the CCL2 gene, for example. [00190] Examples of proteins associated Schizophrenia may include NRG1 , ErbB4, CPLX1, TPH1 , TPH2, NRXN1 , GSK3A, BDNF, DISC I , GSK3B, and combinations thereof.

[00191] Examples of proteins involved in tumor suppression may include ATM (ataxia telangiectasia mutated), ATR (ataxia telangiectasia and ad3 related), EGFR (epidermal growth factor receptor), ERBB2 (v-erb-b2 erythroblastic leukemia viral oncogene homoiog 2), ERBB3 (v-erb-b2 erythroblastic leukemia viral oncogene homoiog 3), ERBB4 (v~erh-b2 erythroblastic leukemia viral oncogene homoiog 4), Notch 1 , Notch2, Notch 3, or Notch 4, for example.

[00192] Examples of proteins associated with a secretase disorder may include PSENEN (presenilin enhancer 2 homoiog (C. elegans)), CTSB (cathepsin B), PSEN1 (presenilin 1), APP (amyloid beta (A4) precursor protein), APH1B (anterior pharynx detective 1 homoiog B (C. elegans)), PSEN2 (presenilin 2 (Alzheimer disease 4)), or BACE1 (beta-site APP-cleaving enzyme 1), for example.

[00193] Examples of proteins associated with Amyotrophic Lateral Sclerosis may include SOD1 (superoxide dismutase 1), ALS2 (amyotrophic lateral sclerosis 2), FITS (fused in sarcoma), TARDBP (TAR DNA binding protein), VAGFA (vascular endothelial growth factor A), VAGFB (vascular endothelial growth factor B), and VAGFC (vascular endothelial growth factor C), and any combination thereof.

[00194] Examples of proteins associated with prion diseases may include SOD 1 (superoxide dismutase 1), ALS2 (amyotrophic lateral sclerosis 2), FUS (fused in sarcoma), TARDBP (TAR DNA binding protein), VAGFA (vascular endothelial growth factor A), VAGFB (vascular endothelial growth factor B), and VAGFC (vascular endothelial growth factor C), and any combination thereof.

[00195] Examples of proteins related to neurodegenerative conditions in prion disorders may include A2M (Alpha-2-MacroglobuIin), AATF (Apoptosis antagonizing transcription factor), ACPP (Acid phosphatase prostate), ACTA2 (Actin alpha 2 smooth muscle aorta), ADAM22 (ADAM metallopeptidase domain), ADORA3 (Adenosine A3 receptor), or ADRAI D (Alpha-ID adrenergic receptor for Alpha- ID adrenoreceptor), for example.

[00196] Examples of proteins associated with Immunodeficiency may include A2M [alpha-2- macroglobulm]; AANAT [arylalkylamine N -acetyl transferase]; ABCA1 [ATP-binding cassette, sub-family A (ABC I), member I]; ABCA2 [ATP-binding cassette, sub-family A (ABC1), member 2]; or ABC A3 [ATP-binding cassette, sub-family A (ABC!), member 3]; for example. [00197] Examples of proteins associated with Trinucleotide Repeat Disorders include AR (androgen receptor), FMR 1 (fragile X mental retardation 1), HTT (huntingtin), or DMP (dystrophia myotonic a-protein kinase), FXN (frataxin), ATXN2 (ataxin 2), for example.

[00198] Examples of proteins associated with Neurotransmission Disorders include SSI^' (somatostatin), NOS1 (nitric oxide synthase 1 (neuronal)), ADRA2A (adrenergic, alpha -2A-, receptor), ADRA2C (adrenergic, alpha-2C-_s receptor), TACR.1 (tachykinin receptor 1), or HTR2c (5-hydroxytryptamine (serotonin) receptor 2C), for example.

[00199] Examples of neurodeveiopmental-associated sequences include A2BP1 [ataxin 2- binding protein 1], AADAT [aminoadipate aminotransferase], AANAT [arylalkylamine N- acetyltransferase] , ABAT [4-aminobutyrate aminotransferase], ABCAl [ATP -binding cassette, sub-family A (ABCl), member 1], or ABCA l 3 [ATP-binding cassette, sub-family A (ABC1 ), member 13], for example.

[00200] Further examples of preferred conditions treatable with the present system include may be selected from: Aicardi-Goutieres Syndrome; Alexander Disease; Allan-Herndon-Dudley Syndrome; POLG-Related Disorders; Alpha-Mannosidosis (Type I and III); Alstrom Syndrome; Angelman; Syndrome; Ataxia-Telangiectasia; Neuronal Ceroid-Lipofuscinoses; Beta- Thalassemia; Bilateral Optic Atrophy and (Infantile) Optic Atrophy Type 1 ; Retinoblastoma (bilateral); Canavan Disease; Cerebrooculofacioskeietai Syndrome 1 [COFS l ]; Cerebrotendinous Xanthomatosis: Cornelia de Lange Svndrome; MAPT-Related Disorders; Genetic Prion Diseases; Dravet Syndrome; Early-Onset Familial Alzheimer Disease; Friedreich Ataxia [FRDA]; Fryns Syndrome; Fucosidosis; Fukuyama Congenital Muscular Dystrophy; Gafactosialidosis; Gaucher Disease; Organic Acidemias; Hemophagocytic Lymphohistiocytosis; Hutchinson-Gilford Progeria Syndrome; Mucolipidosis II; Infantile Free Sialic Acid Storage Disease; PLA2G6- Associated Neurodegeneration; Jervell and Lange- elsen Syndrome; junctional Epidermolysis Bullosa; Huntington Disease; Krabbe Disease (infantile); Mitochondrial DNA -Associated Leigh Syndrome and NARP; Lesch-Nyhan Syndrome; LISl - Associated Lissencephaly; Lowe Syndrome; Maple Syrup Urine Disease; MECP2 Duplication Syndrome; ATP7A-Related Copper Transport Disorders; LAMA2-Related Muscular Dystrophy; Arylsulfatase A Deficiency; Mucopolysaccharidosis Types I, D or HI; Peroxisome Biogenesis Disorders, Zellweger Syndrome Spectrum; Neurodegeneration with Brain Iron Accumulation Disorders; Acid Sphingomyelinase Deficiency; Niemann-Pick Disease Type C; Glycine Encephalopathy; A X-Related Disorders; Urea Cycle Disorders; COL1 A 1/2-Related Osteogenesis Imperfecta; Mitochondrial DNA Deletion Syndromes; PLP1 -Related Disorders; Perry Syndrome; Phelan-McDermid Syndrome: Glycogen Storage Disease Type II (Pompe Disease) ( Infantile); MAPT-Related Disorders; MECP2-Re!ated Disorders; Rhizomelic Chondrodysplasia Punctata Type 1; Roberts Syndrome; Sandhoff Disease; Schindler Disease - Type 1 ; Adenosine Deaminase Deficiency; Smith-Lemli-Opitz Syndrome; Spinal Muscular Atrophy; Infantile-Onset Spinocerebellar Ataxia; Hexosaminidase A Deficiency; Thanatophoric Dysplasia Type 1; Collagen Type VI-Re ated Disorders; Usher Syndrome Type I; Congenital Muscular Dystrophy; Wolf-Hirschhorn Syndrome; Lysosomal Acid Lipase Deficiency; and Xeroderma Pigmentosum.

[00201 J As will be apparent, it is envisaged that the present system can be used to target any polynucleotide sequence of interest. Some examples of conditions or diseases that might be useful Sy treated using the present system are included in the Tables above and examples of genes currently associated with those conditions are also provided there. However, the genes exemplified are not exhaustive.

EXAMPLES

[00202] The following examples are given for the purpose of illustrating various embodiments of the invention and are not meant to limit the present invention in any fashion. The present examples, along with the methods described herein are presently representative of preferred embodiments, are exemplary, and are not intended as limitations on the scope of the invention. Changes therein and other uses which are encompassed within the spirit of the invention as defined by the scope of the claims will occur to those skilled in the art.

Example 1: Improvement of the Cas9 system for in vivo application

[00203] Applicants conducted a Metagenoniic search for a Cas9 with small molecular weight. Most Cas9 homologs are fairly large. For example the SpCas9 is around 1368aa long, which is too large to be easily packaged into viral vectors for deli very.

[00204] Through computational analysis, Applicants found that in the bacterial strain Campylobacter, there are two Cas9 proteins with less than 1000 amino acids. The sequence for one Cas9 from Campylobacter jejuni is presented below. At this length, CjCas9 can be easily packaged into AAV, lentiviruses, Adenoviruses, and other viral vectors for robust delivery into primary ceils and in vivo in animal models. In a preferred embodiment of the invention, the Cas9 protein from 5. aureus is used.

Campylobacter jejuni Cas9 (CjCas9)

MARILAfOJGISSIGWAFSENDEL DCGVRIFT VENP TGESLALPRRLAJlSAJiKRLARR A LNHL HLIANEFKLNYEDYQSFDESLA AYKGSLISPYELRFRALNELLSKQDFAR

VILHIAKRRGYDDI SDDKE GAILiC^IKQNEEKLANYQSVGEYLYKEYTQ FKENSK

EFTNVRNKKESYERCIAQSFL DELKLIFKKQREFGFSFSiG FEEEVLSVAFYKRALKDFS

HLVGNCSFFTDEKRAP SPI.AFMFVAL RIINLLNNLKNTEGn.YTKDDLNALIvNEVL

NGTLTY QTK LLGLSDDYEFKGE GTYFIEFKKYKEFIKALGEHNLSQDDLNEIAKDIT

LI DEIKLKKALA YDLNQNQIDSLSKLEF DHLNISFKJ^L LVTPLMLEGKKYDEACNE

LNL VAiNEDKKDFLPAFNETYYKDEVTNPV\⁷L Al EYRKVLNAIXKKYGK.VHKINiE

LAJIEVGKN SQRA JE EQNENYKAKKDAELECEKLGLKI S NJL LRLF EQKEFCA

YSGE IKISDLQDEKMLEIDHIYPYSRSFDDSYMNKVLVFTK.QNQE LNQTPFEAFGNDS

AKWQKJE\XAKNLPTK QKRILDKNYKDKEQKNFKDRNLNDTRYIARLVLNYTKDYL

DFLPLSDDENTKL DTQ GSKVBVEA SGMLTSALRBTWGFSA DRNNHLHHAIDAVi

LAYANNSIV AFSDF KEQESNSAELYAKKISFLDY N R FFEPFSGFRQ VLDKIDEIF

VS TER XPSGALHEETFRKEEEFYQSYGGKSGVLK, LELGKJRK ^GKI\⁷KNGDMFR

V I .) I !^■ ! I K Ί X K 1 Ύ A V P f Y 1 \ 1 i ) 1 ^'Λ I , \^'I . P X K A V R S K i J I i f K ! ) f I . VI Y□ ·^"(^' FS 1. Y

DSIJLIQT DMQEPEFVYYNAFTSSTVSLIVS FIDN FF LS NQKJLFKNANEKEVIAKS IGIQNLKVFEKYIVSALGE KAEFRQREDFKK.

[00205] The putative tracrRNA element for this CjCas9 is:

[002061 Ί ΑΤΛΛΤί ^'Τί ΛΤΛΑθΛΛΛΤΤ!^'ΛΛΛΛΛθί;θΛ<Ί ΛΛΛΛΤΛΑΛί ;Λί iTTTi iCGi ¾G

ACTCTGCGGGGTTACAATCCCCTAAAACCGCTTTTAAAATT

[00207] The Direct Repeat sequence is:

ATTTTACCATAAAGAAATTTAAAAAGGGACTAAAAC

[00208] An example of a chimeric guideR A for CjCas9 is:

UGCGGGACUCUGCGGGGUUACAAUCCCCUAAAACCGCUUUU

Example 2: Cas9 optimization

[00209] For enhanced function or to develop new functions, Applicants generate chimeric Cas9 proteins by combining fragments from different Cas9 homologs. For example, two example chimeric Cas9 proteins:

[00210] For example, Applicants fused the N-term of StlCas9 (fragment from this protein is in bold) with C-term of SpCas9 (fragment from this protein is underlined).

[00211] St 1 ( )Sp(C)Cas9

MSDLVLGLDIGIGSVGVGIL VTGEIIHKNSRIFPAAQAENNLVRRTNRQGRRLAR KKH Ji VRL RLFEE SG LIT DFT i S IN L P YQL V GLTOELSN E ELFI AL M V HRGISYLDDASDDGNSSVGDYAQIVKENS QLET TPGQIQLERYQTYGQLRGDFT N LTVPTETK LSKEQKNQil ^^ NE AMGPA LFKYIAKLLSCDVADI GY iD

KSGKAEIHTFEAYR MKTLETLDIEQMDRETLDKLAYVLTL TEREGIQEALEHEF

ADGSFSQKQVDELVQFRKANSSIFG GWHNFSVKLMMELIPELYETSEEQMTILTR

LG QKTTSSSN T YiDEKLLTEEiY P\^AKSVRQAIKi\^rNAAIKEYGDFD rVIEM

ARENOTTO GOK SRERJvlKRIEEGIKELGSOILKEHPVENTOLONE LYLYYLQNGRD

MYVDQELDINRLSDYDVDHIVPQSFLKDDSIDNKVLTRSDKNRGISD VPSEEVVKKM

KNYWROLLNAIGJTQRKFDNL^

MNT^

LrK YPKLESEFVYGDY VYDVRKMIAKSEQErGKATAKYFFYSNIMNFF TEiTLANGE

DKLIARK DWDP KYGGFDSPTVAYSVLVVAKVE GKS L SVKELLGITIMERSSFE KXPlDH.Ii Λ K ( } \ ^' I ·. \ ^; K ( ) i Π K I . P YSLFIiLP GkK. R X- 1 ί . A. S A G U .0 K G N i ·. i , A I . P S Y V \ FLYLASHYE L GSPEDNEO OLFVEQHKHYLDEHEOISEFSKR\⁷ILADANLDKVLSAY HiD IREQAENH LFTLTNLGAPAAF YFDTTiDI KRYTST EVLDATLIHQSITGL YET TOLSOLGGD

>Sp(N)Stl(C)Cas9

MDKKYSiGLDiGTNSVGWAYITDEYKYPSKKFKVLGNTDRIISIKK JGALLEDS EATRLKRTARRRYTRR ^RICYLQEIFSNEMAKVDDSFFmLEESFLVEEDKKHERHPIF ( ) X j V PL V A Y 1 Π Y T f Y i Π . R f A^; P S Π ) K. I ) i , PJ . I Ί . A ί . A I S VII Γ i ( ; ί i 1 ·^' j . f ( ^' i j ) ( . N f ^> i ) N S

DVDKLFIOLA TYNQLFEENPR ASGVDAKAILSARL^S SRRLENLIAOLPGEKK GLFG NLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAATGSRLSD

HAILRRQEDFYPFL PNREKIE JLTFRIPYYVGPLARGNSRFAWMTR SEETRRPWNFEE

V VDKGASAQSl lHR \f ΓΝΓΡΚΝΙ.ΡΝΗ v I.P i jSi JA ATTVVNTJ KX' V VTl iMR PA FLSGEOKK VDLLF TNR VKOLK£DYFKJgECFDSVEISGVEDRFNASLGTYHDLL

K]] D DFLDNEENED]LEDIVLTL11.J^TEDREM1

WGRLSRKLR GIRD QSG TILDFL SDGFANRNFMOLIHDDSLTFKEDIOKAOVSGQG

DSLH:EHIANLAGSPAI GILOIY^?"KVVDEL\^ VMGRHKPE IV:I:EMA:REI^'' EDDE KAI

QKIQKANKDE DAJIMLKAANQY GKAELPHSVFHGHKQLATKIRLWHQQGERC

LYTGKTISIHDLINNSNQFEVDHILPLSITFDDSLAN VLVYATANQEKGQRTPYQAL

DSMDDAWSFRELKAFVRESKTLSN^

SRWLNALQEHFRIIH IDTKVSWRGQFTSQLRRHWGIE TRDTYHHHAVDALILA

ASSQLNLW KQKNTLVSYSEDQLLDIETGELISDDEY ESVF APYQHFVDTLKSK.

EFEDSIL.FSYQVDSKF R ISDATIYATRQAKVG D ADET I.GKI DIYTQDGYD

AFM IY DKSKFLMY HDPQTFEKVIEPILE YPNKQINEKG EVPCNPFL YKE

EHGYIRKYSK GNGPEIKSLI^YDS LGNHIDITPKDSNNKVVLQSVSPWRADVYF

N TTG YEILGLKY^{^}ADLQFE GTGTY ISQE Y DI KKEGVDSDSEF FTLYK D

LLLV DTETKEQQLFRFLSRT PKQKHWELKPYD QKFEGGEALIKVLG VANS

GQCKKGLGKSNISRY VRTDVLGNQHIIKNEGDKPKLDF

[00212] The benefit of making chimeric Cas9 include:

a, reduce toxicity b. improve expression in eukaryotic cells

c. enhance specificity

d. reduce molecular weight of protein, make protein smaller by combining the smallest domains from different Cas9 homologs.

e. Altering the PAM sequence requirement

Example 3: Utilization of Cas9 as a generic DNA binding protein

[00213] Applicants used Cas9 as a generic DNA binding protein by mutating the two catalytic domains (D10 and 1 1840) responsible for cleaving both strands of the DNA target. In order to upregulate gene transcription at a target locus Applicants fused the transcriptional activation domain (VP64) to Cas9 (Figure 5). Applicants hypothesized that it would be important to see strong nuclear localization of the Cas9-VP64 fusion protein because transcription factor activation strength is a function of time spent at the target. Therefore, Applicants cloned a set of Cas9-VP64-GFP constructs, transfected them into 293 cells and assessed their localization under a fluorescent microscope 12 hours post-transfection (Figure 8).

[002141 The same constructs were cloned as a 2A-GFP rather than a direct fusion in order to functionally test the constructs without a bulky GFP present to interfere. Applicants elected to target the Sox2 locus with the Cas9 transactivator because it could be useful for cellular reprogram and the locus has already been validated as a target for TALE-TF mediated transcriptional activation. For the Sox2 locus Applicants chose eight targets near the transcriptional start site (TSS). Each target was 20bp long with a neighboring NGG protspacer adjacent motif (PAM ) (Figure 12). Each Cas9-VP64 construct was co-transfected with each PGR generated chimeric crispr RNA (eiiiRNA) in 293 cells. 72 hours post transfection the transcriptional activation was assessed using T-qPCR (Figure 6).

[00215] To further optimize the transcriptional activator, Applicants titrated the ratio of chiRNA (Sox2.1 and Sox2.5) to Cas9 (NLS-VP64-NLS-hSpCas9-NLS-VP64-NLS), transfected into 293 cells, and quantified using RT-qPCR (Figure 11). These results indicate that Cas9 can be used as a generic DNA binding domain to upregulate gene transcription at a target locus.

| 00216| Applicants designed a second generation of constructs. (Table 1 below).

pLenti-EFl a-GFP-2A >xHis-NLS-VP64-NLS-hSpCsnl(D10A,

H840A)-NLS

[00217] Applicants use these constructs to assess transcriptional activation (VP64 fused constructs) and repression (Cas9 only) by RT-qPCR. Applicants assess the cellular localization of each construct using anti-His antibody, nuclease activity using a Surveyor nuclease assay, and DNA binding affinity using a gel shift assay. In a preferred embodiment of the invention, the gel shift assay is an EMS A gel shift assay.

Example 4: Cos9 repressor

[00218] It has been shown previously that dCas9 can be used as a generic DNA binding domain to repress gene expression. Applicants report an improved dCas9 design as well as dCas9 fusions to the repressor domains KRAB and SID4x. From the plasmid library created for modulating transcription using Cas9 in Table 2 below, and Figure 15, the following repressor plasmids were functionally characterized by qPCR: pXRP27, pXRP28, pXRP29, pXRP48, pXRP49, pXRP50, pXRPS L pXRP52, pXRP53, pXRP56, pXRP58, pXRP59, pXRP61, and pXRP62.

[00219] Each dCas9 repressor plasmid was co-transfected with two guide RNAs targeted to the coding strand of the beta-catenin gene (gRNAs were designed by my collaborator at the Broad, Joseph Rosenbiuh). RNA was isolated 72 hours after transfection and gene expression was quantified by RT-qPCR (Figure 16). The endogenous control gene was GAPDH. Two validated shRNAs were used as positive controls. Negative controls were certain plasmids transfected without gRNA, these are denoted as "pXRP## control" in Figure 16. The plasmids pXRP28, pXRP29, pXRP48, and pXRP49 could repress the beta-catenin gene when using the specified targeting strategy. These plasmids correspond to dCas9 without a functional domain (pXRP28 and pXRP28) and dCas9 fused to SlD4x (pXRP48 and pXRP49).

[00220] Table 2

pXRP024-pLend2-EFla-VP64-NLS-FLAG-Lmker-dCas9-NLS

pXRP025-pLenti2-EFla-VP64-NLS-GGGGS₃Linker-dCas9-NLS-gLuc-2A-GFP-WPRE

XRP034- Lenti2- PG -VP64-NLS-GGGGS₃Linker-Cas9-NLS-gLuc-2A-GFP-WPRE XR 0¾

p (R 03^

pXRP037-pLenti2-pPGK-VP64- LS-EAAAK Linker-Cas9-NLS-gL ic-2A-GFP-WPR,E pXRP038-pLenti2-LTR-VP64-NLS-EAAAK LirLker-Cas9-NLS-gLuc-2A-GFP-WPRE pXRP048-pLenti2-EFla--SID4x-NLS-FLAG-Linker-Cas9-NLS-gLiic-2A-GFP-WPRE pXRP049-pL€nti2-EFla-SID4X-NLS-GGGGS₃Linker-Cas9- LS-gL ic-2A-GFP VPRE pXRP050-pLenti2-EFla-SID4X-NLS-^

pXRPOS 1 -pLenti2-EFl a-KRAB-NLS-FLAG-Lmker-Cas9-NLS-gL c-2 A-GFP-WPRE pXBJE )^

pXRP053-pLenti2-EFla-KRAB-NLS-EAAAK₃Liiiker-Cas9-NLS-gLuc-2A-GFP-WPRE pXRP054-pLenti2-EFla-Cas9-Linker-FLAG-NLS-VP64-gLuc-2A-GFP-WPRE

pXRP055-pLenti2-EFla-Cas9-Linker-FLAG-NLS-Sro4X-gJ,uc-2A-GFP-WPRE

pXRP056-pLenti2-EFla-Cas9-Lioker-FLAG-NLS- RAB-gLuc-2A-GFP-WPR^

pXRP057-pLenti2-EFla-Cas9-GGGGGS₃-NLS-VP64-gLuc-2A-GFP-WPRE

pXRP058-pLenti2-EFla-Cas9-GGGGGS₃-NLS-S]D4X-gL c-2A-GFP-WPRE

XRH⁾59^LCT^

pXRP060-pLenti2-EFla-Cas9-EAAAK₃-NLS-VP64-gLuc-2A-GFP-WPRE

pXRP061 -pLenti2-EF 1 a-Cas9-EAAAK₃-NLS-SID4X-gLuc-2A-GFP-WPRE

pXRP062-pI.enti2-EFla-Cas9-EAAAK3-]SlLS-KRAB-gLuc-2A-GFP-WPRE

Example 5: Cas9 transcriptional modulator and nuclear localization

[00221] Cas9 Transcriptional Modulator. Applicants set out to turn the Cas9/gRNA CRISPR system into a generalized DNA binding system in which Applica ts ca execute functions beyond DNA cleavage. Whereby, fusing functional domains onto a eatalytically inactive Cas9, dCas9, Applicants can impart novel functions, such as transcriptional activation/repression, methy!ation/demethyiation, or chromatin modifications. To accomplish this goal Applicants made a eatalytically inactive Cas9 mutant by changing two residues essential for nuclease activity, D10 and H840, to alanine. It has been shown previously thai by mutating these two residues the nuclease activity of Cas9 is abolished while maintaining the ability to bind target DNA. The functional domains Applicants decided to focus on to test Applicants' hypothesis are the transcriptional activator VP64 and the transcriptional repressors SID and KRAB.

[00222] dCas9 Nuclear localization. Applicants hypothesized that the most effective dCas9 transcriptional modulator would be strongly localized to the nucleus where it would have its greatest influence on transcription. Moreover, any residual dCas9 in the cytoplasm could have unwanted effects. In previous work Applicants determined that wild-type Cas9 does not localize into the nucleus without including multiple nuclear localization signals (NLSs). Because multiple NLS sequences were required Applicants reasoned that it is difficult to get Cas9 into the nucleus and any additional domain that is fused to Cas9 could disrupt the nuclear localization. Therefore, Applicants built five dCas9-VP64-GFP fusion constructs to optimize the position and number of NLS sequences. A second version of each construct was made for functional testing, and these constructs were not directly fused to GFP. A schematic of these designs is shown in Figure 7. These constructs were cloned into a plenti2 backbone under the expression of the human EF! a promoter. The W PRE element was also added for more robust protein expression. Each constmct was transfected into HEK 293FT cells using Lipofectame 2000 and imaged 24 hours post- transfection (Figure 8). Figure 8 shows that the best nuclear localization is obtained when the fusion proteins have NLS sequences on both the N- and C-term of the fusion protein. The highest observed nuclear localization occurred in the construct with four NLS elements.

[00223] To more robustly understand the influence of NLS elements on dCas9 Applicants made 16 dCas9-GFP fusions by adding the same alpha importin NLS sequence on either the N- or C-term looking at zero to three tandem repeats. The same cloning strategy was used as explained previously. Each construct was transfecte into HEK 293 FT cells using Lipofectame 2000 and imaged 24 hours post-transfection (Figure 9). Notably, the number of NLS elements does not directly correlate with the extent of nuclear localization. Adding an NLS on the C-term has a greater influence on nuclear localization than adding on the N-term. For future applications it is more favorable to have smaller proteins. Therefore, the optimal NLS architecture for dCas9 was having one NLS on the N-term and C-term (pXRPNLS006).

[00224] One potential confounding factor of using a GFP fusion to determine nuclear localization is that the GFP itself could have a large influence on where the protein localizes in the cell. Therefore, Applicants determined that a good approach would be to include a (SxHis tag to dCas9, transfect into 293 FT cells, and then stain with an anti-6xHis antibody. Applicants made six versions utilizing this idea (Figure 10). Three were constructed for transcriptional activation (VP64 fusions), and the other three were for transcriptional repression (no functional domain). These constmcts were also made so Applicants could purify the recombinant protein using a nickel column. There are many applications of the 6xHis-dCas9 constmcts, such as, to perform an electromobility gel shift assay to show that mutated Cas9 can indeed bind its DNA target. The repression constructs (pXRPOB, pXRPQ14, pXRPOl S) were transfected in HEK 293 FT cells and were immunostained and imaged after 24 hours (Figure 1 1). Under this specific context, dCas9 requires two NLS signals on the N-terai to be localized into the nucleus. Interestingly, one LS on each terminus did not cause dCas9 to be strongly nuclear localized. Taken together, what this data suggests is that there is no generalized rule that can be made to conclusively say that a dCas9 fusion protein wi ll be localized into the nucleus. The construct of interest must be validated in the system it will be used to determine if it is in fact localized to the nucleus.

[00225] Cas9 Transcriptional Modulator Functional Testing. Applicants functionally tested the dCas9-VP64 protein by targeting the Sox2 locus and quantifying transcriptional activation by RT-qPCR. Eight DNA target sites were chosen to span the promoter of Sox (Figure 12). The gRNA expression cassettes were cloned into a pAAV-U6~gRNA/trcrRNA backbone plasmid, pA6. The plasmid utilizes the type lis enzyme Bbsi to reveals sticky ends for annealed ol go ligation. So for each target ail one needs is two complimentary oligos with the appropriate sticky- ends.

[002261 Each dCas9 containing construct was co-transfected with pA6 plasmids into HEK 293FT cells using Lipofectame 2000. 72 hours post-trans fection total RNA was extracted from the cells. 1 ug of RNA was reverse transcribed into cDNA (qScript Supermix) in a 40 u reaction. 2 ui of reaction product was added into a single 20 ul TaqMan assay qPCR reaction. Each experiment was performed in biological and technical triplicates. No RT control and no template control reactions showed no amplification. The results of this experiment are shown in Figure 13. Constructs that do not show strong nuclear localization, pXRP02 and pXRP04, result in no activation. For the construct that did show strong nuclear localization, pXRPOS, moderate activation was observed. Statistically significant activation was observed in the case of gRNAs Sox2.4 and Sox2.5. Of the 6xHis-dCas9 constructs (pXRPOl l , pXRPOB, pXRP015) were also tested using the same Sox2 targets (Figure 14). Compared to no gRNA mock controls Applicants could repress or activate Sox2.

[00227] To further optimize the dCas9 transcriptional activator and repressor Applicants built 31 constructs to explore different linkers, functional domains, and N- and C~term fusions. The list of constructs and the critical elements are shown in Figure 15. Three linkers were tested and the first was an unusual linker that was published by Shen and collegues (Shen et al. 2013, Cell Research paper from Xingxu Huang's lab: Ceil Research 23, 720-723 (May 2013)) where they showed it drastically improved nuclear localization and nuclease activity of Cas9. The second and third linkers were very common linkers known to be flexible (GGGGS3) and rigid (EAAAK3). The functional domains tested were VP64 for activation and SID4x and KRAB for repression, dCas9 without a functional domain was also made to test repression. The promoters tested were human EFl a, human pPGK, SV40, and the Sack of a promoter where expression is driven by the viral LTR.

[00228] All transcriptional activator constructs were targeted to the Sox2 locus using a combination of two gRNAs, iiSox2.1 and hSox2.4. The dCas9 activator constructs were co- transfeeted with the gRNAs into HEK 293FT cells and analyzed by qPCR. after 72 hours (Figure 16).

[00229] A luciferase Sox2 reporter assay was adopted to simplify the methods associated for determining levels of activation. The assay works by eo-transfeeting in three p!asmids, 1 ) dCas9, 2) gRNA, 3) Sox2 responsive element driving luciferase. So the level of luciferase is proportional to the amount of Sox2. The Sox2 responsive plasmid was purchased from BioCat. The Sox2 locus was targeted using different combinations of gRNAs and the constructs pXRP024 and pXRP025. A "No dCas9" control was used to determine the basal level of activation. The results shown in the top panel of Figure 11 suggest thai 3-fold activation could be reached compared to "No dCas9" and "No gRNA" controls.

[00230] A similar luciferase assay was adopted to test dCas9 transcriptional repression. The candidate gene Applicants chose to repress was beta-catenin and the targets were located near the 5' end of the gene body on the non-coding strand. The first experiment utilizing this assay compared the repressor pXRPNLS006 to the "dCas9" repressor published by Qi and coilegues (Qi et al. 2003, Cell paper from Wendell Lim's lab: http://www.sciencedirect.com/science/articIe/pii/S0092867413002110). The luciferase assay results (bottom panel of Figure 11) show that 3 -fold repression can be reached and the pXRPNLS006 plasmid reported here works significantly better than the current standard, "dCas9".

Example 6: Cas9 transcriptional activator in murine and human cell lines

[00231 ] Applicants previously demonstrated the capacity for CRISPR/Cas9 to act as a transcriptional activator. In this example Applicants further test this capability in a murine cell line. Applicants also examined the unguided basal activity of the dCas9~VP64 (double mutant DIOA H840A Cas9 fused to the VP64 transcriptional activation domain). Applicants delivered the Cas9 activator system to mouse cells and, separately, characterized the unguided effects of dCas9-VP64 for several human genes.

[00232] Mouse Ceil Line Experiments: Applicants selected the locus for the mouse gene Neurog2 for testing dCas9-VP64 transcriptional activation in Neuro 2A cells. Applicants also selected 7 sgRNA targeting sequences from a region 300 bp upstream to 100 bp downstream of the annotated Neurogl transcriptional start site. These guide sequences were cloned by the golden gate method into the px362 plasmid containing the U6 promoter upstream of a chimeric sgRNA cloning backbone.

[00233 J Neuro 2A cells were cultured in medium consisting of a 1 : 1 ratio of D5 (100:5: 1 DMEM high glucose w/Glutamax and sodium pyruvate: fetal bovine serum: peneciliin/stretomycin). For transfection, 120 cells in 0.5 mL culture medium were plated in each well of a 24 well plate. After 22 h in culture, each well of Neuro 2A cells was transfected with 1 ug of DNA using 5 uL of Lipofectamine following the recommended steps of the manufacturer (Life Technologies). For all dCas9-VP64 + sgRNA samples, 0.5 ug dCas9-VP64 plasmid and 0.5 ug sgRNA expression plasmid were used. For control samples, plasmid masses replaced GFP expressing plasmid as necessary. 4h after transfection, the medium was replaced with 1 mL culture medium. 48h after transfection, RNA was purified using the Macherey Nagel Nueleospin 96 RNA kit. Reverse transcription was performed with qScript cDNA supermi according to the manufacturer's protocol. qPCR was performed using Taqman probes and Taqman Fast Advanced Master Mix from fife Technologies on a Roche LightCycler 480 II realtime PCR machine.

[00234] Human Cell Line Experiments: Applicants selected 8 previously available sgRNA sequences for testing in 293FT cells using Applicants' pXRP057 dCas9-VP64 activator construct. Guide sequences were cloned by the golden gate method into the px362 plasmid containing the U6 promoter upstream of a chimeric sgRNA cloning backbone.

[00235] 293FT cells were cultured in D10 medium (100: 10: 1 ratio of DMEM high glucose w/Gfutamax and sodium pyruvate: fetal bovine serum: lOOx FIEPES solution). For transfection, 100K ceils in 0,5 mL culture medium were plated in each well of a 24 well plate. After 22 h in culture, each well of 293FT cells was transfected with 1 ug of DNA usin g 5 uL of Lipofectamine following the recommended steps of the manufacturer (Life Technologies), For all dCas9-VP64 + sgRNA samples, 0.5 ug dCas9-VP64 plasmid and 0.5 ug sgRNA expression plasmid were used. For control samples, including those analyzed for unguided transcriptional effects, plasmid masses were replaced by GFP expressing plasmid as necessary. 4h after transfeetion, the medium was replaced with 1 mL culture medium. 8h after transfeetion, RNA was purified using the acherey Nagel Nucleospin 96 RNA kit. Reverse transcription was performed with qScri.pt cDNA supermix according to the manufacturer's protocol. qPCR was performed using Taqman probes and Taqman Fast Advanced Master Mix from Life Technologies on a Roche LightCycler 480 I I real-time PGR machine.

[00236] Experimental results for Mouse Cel l Line Experiments: As shown in Fig. 20, 6 out of 7 sgRNAs targeted to the mouse eurog2 locus were able to induce upregulation of Neurog2 mRNA as measured by qPCR. With these results, Applicants demonstrated the utility of the Cas9 activator system for gene modulation in a mouse cellular model. The 7 sgRNa sequences are listed below:

[00213 J Experimental results for Human Cell Line Experiments: As shown in Fig. 21 , sgRNAs targeted to several human genes (ASCLl , MYOD1, VEGFA, and NTF3) successfully induced upregulation of the desired mRNA using Applicants pXRP057 dCas9-VP64 construct ( onermann et al, Optical control of mammalian endogenous transcription and epigenetic states. Nature. 2013 Aug 22;500(7463):472-6). Applicants showed that samples transfected with the dCas9-VP64 construct, but without an sgRNA had significant changes in expression level for several genes and further characterization is to be carried out (Fig. 22). The PAM counts (-100 to +100 bp of TSS) are indicated below:

Gene Basal Fold Change NGG + NAG counts

Neurog2 0.60 213 NTF3 0.94 203

ASCL1 4.19 235

MYOD1 0.90 204

Example 7: Further studies on the Cas9 modulator- activator and repressor data

[00237] Applicants carried out studies to further develop the dCas9 activator (pXRP57) and repressor (pXRP48) (Fig. 23). Applicants cloned piasmids pXRP57 and pXRP48 (Konermann et al., Optical control of mammalian endogenous transcription and epigenetie states. Nature. 2013 Aug 22:500(7463 ):472-6). The Cas9 activator sequence is indicated in Fig. 24 and the Cas9 repressor sequence is indicated in Fig. 25. Additional data was collected for the activator (Fig. 26), and repressor (Fig. 27). A list of guide RNAs used in the experiment is listed below:

KNA

hOct4-2 GAGTGATAAGACACCCGCTT

hOct4-3 G CAG CTGG CC ATTGTG CTTA

hOct4-4 GGAGAGGGGGTCAAGCACCT

hOct4-5 GCGGGTTGGGAGTTGAAAGT

hOci4-6 GCTCCAGCCTCCTAAGTGGC

hOct4-7 GGAGGTGGGGGGAGAAACTG

hOct4-8 G GTG A A ATG AGGGCTTGCGA

Example 8: CRISPR/Cas9 activator system with the light-inducihility of the LITE system

[00238] Applicants combined the RNA guidance of the CRISP /Cas9 activator system with the light-inducibility of the LITE system. An inducible expression system based on CRISPR/Cas9 .may make the inducible screen of many gene targets much faster and easier than previously possible, while also providing the opportunity to easily multiplex different targets by combining sgRNAs targeted to disparate genetic loci,

[00239] Materials and methods: The CasLlTE system consists of 3 components: a dCas9- CIB1 fusion protein, the CRY2PHR-VP64 construct, and an sgRNA guide sequence. Applicants synthesized 3 different versions of dCas9-QBl : (1) dCas9-GS-NLS-CIBl comprising the double mutant (D10A H840A) dCas9 from our pXRP057 piasmid, a glycine serine linker, SV40 nuclear localization signal, and CIBl from LITE l .O. (2) dCas9-GS-NLS-NLS-CIBl comprising the double mutant dCas9, glycine serine linker, 2 SV40 LS sequences, and CIB l from LITEl .O. (3) dCas9-G S-CIB 1 (mNLS d318-334) comprising the double mutant dCas9, glycine serine linker from LITE2.0, and CIBl from L1TE2.0. Vectors used in the practice of the invention are illustrated in Figs. 28, 29, 30.

[00240] Applicants selected sgR A sequences targeted to ASCL1 and MYOD1 , previously validated with a constitutive dCas9-VP64 activator, for testing the CasLITE systems in human cells. Guide sequences were cloned by the golden gate method into the px362 piasmid containing the U6 promoter upstream of a chimeric sgRNA cloning backbone.

[00241] 293FT cells were cultured in DIG medium without HEPES (10: 1 ratio of DMEM high glucose w/Glutamax and sodium pyruvate: fetal bovine semm). For transfection, 100 cells in 0,5 mL culture medium were plated in each well of a 24 well plate. After 22 h in culture, each well of 293FT cells was transfected with 1 .5 ug of DMA using 7.5 uL of Lipofectamine following the recommended steps of the manufacturer (Life Technologies). For all CasLITE + sgRNA samples, 0.5 ug dCas9-Cffil plasmid, 0.5 ug of CRY2PHR-VP64 plasmid (LITE1.0 or

LITE2.0 to match CIB1), and 0.5 ug sgRNA expression plasmid were used. Experiments with 4 sgR As used equal masses of each of 4 sgRNAs totaling 0.5 ug. For control samples, plasmid masses were replaced by GFP expressing plasmid as necessary. 4h after transfection, the medium was replaced with 1 mL culture medium. 48h after transfection excitation was started on light stimulated samples using 5 mW/cm2 475 nm blue light. 12h after starting stimulation, all samples, including all controls, were harvested for RNA using the Macherey Nagel Nucleospin 96 RNA kit. Reverse transcription was performed with qScript cDNA supermix according to the ma ufacturer's protocol . qPCR was performed using Taqman probes and Taqman Fast Advanced Master Mix from Life Technologies on a Roche LightCycIer 480 II real-time PGR machine,

[00242] Results: CasLITE constructs exhibited varying levels of light-inducible transcriptional activation (Fig. 31). Though the initial functionality of the system appears to be modest, calling for repeated experimentation, these results suggest the possibility for light- inducible RNA-guided transcriptional activation.

Example 9: Cas9 mouse model and validation of mouse embryonic stem cell line

[00243] Applicants validated a mouse embryonic stem cell line that was modified to i clude the Cre-dependent Cas9 cassette ( ί VI s into the Rosa26 locus (Fig. 32) and obtained geiiotyping results for germ line transmitted founders (Fig, 33).

[00244] To validate that the Cas9 cassette was functional, the modified mESC line was eleetroporated with the designated constructs in Fig. 32. The mESC line was used for blastocyst injection into C57BL/6J recipients (performed by the DCM at MIT). Six chimeric progeny were produced and then backcrossed to the C57BL/6J background. Successful germ line transmission was identified on the basis of agouti coat color. Two of the six chimerics produced germ line transmitted pups. Genomic D A was extracted from tissue from the Cas9 mice and Rosa26 short arm genotyping PGR was performed (Fig. 33), A 1.5kb band is the correct size for correctly inserted transgenes into the Rosa26 locus. These results demonstrate the successful germ line transmissio of the Cre-dependent Cas9 transgene in the Rosa26 locus. [00245] The benefit of the osa26 Cre-dependent Cas9 knockin line is that it can be crossed to any Cre driver line to enable Cas9 expression. Moreover, Cas9 can be activated by the delivery of Cre by viral vector or other delivery means. This enables ceil type, tissue, and developmental specificity of Cas9 expression. An additional benefit is that the mouse can be used for isolation of primary cells. This would be particularly useful in the case of a primary cell type that is not amenable to the delivery of nucleic acids or cannot be cultured long enough for the utilization of viral vectors.

Example 10: RNA-targeted CRISP R-hased platform for mammalian epigenome engineering

[00246] Applicants develop an RNA-targeted CRIS PR-based platform for mammalian epigenome engineering. Two RNA-targeted CR ISPR-mediated immune systems, CR ISPR/Crnr loci, were recently characterized from Pyrococcus furiosus and Sulfolobus solfataricus. Based on protein homology these CRISPR/Crnr loci are pari of a much larger family that exists within a diversity of bacterial and archaeai genomes. Similar to RNAi and Cas9 the interference mechanism of a CRISP /Cmr locus is based on the homology of a short stretch of nucleotides and is thus amenable to genome-wide screens. Moreover, the homology region to the target site is significantly increased making the potential for specificity much greater.

[00247] Applicants conduct a metagenomie analysis of the CRISPR/Crnr family, development of an in vitro assay system to identify functional loci, and characterization of the specificity and capacity for multiplexing in mammalian cells. A site-specific RNA-targeted CRISPR-based genome engineering platform (Fig. 34) can replace the many utilities of RNAi and provide a system for perturbing RNA biology that has never before been possible.

[00248] Preliminary work with the CRISPR/Cmr locus from P. furiosus: Based on the extensive knowledge base on the CRISPR Cmr locus from P. furiosus Applicants investigated the feasibility of expressing the Cmr genes within mammalian cells. Genomic DNA from P. furiosus was obtained from ATCC and used as a PGR. template to amplify the six Cmr genes (Cmr 1-6). Applicants also amplified another protein within the locus, Cas6. Cas6 is involved with the processing of crRNA into its mature form. Although only five Cmr genes (Cmr1 ,2,3,4,6) are essential Applicants considered that Cas6 may aid in troubleshooting if the five Cmr genes happened to be insufficient in the mammalian context. [00249] Cmrl -6 and Cas6 were cloned into mammalian expression plasmids and transfected into HEK 293FT cells. For easy visualization the cloning plasmid contained an HA tag and a P2A-EGFP sequence. The P2A sequence causes a ribosomal skip resulting in two mature proteins from the same transcript. 72 hours post-transfeetion EGFP fluorescence was observed for each Cmr expression plasmid (Fig. 35 A), suggesting that Cmrl -6 and Cas6 are successfully being expressed. To validate that the proteins are stable within the mammalian cell environment and are also the correct size Applicants performed a western blot (Fig. 35B). Within each lane there is a band of the expected size, suggesting thai each protein is being expressed and is stable within mammalian cells. The larger second band that appears within each lane may be a result of failure of the P2A sequence to cause a ribosomal skip and thus one protein fusion is created and not two individual protein products. The band located above the predicted size is -30 kDa larger than the expected size, which corresponds to P2A-EGFP. Applicants will confirm this by immunostaining the same blot using an anti-EGFP antibody and should see two bands per lane, one that is the size of P2A-EGFP and another larger band the size of Cmr-P2A-EGFP. The western blot results also show variable expression for the seven proteins, whereas, Cmrl , Cmr3, and Cmr6 have low expression while Cmr2, Cmr4, and Cmr5 have high expression. Applicants demonstrated that it is indeed possible to express Cmr proteins from P. furiosus within mammalian cells.

[00250] In this example, Applicants identify putative RNA-targeted CRISPR/Cmr loci and validate the expression of individual proteins and corresponding crRNAs in mammalian cells. Using a homology-based approach Applicants identify putative RNA-targeted CRISPR'Cmr loci across a diversity of bacterial and archaeal genomes. Cmr proteins and crRNAs from each locus are identified and validated through cloning, transfection into mammalian ceils, and detection by western blot and northern blot, respectively. The methodology is as follows:

[002511 1 . Identify RNA-targeted CRISPR loci: Identification of RNA-targeted CRISPR loci from published work is the first step in understanding the essential components of a functional Type III-B CRISPR/Cmr system. Two RNA-targeted loci from two different organisms have been published and characterized to different extents.

[00252] 2. Identify putative RNA-targeted CRISPR loci across a diversity of bacterial and archaeal species: Extensive work has been done towards classifying all known CRISPR loci into phylo genetic groups and has thus resulted in high confidence databases of orthoiogous proteins. Using the most extensive and manually curated databases Applicants identify putative CRISPR/Cmr loci based on the presence of multiple Cmr protein orthologs. 1 will pick a subset that spans the diversity of CRISPR' Cmr loci for further molecular characterization in a broad attempt to sample the natural diversity.

[00253] 3. Identify Cmr proteins and crRNAs within CRISPR Cmr loci: CRISPR/Cmr loci are well studied and many bacterial and archaeal genomes have been extensively annotated so the identification of Cmr proteins should be straightforward in these cases. However, in the absence of good annotation the problem will be more complicated. For this reason Applicants preferentially select CRISPR/Cmr loci from organisms where good annotations are available. If these strategies do not provide comprehensive coverage of the diversity CRISPR/Cmr loci Applicants use a homology-based approach combined with ORF prediction algorithms to identify the Cmr proteins. CRISPR repeat arrays have predictable structures and are located near the Cmr CRISPR associated proteins. The CRISPR array consists of a leader sequence that drives expression of the entire array of repeats and spacers creating a primary transcript that is extensively processed to make mature CRISPR NAs (crRNA)s. Existing computational tools (CRISPRFinder) will allow for identification of the repeat arrays. Predicting the mature crRNA from each locus may not be as straightforward and may require optimization. There are general features known about mature crRNAs from Type III-B CRISPR/Cmr loci that Applicants use to predict novel crRNAs. All identified mature crRNAs from Type III-B CRISPR loci have a 5' handle that is part of the repeat sequence followed by a spacer. The 5' handle functions in the recognition of the crRNA by the Cmr complex and the spacer guides the Cmr complex to target RNA through Watson-Crick base pairing. Applicants design a panel of likely crRNA architectures that are of different total length and have 5' handles of different length as it is difficult to predict any specific unique features of novel crRNAs a priori.

[00254] 4. Clone Cmr proteins and crRNAs into mammalian expression vectors: Cmr proteins are individually cloned into two different mammalian expression vectors (Fig. 36). The first vector (VI .0) expresses individual Cmr proteins using a C V promoter, bovine growth hormone polyA tail sequence, and a WPRE element to maximize protein expression. The second vector (V I .2) uses the same elements as in VI .0 but will include an N-term FIA tag and a C-term P2A-EGFP sequence. The HA tag enables protein detection and quantification and the P2A- EGFP enables an easy visual method for detecting expression in mammalian cells. Applicants make both versions because the impact of adding an HA tag and a P2A peptide on Cnrr proteins and how that influences correct formation of the Cmr complex is unknown. crRNAs is expressed using the human U6 promoter, which has been successfully used to express noncoding RNAs utilized for RNAi and DNA-targeted C ISPR/Cas9.

[00255] 5. Validate Cmr protein and crRNA expression: Cmr protein expression is validated by transfecting VI .2 plasmids into HEK 293FT ceils and observing EGFP expression. To further validate that the protein is expressed and the correct size Applicants prepare protein lysates from transfected cells and perform a western blot using an anti-HA tag antibody. To validate crRNA expression Applicants purify small RNAs from transfected cells and probe by northern blot.

[00256] Applicants demonstrate NA cleavage in an in vitro mammalian cell lysate assay- using naturally encoded crRNAs. Applicants develop a simple mammalian ceil Sysate in vitro assay to rapidly validate putative CRISPR/Cmr loci. Cell lysates of mammalian ceils transfected with Cmr proteins are prepared and incubated with naturally encoded crRNAs and a corresponding RNA target. Functioning CRISPR/Cmr loci are identified on the bases of correctly sized cleavage products using gel electrophoresis. The methodology is as follows:

[00257] 1 . Expression of Cmr proteins in mammalian ceils and preparation of cell lysates: Applicants transfect individual expression plasmids for all Cmr proteins of a species into HEK 293 FT cells and wait 72 hours for robust protein expression to occur. The cells are iysed, homogenized, and aliquoted for future use. Although not all cells are transfected with each Cmr plasmid, once the lysates are prepared all Cmr proteins will be in the same mixture. This is a beneficial over the live cell model where cotransfection of seven components may be challenging. Moreover, this will give Applicants absolute control over the final concentration of the crRNA and target RNA in the reaction.

[00258] 2. Preparation of crRNAs: For each CRISPR/Cmr locus Applicants make mature crRNAs containing the endogenous spacer. Specifically Applicants utilize the spacer sequence of the crRNA nearest the leader. As was discussed previously Applicants experiment with different crRNA architectures with different 5' ends. A direct method for creating mature crRNA of a defined sequence is in vitro transcription using commercially available T7 transcription kits.

[00259] 3. In vitro transcribe RNA harboring crRNA target sequences: T7 expression plasmids are cloned to uniquely harbor sequences targeted by the endogenous spacer of each CRISPR/Cmr locus. This target will be cloned into the middle of a ~1 kb piece of RNA so that- resulting cleavage products will be easily visualized on an agarose gel.

[00260] 4. Perform and optimize in vitro mammalian cell lysate cleavage experiment: Once all of the components are prepared Applicants combine and incubate the cell lysates, individual crRNAs, and target RNA followed by visualization o an agarose gel. Functional CRISPR systems are identified on the basis of cleavage products of the correct size. Certain parameters are kept in mind. Parameters for optimization are Cmr protein identity and concentration, crRNA architecture and concentration. Less significant parameters for optimization are buffer content and concentration, crRNA and RNA stability, reaction time, and RNA visualization.

[00261] Applicants demonstrate and characterize knockdown of endogenous mammalian genes using novel crRN As. crRNAs are engineered to target endogenous mammalian genes and cotraiisfected with Cmr expression plasmids into mammalian cells. mRNA a d protein knockdown are quantified by quantitative PCR and western blot. The multiplexing capability is investigated by targeting multiple genes at the same time. The specificity is characterized and compared to RNAi using RNA-seq. The methodology is as follows:

[00262] 1 . Target crRNAs to endogenous mammalian genes: With functionally validated RNA-targeted CRISPR/Cmr loci Applicants design novel crRNAs targeting three genes that are therapeutically validated RNAi targets, namely, P53, VEGF, and CTNNB l (Beta-catenin). Applicants pick eight target sites within each gene to help resolve any sequence-specific limitations of the technology. For different CRISPR/Cmr loci the exact target sight may differ by a few bases because of the unique required features of each crRNA but Applicants target a consistent region to aid in comparisons.

[00263] 2. Quantify and characterize mRNA knockdown: Applicants test the CRISPR/Cmr systems in HEK 293FT cells by iransfeetmg mammalian expression plasmids for Cmr protein components and individual crRNAs. Cleaved mRNAs are rapidly degraded in the cell, whereas, the resulting RNA fragments do not have both a 5 ' cap and a po!yA tail. Applicants quantify the extent of mRNA knockdown by performing quantitative PCR. When mRNA knockdown is observed Applicants perform a western blot for the targeted protein.

[00264] In addition to single crRNA transfection experiments Applicants add multiple crRNAs targeted to the same gene. It was observed previously that other transcriptional modulators work synergistically when targeted to multiple sites within the same region. This is also a useful strategy to identify suboptimal CRISPR/Cmr systems that do not function when using single crRNAs but can function overall and just need to be optimized for one reason or another. Applicants also add multiple crRNAs targeting different genes in the same condition to further consider multiplexing in this system. This has broad implications for pathway engineering and genome-scale screens.

[00265] 3. Characterize specificity by NA-seq: A major motivation of this work is to develop an RNA-targeting platform with greater specificity than RNAi. Inherently there is a greater opportunity for the CRISPR/Cmr system to have better specificity because the extended complementarity to the target site. However, each base pair within the guide may not be necessary or there may be some tolerance to mismatches. To understand these characteristics of the CRISPR/Cmr system Applicants will use an HEK 293T derived cel l line that expresses a single copy of EGFP. Applicants target EGFP for knockdow usi g 24 unique crRNAs. Using a HEK/GFP cell line makes the off-target analysis straightforward because EGFP may be considered an innocuous protein that has no influence on cellular processes so any altered transcripts are likely off-target effects. Results are compared to an siRNA targeting EGFP with known off-target effects. Due to the extended base pairing capacity of the CRISPR/Cmr complex Applicants expect the off-targets to be reduced. The tolerance to mismatches is also explored and this will be important for future development of the CRISPR/Cmr platform.

[00266] Given that an RNA-targeted CRISPR/Cmr system functions in mammalian cells Applicants initially pursue two applications: genome-scale screens and a catalytical ly inactive RNA-binding platform. A genome-scale RNAi screen is a powerful method for probing biology. However, high off-target effects severely limit the approach. A platform with higher specificity could either replace RNAi genomic-screens or provide an orthogonal approach that would aid in identifying true positives. An RNA-targeted CRISPR/Cmr platform is amenable to genomic screens because each target is programed by only a few nucleotides, whereby, a complex library could easily be synthesized and delivered.

[00267] A catalytically inactive RNA-binding platform is an enabling technology for the development of effector complexes that aid in the probing of RNA. Applicants identify the catalytically active components of the Cmr complex and mutate the specific residues responsible. This has been done successfully in a number of cases, e.g. this was done for CRJSPR/Cas9 to create a nickase and a transcriptional modulator. Utilizing this platform Applicants develop a technology to detect and image RNA transcripts inside the cell. This has applications for understanding the influence of RNA localization on cellular processes and in vivo detection and quantification of RNA. Alternatively Applicants add effector molecules onto an RNA-biiiding platform towards probing and understanding areas of RNA biology that are not well understood, namely RNA editing and epigenetics.

[00197] While preferred embodiments of the present invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the invention. It should be understood that various alternatives to the embodiments of the in vention described herein may be employed in practicing the invention.

[00198] References:

Barrangou, R., Fremaux, C, Deveau, PL, Richards, M., Boyavai, P., Moineau, S., ... Llorvath, P. (2007). CRISPR provides acquired resistance against viruses in prokaryotes. Science (New York, N.Y.), 315(5819), 1709-12. doi: 10.1 126/science, 1 138140

Birmingham, A., Anderson, E. M., Reynolds, A., llsley-Tyree, D., Leake, D., Fedorov, Y., ... Khvorova, A. (2006). 3' UTR seed matches, but not overall identity, are associated with RNAi off-targets. Nature methods, 3(3), 199-204. doi: 10.1038/nmeth854

Brouns, S. J. J., Jore, M. M., Lundgren, M., Westra, E. R., Siijkhuis, R. J. H., Snijders, A. P. L., ... van der Oost, J. (2008). Small CR ISPR RNAs guide antiviral defense in prokaryotes. Science (New York, N.Y.), 321(5891), 960-4. doi: 10.1126/science.l 159689

Burnett, J. C, Rossi, J. J., & Tiemann, K. (201 1). Current progress of siRNA/shRNA therapeutics in clinical trials. Biotechnology journal, 6(9), 1 130-46. doi: 10.1002/biot.201 100054 Cheong, C.-G., & Hall, T. M. T. (2006). Engineering RNA sequence specificity of Pumilio repeats. Proceedings of the National Academy of Sciences of the United States of America, 103(37), 13635-9. doi: 10.1073/pnas.0606294103

Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., ... Zhang, F. (2013). Multiplex Genome Engineering Using CRISPR/Cas Systems. Science (New York, N.Y.). doi: 10.1126/science.1231 143 Eibashir, S. M., Harborth, J., Lendeckel, W,, Yalcin, A., Weber, K., & Tuschl, T. (2001). Duplexes of 21 -nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature, 411(6836), 494-8. doi: 10.1038/35078107

Fire, A., Xu, S., Montgomery, M. ., Kostas, S. A., Driver, S. E., & Meilo, C. C. (1998). Potent and specific genetic interference by double-stranded RNA in Caenorhabditis eiegans. Nature, 391 (6669), 806-11. doi: 10.1038/3588S

Hale, C, Kleppe, ., Terns, R. M., & Terns, M. P. (2008). Prokaryotic silencing (psi)RNAs in Pyrococcus furiosus. RNA (New York, N.Y.), 14(12), 2572-9. doi:10.126J/raa.l246808

Hale, C. R., Majumdar, S., Elmore, J., Pfister, N., Compton, M., Olson, S., ... Terns, M. P. (2012). Essential features and rational design of CRISPR RNAs that function with the Cas RAMP module complex to cleave RNAs. Molecular cell, 45(3), 292-302. doi: 10.1016/j .molcei.2011.10.023

Hale, C. I ., Zhao, P., Olson, S., Duff, M. <).. Graveley, B. R., Wells, L., ... Terns, M. P. (2009). R A-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell, 139(5), 945-956. Hou, Z., Zhang, Y., Prop son, N. E., Howden, S. E., Chu, L.-F., Sontheimer, E. J., & Thomson, J. A. (2013). Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis. Proceedin gs of the National Academy of Sciences of the United States of America, 1 10(39), 15644-9. doi: 10.1073/pnas.l313587110

Ishino, Y., Shinagawa, H., Makino, ., Amemura, M., & Nakata, A. (1987). Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. Journal of bacteriology, 169(12), 5429- 33.

Jackson, A. L., Bartz, S. R., Scheiter, 1, obayashi, S. V, Burchard, J., Mao, M., ... Linsley, P. S. (2003). Expression profiling reveals off-target gene regulation by RNAi. Nature biotechnology, 21 (6), 635-7. doi: 10.1038/nbt831

Jackson, A. L., Burchard, J., Leake, D., Reynolds, A., Scheiter, J., Guo, J., ... Linsley, P. S. (2006). Position-specific chemical modification of siRNAs reduces "off-target" transcript silencing. RNA (New York, N.Y.), 12(7), 1197-205. doi:10.1261/ma.30706

Jansen, R., Embden, J. D, A. van, Gaastra, W., & Schouls, L. M. (2002). Identification of genes that are associated with DNA repeats in prokaryotes. Molecular microbiology, 43(6), 1565-75, Konermann, S., Brigham, M, D., Trevino, A, E., Hsu, P. D., eidenreich, M., Cong, L,, , , , Zhang, F. (2013). Optical control of mammalian endogenous transcription and epigenctic states. Nature, 500(7463), 472-6. doi: 10.1038/naturel2466

Mackay, j. P., Font, J., & Segal, D, J, (2011). The prospects for designer single-stranded R A- binding proteins. Nature structural & molecular biology, 18(3), 256-61. doi: 10.1038/nsmb.2005 Makarova, , S., Haft, D. FI., Barrangou, R., Brouns, S. J. J., Charpentier, E,, Horvath, P., ... Koonin, E. V. (2011 ). Evolution and classification of the CRISPR-Cas systems. Nature reviews. Microbiology, 9(6), 467-77. doi: 10.1038/nrmicro2577

Mali, P., Yang, L., Esveit, K. M., Aach, J., Gueli, ML, DiCario, J. E., ... Church, G. M. (2013). RNA-guided human genome engineering via Cas9. Science (New York, N.Y.), 339(6121), 823— 6. doi: 10.1126/science.1232033

Marraffini, L, A., & Sontheimer, E. J. (2010). CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nature reviews. Genetics, 1 1 (3), 181-90. doi: 10.1038/rsrg2749 Mojica, F. J., Diez-Viilasenor, C, Soria, E., & Juez, G. (2000). Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria. Molecular microbiology, 36(1), 244-6.

Mojica, F. J. M., Diez-Viliasefior, C, Garcia-Martinez, J., & Soria, E. (2005). Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. Journal of molecular evolution, 60(2), 174-82. doi: 10.1007/s00239-004-0046-3

Peabody, D. S. ( 1993). The RNA binding site of bacteriophage MS coat protein. The CM BO journal, 12(2), 595-600. Qi, L. S., Larson, M. EL, Gilbert, L. A., Doudna, J. A., Weissman, J. S., Arkin, A. P., & Lim, W. A. (2013). Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell, 152(5), 1173-83. doi: 10.1016/j xell.2013.02.022

Sapranauskas, R., Gasiunas, G., Fremaux, C, Barrangou, R., Horvath, P., & Siksnvs, V. (2011). The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli. Nucleic acids research, 39(21), 9275-82. doi: 10. 1093 nar gkr606

SenGupta, D. J., Zhang, B., Kraemer, B., Pochart, P., Fields, S., & Wickens, M, (1996). A three- hybrid system to detect RNA-protein interactions in vivo. Proceedings of the National Academy of Sciences, 93(16), 8496-8501. doi: 10.1073/pnas.93.16.8496 Valencia-Burton, M„ McCullough, R. M., Cantor, C. R., & Broude, N. E. (2007). RNA visualization in live bacterial ceils using fluorescent protein com lementation. Nature methods, 4(5), 421-7. doi: 10.1038/nmetiil023

Wang, X., McLachlan, J., Zamore, P. D., & Hall, T. M. T. (2002). Modular Recognition of RNA by a Human Pumilio-Homology Domain. Ceil, 1 10(4), 501-512.

Zhang, J., Rouil lon, C, erou, M ., Reeks, J., Brugger, K„, Graham, S., . .. White, M. F. (2012). Structure and mechanism of the CMR complex for CRISPR-mediated antiviral immunity. Molecular cell, 45(3), 303-13. doi: 10.1016/j.molcel.201 1.12.013

Claims

What is claimed is:

1. A non-naturally occurring or engineered composition comprising a vector system comprising one or more vectors comprising

1. a first regulatory element operabl linked to a CRISPR/Cas system chimeric A (chiRNA) polynucleotide sequence, wherein the polynucleotide sequence comprises

(a) a guide sequence capabl e of hybridizing to a target sequence in a cell,

(b) a tracr mate sequence, and

(c) a tracr sequence, and

II. a second regulatory element operably linked to an enzyme-coding sequence encoding a CR1SPR enzyme comprising at least one or more nuclear localization sequences,

wherein (a), (b) and (c) are arranged in a 5' to 3 ^"orientation,

wherein components I and II are located on the same or different vectors of the system, wherein when transcribed, the tracr mate sequence hybridizes to the tracr sequence and the guide sequence directs sequence-specific binding of a CRISPR complex to the target sequence,

wherein the CRISPR complex comprises the CRISPR enzyme complexed with (1) the guide sequence that is hybridized to the target sequence, and (2) the tracr mate sequence that is hybridized to the tracr sequence,

wherein the CRISPR enzyme comprises two or more mutations, such that the enzyme has altered nuclease compared with the wild t pe enzyme, and

wherein the enzyme-coding sequence further encodes one or more heterologous functional domains.

2. A multiplexed CRISPR enzyme system composition comprising a vector system comprising one or more vectors comprising

I. a first regulatory element operably linked to a CRISPR/Cas system chimeric RNA (chiRNA) polynucleotide sequence, wherein the polynucleotide sequence comprises

(a) a guide sequence capable of hybridizing to a target sequence in a cel l,

(b) a tracr mate sequence, and

(c) a tracr sequence, and

II. a second regulatory element operably linked to an enzyme-coding sequence encoding a CRISPR enzyme comprising at least one or more nuclear localization sequences, wherein (a), (b) and (c) are arranged in a 5' to 3' orientation,

wherein components I and I I are located on the same or different vectors of the system, wherein when transcribed, the tracr mate sequence hybridizes to the tracr sequence and the guide sequence directs sequence-specific binding of a CRISPR complex to the target sequence,

wherein the CR ISPR complex comprises the CRISPR enzyme complexed with (1 ) the guide sequence that is hybridized to the target sequence, and (2) the tracr mate sequence that is hybridized to the tracr sequence,

wherein the CRISPR enzyme comprises two or more mutations, such that the enzyme has altered nuclease activity compared with the wild type enzyme,

wherein the enzyme-coding sequence further encodes one or more heterologous functional domains, and

wherein in the multiplexed system composition multiple ch.iR.NA. polynucleotide sequence are used.

3. A non-naturally occurring or engineered composition comprising a vector system comprising one or more vectors comprising

I. a first regulatory element operably linked to

(a) a guide sequence capable of hybridizing to a target sequence in a cell, and

(b) at least one or more tracr mate sequences,

Π. a second regulatory element operably linked to an enzyme-coding sequence encoding a CRISPR enzyme, and

III. a third regulatory element operably linked to a tracr sequence,

wherein components I, II and III are located on the same or different vectors of the system,

wherein when transcribed, the tracr mate sequence hybridizes to the tracr sequence and the guide sequence directs sequence-specific binding of a CRISPR complex to the target sequence,

wherein the CRISPR complex comprises the CRISPR enzyme complexed with (1) the guide sequence that is hybridized to the target sequence, and (2) the tracr mate sequence that, is hybridized to the tracr sequence, wherein the CRISPR enzyme comprises two or more mutalions, such thai the enzyme has altered nuclease compared with the wild type enzyme, and

wherein the enzyme-coding sequence further encodes one or more heterologous functional domains.

4. A multiplexed CRISPR enzyme system composition comprising a vector system comprising one or more vectors comprising

I. a first regulatory element operabiy linked to

(a) a guide sequence capable of hybridizing to a target sequence in a cell, and

(b) at least one or more tracr mate sequences,

II. a second regulatory element operabiy linked to an enzyme-coding sequence encoding a CR ISPR enzyme, and

III. a third regulatory element operabiy linked to a tracr sequence,

wherein components I, I I and III are located on the same or different vectors of the system,

wherei when transcribed, the tracr mate sequence hybridizes to the tracr sequence and the guide sequence directs sequence-specific binding of a CRISPR complex to the target sequence,

wherein the CRISPR complex comprises the CRISPR enzyme complexed w th ( 1) the guide sequence that is hybridized to the target sequence, and (2) the tracr mate sequence that is hybridized to the tracr sequence,

wherein the CRISPR enzyme comprises two or more mutations, such that the enzyme has altered nuclease compared with the wild type enzyme,

wherein the enzyme-coding sequence further encodes one or more heterologous functional domains, and

wherein in the multiplexed system composition multiple guide sequences capable of hybridizing to multiple target sequences are used.

5. The composition of any preceding claim, wherein the CRISPR enzyme comprises one or more mutations in two or more catalytically active domains.

6. The composition of any preceding claim, wherein the CRISPR enzyme has reduced or abolished nuclease activity compared with the wild type enzyme.

7. The composition of any preceding claim, wherem the two mutations are D10A SpCas9 in a first catalytically active domain and H840A SpCas9 in a second catalytically active domain or corresponding residues of other CRISPR enzymes.

8. The composition of any preceding claim, wherein the CRISPR enzyme comprises two or more mutations in a residue selected from the group consisting of DIO, E762, H840, ^'N854, ^'N863, or 1)986.

9. The composition of any precedmg claim, wherein the CRISPR enzyme comprises two or more mutations selected from the group comprising D10A, E762A, H840A, N854A, N863A or D986A.

10. The composition of any preceding claim, wherein the CRISPR enzyme is a DNA binding protein that does not direct cleavage of either strand at the location of the target sequence.

1 1. The composition of any preceding claim, wherein each of the two or more mutations is in a catalytically active domain of the CRISPR enzyme selected from the group comprising RirvCI, RuvCII, RuvClII or I INI I domain.

12. The composition of any preceding claim, further comprising at least two or more nuclear localization sequences.

13. The composition of any precedmg claim, wherein the functional domain is a transcriptional activation domain

14. The composition of claim 13, wherein the transcriptional activation domain is

VP64.

15. The composition of any precedmg claim, wherein the functional domain is a transcriptional repressor domain.

16. The composition of claim 15, wherem the transcriptional repressor domain is a KRAB domain.

17. The composition of claim 15, wherein the transcriptional repressor domain is a SID domain or a SID4X domain,

18. The composition of any preceding claim, wherein the enzyme coding sequence encodes one or more heterologous functional domains fused to the CRISPR enzyme.

19. The composition of any preceding claim, wherein the enzyme coding sequence encodes two or more heterologous functional domains.

20. The composition of any preceding claim, wherein the enzyme coding sequence further comprises one or more linker sequences between any two domains.

21. The composition of any preceding claim, wherein the one or more functional domains have one or more of the following activities: methylase activity, demethylase activity, transcription activation activity, transcription repression activity, transcription release factor activity, histone modification activity, RNA cleavage activity and nucleic acid binding activity.

22. The composition of any preceding claim, wherein the functional domain binds

DNA.

23. The composition of any preceding claim, wherein the functional domain affects transcription of the target nucleic acid.

24. The composition of any preceding claim, wherein the cell is a prokaryotic or eukaryotic cell.

25. The composition of any preceding claim, wherein the cell is a eukaryotic cell.

26. The composition of claim 25, wherein the eukaryotic cell is a mammalian cell.

27. The composition of claim 26, wherein the mammalian cell is a human cell.

28. The composition of any preceding claim, wherein the CRISPR enzyme is codon optimized for expression in a eukaryotic cell.

29. The composition of any preceding claim, wherein the CRISPR enzyme is a type II CRISPR enzyme.

30. The composition of any preceding claim, wherein the CRISPR enzyme is a Cas9 enzyme.

31. The composition of any preceding claim, wherein the Cas9 enzyme is from an organism selected from the group comprising of genus Streptococcus, Campylobacter, Nitratifraclor, Staphylococcus, Parvibaculum, Roseburia, Neisseria, Oluconacetobacter, Azospirillurn, Sphaerochaeta, Lactobacillus, Eubacterium or Corynebacter.

32. The composition of any preceding claim, wherein the vectors of the system are viral vectors selected from the group comprising of a lentiviral vector, an adenoviral vector or an AAV vector.

33. A method of modulating gene expression at a genomic locus of interest in a cell by contacting the cell with the composition of any of the preceding claims.

RECTIFIED SHEET (RULE 91) ISA/EP