CRISPR Handbook

Enabling Genome Editing and

Transforming Life Science Research

www.GenScript.com
GenScript USA Inc.
860 Centennial Ave.
Piscataway, NJ 08854 USA
Phone: 1-732-885-9188
Toll-Free: 1-877-436-7274
Fax: 1-732-885-5878

Table of Contents
CRISPR Reagents and Services
from GenScript
gRNA sequence databases
Validated gRNA sequences for ecient,
specic targeting of WTCas9 or SAM

CRISPR Plasmids
Validated all-in-one, dual, non-viral and
viral vectors for Cas9 & gRNA constructs

CRISPR gRNA Libraries

Validated GeCKO and SAM libraries for
genome-scale loss- or gain-of-function
screens

SAM Transcription Activators

A
S M

Validated SAM guide RNA sequences and

ecient lentiviral vectors for robust
transcriptional activation of endogenous
genes or lncRNA

CRISPR KO/KI mammalian cell lines

CRISPR genome editing service generates KO
or KI mammalian cell lines

Microbial genome editing

Ecient bacterial genome editing using
Red CRISPR/Cas technology

This handbook describes CRISPR/Cas9 genome editing and other research

applications for CRISPR technology.

The CRISPR Genome Editing Revolution

Discovery of CRISPR in bacterial immune system
Evolution of Genome Editing technology
Advantages of CRISPR genome editing
Improving the specicity of CRISPR genome editing
Improving gRNA and Cas9 delivery ecacy
Expanding the applicability of CRISPR genome editing
Regulating Cas9 expression

2
4
7
8
10
11
12

Putting CRISPR into Practice: Workows and

Case Studies
Design guide RNA and generate expression constructs
Deliver CRISPR reagents to target cells
Check for intended KO/KI and o-target eects
Case studies

13
14
16
17

Expanding the Research Applications for CRISPR

Genome-wide screens using CRISPR libraries
Adapting CRISPR for transcriptional regulation
Epigenetic Modications
Stem Cell Dierentiation
Therapeutics

21
22
24
25
25

Future of CRISPR

28

References

29

To download this handbook as a PDF, please visit

www.genscript.com/CRISPR-handbook.html
www.genscript.com

Figure 1: Mechanism of CRISPR-mediated immunity in bacteria

viral DNA

Discovery of CRISPR in bacterial immune systems

Microbes have adapted many strategies to evade infection by viruses and phages,
from blocking virus adsorption to preventing DNA insertion. Over the past 10
years, a new bacterial immune system has been discovered, employing a novel
technique to prevent infection. This immune system allows bacteria to both
prevent foreign DNA from being inserted into the genome, and also target the
invasive DNA for destruction (Horvath et al., 2010).
This system was rst brought to light in 1987. Nakata and colleagues were
studying the iap enzyme when they discovered curious repeat and non-repeat
sequences downstream of the iap gene (Ishino et al., 1987). Just 5 years later,
these repeat arrays would become referred to as CRISPR, or Clustered Regular
Interspaced Short Palindromic Repeats (Jansen et al., 2002); however, their function
was still a mystery. In 2005, Mojica and colleagues revealed that these sequences,
or spacers, actually contained DNA from bacteriophages (Mojica et al., 2005).
Shortly after this discovery, Bolotin et al also observed the presence of cas genes,
which encode for a DNA endonuclease, in close proximity to CRISPR structures,
strongly suggesting that foreign DNA degradation may be a primary function of
CRISPR/Cas (Bolotin et al., 2005). The specicity of this system for foreign DNA
was further elucidated a few years later with the discovery of conserved motifs

www.genscript.com

Cas1/Cas2

DNA is cleaved and new

spacer unit is inserted

repeat + spacer
TracrRNA Cas complex

crRNA-tracrRNACas complex

+
immunity

The ability to manipulate DNA has been a signicant breakthrough in the

scientic community making it possible to better understand the relationship
between the genome and its functions. From inhibiting gene function to
altering its expression, genome editing can provide tremendous insight into
the basis of disease and identication of new targets for medical intervention
(Hsu et al., 2014). For this to become a reality, researchers need the ability
to make specic, targeted changes to the genome, a simple principle that has
been challenging in practice. Over the last 20 years, advances in genome
editing technologies have overcome many of these challenges, allowing
researchers to more precisely manipulate genomes in cell lines and animal
models to more accurately model disease pathologies. Of these advances,
one of the most exciting has been CRISPR/Cas, a system adapted from the
bacterial immune system that is ecient, rapid, and easy to use (Doudna et
al., 2014). In this handbook, we will discuss how CRISPR technology has
fueled a genome editing revolution, as well as how it has been adapted for
other biological applications and how it is expected to transform medicine.

within the genome. Just upstream of the protospacers, or target genomic

sequences on the foreign DNA, are conserved motifs called protospacer adjacent
motifs (PAM). These motifs are preferential targets for the Cas endonucleases
(Horvath et al., 2008, Deveau et al., 2008), and allow the system to discern
between self- and non-self DNA (Mali et al., 2013). Together, by the end of the

immunization

The CRISPR Genome Editing Revolution

RNA Pol III

viral DNA
cleavage
viral DNA

early 2000s, the signicance of the CRISPR as a defense strategy in bacteria was
coming to light.
By 2010, three CRISPR systems had been identied in bacteria: Type I, II and III.
Type II CRISPR interference, because of its relative simplicity, would eventually
become the system adapted for genome editing in mammalian cells (Sapranauskas et al., 2011) (Figure 1). CRISPR-based immunity is composed of two main
phases: immunization and immunity. In the immunization phase, Cas proteins
(Cas1/Cas2) form a complex that cleaves the foreign, viral DNA (Jiang et al.,
2015). This foreign DNA is then incorporated into the bacterial CRISPR loci as
repeat-spacer units. In the immunity phase, following re-infection, the repeat
spacer units are transcribed to form pre-CRISPR RNA (pre-crRNA). The Cas9
endonuclease and trans-activating crRNA (tracrRNA, which helps guide Cas9 to
crRNA) then bind to the pre-crRNA. A mature crRNA-Cas9-tracrRNA complex is
formed following cleavage by RNA polymerase. This crRNA-Cas9-tracrRNA
complex is essential to target and destroy the foreign DNA.

www.genscript.com

Evolution of Genome Editing technology

Prior to the dawn of genome editing in the early 2000s, studying gene function
was primarily limited to transgenesis. The concept of gene editing began in the
late 1980s: in 1989, homologous recombination (HR) was used to target specic

which recognizes 34-bp loci called loxP (Sauer et al., 1998). Recombination at
these sites leads to knock-out of desired genes, which has been particularly
useful for the development of transgenic mouse models. While easier to control
than HR, the Cre-lox system was less ecient as the genetic distance increased
between loxP sites (Zheng et al., 2000).

Figure 2: Advancements in genome editing

Figure 3: DNA repair by targeted genome editing

1989

1998

2009

First study describing

genome editing via
HR in mouse ES cells
(Capecchi et al).

Discovery of zinc-nger
proteins that can target
specic DNA sequences
(Beerli et al).

DNA binding proteins

discovered in Xanthomonas
bacteria (Boch et al).

HR-mediated
targeting

Zinc-nger nucleases
(ZFNs)

1992

2000

The Cre-lox editing

technology was successfully used for site-specic
recombination in mice
(Orban et al).

The CRISPR defense

system is rst identied
in prokaryotes (Mojica
et al).

Cre-lox

Bacterial CRISPR/Cas

Transcription-like eector
nucleases (TALENs)

CRISPR/Cas genome
editing
First demonstration that
the CRISPR/Cas system can
be used for mammalian
cell genome editing (Mali
et al, Cong et al).

As the need for relevant animal disease models rose, so did the need for
sophisticated and more ecient genome editing tools. The Cre-lox technology
became one of the most eective gene editing tools in the early 1990s, allowing
scientists to control gene expression both spatially and temporally (Utomo et al.,
1999, Orban et al., 1992). Cre-lox uses a site-specic DNA endonuclease Cre,

www.genscript.com

Donor DNA

Non-homologous end joining (NHEJ)

Homology directed repair (HDR)

Insertion/deletion mutations (indels)

Precise alteration/correction

Knock-out

Knock-in

2013

genes in mouse embryonic stem cells to generate knock-in (KI) and knock-out
(KO) cells (Capecchi et al., 1989) (Figure 2). Since HR occurs rather infrequently in
mammalian cells, the recombination frequency was low (1 in every 3104 cells);
however, this work provided new ideas for how genes can be targeted and
altered in specic ways.

Double-Strand Break

Since HR alone rarely results in gene integration in mammalian cells, the introduction
of double strand breaks (DSB) into the genome can increase recombination
signicantly (Choulika et al., 1995). DSB resolution occurs by either HDR or
error-prone nonhomologous end joining (NHEJ) (Figure 3). If there is no donor
DNA present, resolution will occur by NHEJ, resulting in insertion/deletions (indels)
that will ultimately knock-out gene function. Alternatively, if donor DNA
sequences are available, the DSBs will be repaired by HDR, resulting in gene
knock-in (Bibikova et al., 2002). Combined, these strategies represented new and
more eective approaches for modifying the eukaryotic genome (Hsu et al.,
2014).

www.genscript.com

CRISPR aside, the most eective genome editing techniques employing

DSB-mediated repair have been zinc-nger (ZF) domains (Beerli et al., 1998) and
transcription activator-like eectors (TALEs) (Moscou and Bogdanove, 2009; Boch
et al., 2009). Both of these systems use DNA binding proteins with nuclease
activity that bind to DNA and create site-specic DSBs. While eective, both of
these methods require extensive expertise in protein engineering, which has
been a bottleneck for many research labs use of this technology (Perez-Pinera et
al., 2012).
Figure 4: CRISPR/Cas system for genome editing in mammalian cells
CMV

Human codon optimized Cas9

SV40

Target

Table 1: Key dierences between TALENs, ZFNs, and CRISPR/Cas

gRNA scaold

Cas 9

The adaptation of CRISPR for mammalian cells has revolutionized genome editing
not only for its accuracy but also for its ease of use in any lab regardless of
molecular biology expertise. Unlike ZF and TALE nucleases, CRISPR/Cas does not
require protein engineering for every gene being targeted. The CRISPR system
only requires a few simple DNA constructs to encode the gRNA and Cas9, and, if
knock-in is being performed, the donor template for HR. In addition, multiple
genes can be edited simultaneously. The table below summarizes the key
dierences and advantages between the most common DSB-mediated genome
editing technologies.

TK pA

+
U6

Advantages of CRISPR genome editing

TTTTTT

TALEN
(transcription
activator-like eector
nucleases)
Protein: DNA

Protein: DNA

Construct

Proteins containing
DNA-binding domains
that recognize specic
DNA sequences down
to the base pair

Zinc nger DNA

binding motifs in a
conguration,
the -helix
recognizes 3 bp
segments in DNA

www.genscript.com

(gRNA-Cas9): DNA

PAM

gRNA

The use of CRISPR/Cas as a gene editing tool began in 2013, with the observation
that type II CRISPR systems from S. Thermophilus and S. Pyogenes (SpCas) could
be engineered to edit mammalian genomes (Mali et al., 2013, Cong et al., 2013).
To further adapt the system for mammalian cells, a two-vector system was
optimized (Mali et al., 2013). The two major components include (1) a Cas9
endonuclease and (2) the crRNA-tracrRNA complex; when co-expressed, they
form a complex that is recruited to the target DNA sequence. The crRNA and
tracrRNA can be combined to form a chimeric guide RNA (gRNA) with the same
function to guide Cas9 to target gene sequences (Jinek et al., 2012). These
components can then be delivered to mammalian cells via transfection or
lentiviral transduction.

CRISPR/Cas

Target

Target DNA

Target Sequence

ZFN
(zinc nger
nucleases)

Design
feasibility

References

Easy:
- all-in-one
gRNA-Cas9 vector
system
- multigene editing
is feasible

Dicult:
-Need a customized protein for each gene
sequence
-Low delivery eciency

Moscou and
Bogdanove, 2009
Boch et al., 2009
Gaj et al., 2013

20nt crRNA (CRISPR

RNA) fused to a
tracrRNA and Cas9
endonuclease that
recognize specic
sequences to the
base pair

Beerli et al., 1998

Perez-Pinera et al.,
2012
Gaj et al., 2013

Mali et al., 2013

Cong et al., 2013
Jiang et al., 2015

www.genscript.com

Improving the specicity of CRISPR genome editing

Several systematic eorts have been undertaken to empirically determine the
rules governing gRNA eciency and specicity. One study looked at all possible
targetable sites tiling across 6 mouse and 3 human genes -- 1,841 sgRNAs in total
and quantied their ability to create null alleles as assayed by antibody staining
and ow cytometry. The results were used to construct a predictive model of
sgRNA activity to improve sgRNA design for gene editing and genetic screens.
(Doench et al. 2014) The gRNA design tool, which returns a score predicting the
activity of any sgRNA based on empirical rules determined by this study, is freely
available at http://www.broadinstitute.org/rnai/public/analysis-tools/sgrna-design.
Another more recent study measured sgRNA activity across ~1,400 genomic loci,
across multiple human cell types, using two Cas9 orthologs with dierent PAMs
(S. Pyogenes and S. Thermophilus), to uncover parameters that govern gRNA
eciency based not only on the nucleotide sequences but also on epigenetic status
(Chari et al., 2015). These results power an interactive web tool that can identify
putative CRISPR/Cas9 sites) and assign a predicted activity, freely available at
http://crispr.med.harvard.edu/sgRNAScorer.
Although it is rare for a 20 bp gRNA sequence to have 100% homology at multiple
sites throughout the genome, sgRNA-Cas9 complexes are tolerant of several mismatches
in their targets. Cas9 binds to many locations throughout the genome that display
several mismatches to the guide (Kusco et al., 2014), but the enzyme only creates
DSBs at a small subset of those locations. Still, DSBs have been observed at sites
containing ve or more mismatched nucleotides relative to the guide RNA sequence
(Tsai et al., 2015). Therefore, there has been a major eort to develop modied
CRISPR/Cas9 systems with improved specicity.
One strategy for improving gRNA-Cas9 targeting specicity is to require a pair of
guides that target very nearby regions. Feng Zhangs laboratory at the Broad
Institute and Keith Joungs laboratory at Harvard/MGH both developed systems
that implement this strategy in slightly dierent ways.
The Zhang lab observed that an aspartate-to-alanine (D10A) mutation in the RuvC
catalytic domain of Cas9 causes it to create single strand breaks (nicks) instead of
double strand breaks. Targeting this nickase mutant (Cas9n) to two loci within
close proximity, but occurring on opposite strands of the genomic DNA, causes
Cas9n to eectively nick rather than cleave DNA to yield single-stranded breaks.
Appropriately oset sgRNA pairs can guide Cas9n to simultaneously nick both
strands of the target locus to mediate a DSB, thus eectively increasing the specicity
of target recognition. Although each gRNA might have o-target binding sites
throughout the genome, the Cas9n would cause only single strand breaks (SSB) at
those locations; SSBs are preferentially repaired through HDR rather than NHEJ,

www.genscript.com

which can potentially decrease the frequency of unwanted indel mutations from
o-target DSBs.
Figure 5. Increasing specicity through paired guides: Nickase or RFN
Double-Nicking Cas9n D10A mutant
sgRNA 1

N-bp sgRNA offset

Cas9n

Target 2

5
3

3
5

Target 1
sgRNA 2

5 overhang

RNA-guided Fokl nuclease (RFN)

d Cas9
gRNA 1

5
3

Fok 1

Fok 1

3
5
gRNA 2

Another strategy to improve specicity has focused on the gRNA itself. Although
20 bp regions were initially used, it was observed that mismatches were tolerated
most often in the 3 end of the gRNA, and some wondered if these nal nucleotides
were necessary. Researchers in the Joung lab found that gRNAs with 17 or 18
nucleotides of complementarity functioned as eciently as (or, in some cases,
more eciently than) 20 bp sequences to introduce mutations by means of NHEJ
or HDR at on-target sites, and they showed reduced mutagenic eects at closely
matched o-target sites (Fu et al., 2014). These truncated gRNAs (tru-gRNAs) can
be used with WT SpCas9 or in combination with the RNA-Fok1 nuclease described
above (Wyvekens et al., 2015).
O-target binding of Cas9 throughout the genome has been observed to be
concentration-dependent (Wu et al., 2014) This nding spurred investigations of
whether the frequency of o-target cleavage events could be reduced by delivering
a short-lived Cas9 protein rather than plasmid that would drive expression of Cas9
for a longer period of time than was strictly necessary. A puried Cas9 protein
can be complexed to its guide RNA in vitro to form a ribonucleoprotein (RNP),
which will cleave chromosomal DNA almost immediately after delivery and then
be degraded rapidly in cells, reducing o-target eects. RNPs can be eciently
delivered to hard-to-transfect cells such as human broblasts and pluripotent stem
cells. Another advantage is that RNP delivery may be less stressful for cells than
plasmid transfection (Kim et al., 2014).

www.genscript.com

Improving gRNA & Cas9 delivery eciency

Some of the most widely-used model systems for biomedical research are primary
mammalian cell cultures or hard-to-transfect cell lines in which transfection
eciency via lipofection or electroporation can be quite low. Lentiviral vectors are
preferred for these cell types (Figure 6).
Figure 6 : Optimized Lentiviral Vectors for CRISPR genome editing in mammalian
cells

Option 1: An all-in-one vector, pLentiCRISPRv2, enables CRISPR editing in any cell type of
interest without generating stable Cas9-expressing cell line rst.
AmpR

G(N)20 gRNA
gRNA scaffold

LTR

pLentiCRISPR v2
13kb

Pu

AmpR
O

s
Ca

P2A

G(N)20 gRNA
gRNA scaffold
HIV-1 cPPT

LTR

U6 promoter

HIV-1

EF1a

HIV-1 RRE

HIV-1 RRE

pro
mo
te
r

Bleo
R

HIV-1

LTR

roR

EFS promoter

Pu

HIV-1 cPPT

pLentiGuide-Puro
8.3kb

WPR
s
Ca

i
Or

10

P2A

LT
R

E
sd
R

DYK

W PR E

LTR

pLentiCas9-Blast
12.8kb

Use smaller Cas9 orthologues from other species, such as

Staphylococcus aureus (SaCas9), which are small enough to be packaged
along with a single guide RNA expression cassette into a single AAV
vector (Ran et al., 2015)

One limitation of the rst CRISPR genome editing protocol was the constraint on
genomic sequences that could be targeted. The SpCas9 enzyme requires the
presence of the PAM sequence "NGG" at the end of the ~20-mer. Guide RNA
expression was typically driven by the U6 human pol III promoter due to its
eciency at initiating transcription, which initiates transcription from a guanosine
(G) nucleotide. Therefore, U6-driven gRNAs used with SpCas9 needed to be
selected from genomic sequences that t the pattern GN19NGG which might
occur infrequently in a gene of interest.

Option 2: A two-vector system; sequential transduction with, and selection for,

pLenti-Cas9-Blast followed by pLentiGuide-Puro, shows 10-fold higher eciency compared
to pLentiCRISPRv2.

ri

Develop a split-Cas9 system using split-inteins (Truong et al., 2015).

Expanding the applicability of CRISPR genome editing

EFS promoter

E
WPR
ro
R

DYK

U6 promoter

Bleo
R

Create transgenic animal lines that express Cas9, either constitutively or

in an inducible manner, and then to deliver only the guide RNAs and any
necessary inducer at the time of the experiment (Platt et al., 2014).

HIV-1
HIV-1 RRE
HIV-1 cPPT

LTR

ri

CRISPR/Cas9 system components can be delivered in vivo using modied viral

vectors or any number of non-viral drug delivery systems. Modied recombinant
adeno-associated virus (rAAV) particles are a preferred vehicle for in vivo gene
delivery, but the size of the SpCas9 gene (> 4 kb) exceeds the typical cargo limit
of AAV vectors. Solutions that have been developed to date include:

One strategy to expand the possibilities for CRISPR-mediated genome editing was
to drive gRNA expression from a dierent promoter. The H1 promoter can initiate
transcription from A or G; therefore, H1-driven gRNAs can also target sequences
of the form AN19NGG, which occur 15% more frequently than GN19NGG within
the human genome. This small change in the gRNA expression cassette more
than doubles the number of targetable sites within the genomes of humans and
other eukaryotes.
Another strategy has been to search for ways to relax the restriction on the PAM
sequence, as SpCas9s requirement for NGG presents a tight constraint. One
approach to this has been to use protein engineering techniques to create novel
engineered Cas mutants that recognize alternative PAM sequences (Kleinstiver et

Am p R

www.genscript.com

www.genscript.com

11

al., 2015). Through a painstaking process that used structural information,

bacterial selection-based directed evolution, and combinatorial design, researchers
developed several mutant Cas9 that could recognize alternative PAMs.
Engineered Cas9 nucleases can cleave at PAM sites consisting of NGA and NGCG,
which allows targeting 50% more sites than can be reached with the NGG PAM
alone. Additionally, there is data showing that these newly engineered Cas9s
have lower o-target activity compared to wt SpCas9.

Putting CRISPR into Practice:

Workows and Case Studies
With CRISPR genome editing, modied clonal cell lines can be derived within 23
weeks starting from the guide RNA design stage; transgenic animal strains can be
created in a single generation; and clinically relevant animal models of disease
can be rapidly created through introducing somatic mutations in vivo. To
jump-start your CRISPR experiments, the workow and references below may
help.

Regulating Cas9 expression

In order to make Cas9 active only at specic times or in specic tissues, several
research groups have engineered CRISPR/Cas9 systems that are inducible or
conditional. For example, spatial and temporal control of genome editing can be
accomplished using a photoactivatable Cas9 (paCas9) that was created by splitting
Cas9 into two fragments each fused to a photoinducible dimerization domain;
upon blue light irradiation, paCas9 dimerizes and becomes active, creating targeted
genome edits via NHEJ or HDR only while the optical stimulus is present
(Nihongaki et al., 2015).
Tissue-specic genome editing can be accomplished by using tissue-specic
promoters to drive Cas9 expression. Many mouse strains have been developed
that stably express Cre recombinase under the control of tissue-specic specic
promoters (cre-driver mice); these can easily be crossed with mice harboring a
CRE-driven Cas9 cassette to enable tissue-specic genome editing upon delivery
of guide RNA (Platt et al. 2014). Heritable tissue-specic Cas9 expression has also
been achieved in diverse species other than mice, including zebrash (Ablain et
al., 2015; Yin et al., 2015), sea squirt Ciona intestinalis (Stol et al., 2014), and
drosophila (Xue et al. 2014). Tissue-specic promoters are also useful for
constraining Cas9 activity after in vivo delivery via AAVs, which can infect many
dierent cell types (Cheng et al. 2014).

Design guide RNA and generate expression constructs

To perform CRISPR/Cas9-mediated gene editing, the rst step is to select the
nuclease you will use (e.g. WT SpCas9, Paired-nickase with Cas9D10A, etc) and
then to design, or select from a pre-existing database, the guide RNA sequences
appropriate for your nuclease.
Gene sequence analysis: It is advisable to
sequence the region of interest within the
host genome of the cell line or animal model
you are using, rather than assuming that it
will perfectly match the NCBI ref seq for your
species/strain.

GenScript oers custom gRNA

design services for any target in
any species, as well as
searchable online databases of
validated gRNAs for human and
mouse

Designing gRNA for single DSB-induced gene KO: Designing gRNAs against early
exons tends to disrupt expression, reducing the chance of having truncated forms
of the protein expressed. Alternatively, targeting a functional site can generate a
loss-of-function mutant. For genes with multiple splice variants, care should be
taken to ensure that a constitutive exon is targeted if the goal is to knock out all
splice variants.
Designing guides for paired nickase: Guide RNA for use with Cas9n should be
designed to target opposite strands of the genomic DNA with an oset of 0-20 bp
from the 5 ends of the gRNA (i.e. a 40-60bp oset between PAM sequences).
Designing constructs for knock-in: As a general rule, WT Cas9 is more ecient at
mediating homologous recombination than Cas9 nickase; although using a paired
nickase strategy can reduce the risk for o-target activity, the eciency of HDR
mediated by Cas9 nickase is highly dependent on the cell type (Ran et al., 2013).
To introduce a specic change within the genome, for example a point mutation
that will cause a specic amino acid substitution in the protein product, it is

12

www.genscript.com

www.genscript.com

13

necessary to supply a donor template that

GenScript oers custom gRNA
can be used for HDR after Cas9 creates a DSB.
constructs built from vectors
HDR templates may be delivered in plasmids
developed in Feng Zhangs
or as single-stranded oligos (ssODN). To assist
laboratory, oered through a
in detecting successful HDR and quantifying
license with the Broad Institute.
knock-in eciency, donor templates are often
designed to include several synonymous
mutations so that sequencing can easily distinguish between the donor and the
wild-type sequences. To prevent the cleavage of donor templates or of the
genomic DNA after successful HDR, the donor template should be designed with
mutations in the PAM sequence.
Making gRNA and Cas9 Constructs
Once you have designed your gRNA, you need to synthesize them and clone them
into your vector of choice. The plasmid vector you choose will depend upon your
host and delivery method (Table 2).

Deliver CRISPR reagents to target cells

CRISPR/Cas9 technology for precise genome editing has already proven successful
in many cell lines and species, including C. elegans (Friedland et al., 2013; Waaijers
et al., 2013), Xenopus tropicalis (Guo et al., 2014), plants (Jiang et al., 2013), and
even monkeys (Niu et al., 2014). Although the basic components are the same
regardless of the target organism, the delivery method varies widely, and choosing
the most appropriate vector for your host is critical for success.
In vitro genome editing:
For easy-to-transfect cell lines, plasmids encoding gRNA and Cas9 can be
delivered with high eciency via lipofection. CRISPR plasmids typically contain
selection markers such as genes conferring antibiotic resistance, or uorescent
proteins for easy visualization or FACS. For dicult-to-transfect cell lines or
primary cells, lentiviral vectors are preferred. gRNA may be delivered either via
an all-in-one plasmid that also encodes the Cas9 nuclease, or a separate plasmid
that can be delivered into cells already expressing Cas9. Alternatively, gRNA may
be introduced via a PCR-generated U6-sgRNA expression cassettes expression.
Cleavage eciency is typically lower than when gRNA is expressed from a
plasmid; however, PCR-generated cassettes may be used for rapid comparison of
sgRNA eciencies so that the most optimal sgRNA, in terms of both eciency
and specicity, can be identied before subsequent cloning into pSpCas9 (Ran et
al., 2013).

14

www.genscript.com

In vivo genome editing:

As with prior methods for creating transgenic animal strains, CRISPR/Cas9 system
components can be delivered to germ line cells to create heritable mutations;
stable, homozygous mutations at multiple loci can be achieved in a single
generation in mice (Wang et al., 2013). CRISPR genome editing can also be used
to generate precise mutations in somatic tissues of adult animals, and to modify
multiple genes at once in the same cells (Cong et al., 2013, Mali et al., 2013). This
is especially valuable for creating clinically relevant in vivo cancer models,
because human tumors often contain a combination of gain-of-function
mutations in oncogenes and loss-of-function mutations in tumor suppressor
genes (Platt et al., 2015).
In addition, CRISPR can be used to generate chromosomal rearrangements seen
in human cancers, such as the EML4-ALK inversion observed in human non-small
cell lung cancer. Viral-mediated delivery of CRISPR/Cas9 system to somatic cells in
the lung of adult mice yielded a new clinically faithful mouse model of Eml4-Alk
human lung cancer and presents a new paradigm for accurately modeling human
cancers in mice (Maddalo et al., 2014).
Table 2: gRNA & Cas9 Delivery Methods used for dierent hosts
Host

Delivery Method

Reference

Mammalian cells

- Lipofection-based transfection of
DNA plasmids
- Electroporation of DNA plasmids or
RNP
- Lentiviral transduction of DNA
plasmids

Cong et al., 2013,

Mali et al., 2013
Schumann et al.,
2015
Shalem et al., 2014

Microbial
organisms

- Transformation of plasmids into

competent cells

Jiang et al., 2015

Pyne et al., 2015

Plants

- Agrobacterium mediated
transformation of sgRNA and Cas9
vector

Gao et al., 2014,

Zhou et al., 2014

Mouse:
heritable mutations

- Direct injection into embryos

- Electroporation into zygotes

Wang et al., 2014

Qin et al., 2015

Mouse:
mutations to
adult somatic tissue

Direct injection of AAV into tissue

- of interest

Cheng et al., 2014

Maddalo et al., 2014

Yeast

- Electroporation of plasmids and

galactose induction of Cas9

DiCarlo et al., 2013

www.genscript.com

15

Figure 7: Knock-out targeting strategy for K-Ras

K-ras locus

Exon1

16

www.genscript.com

Exon3

Exon4

Exon5

Exon6

Exon7

Exon8

gRNA and Cas9 complex

K-ras exon 4 is targeted for

double stranded DNA break
(DSB)

K-ras knock-out

How to ensure that o-target Cas9 activity wont confound your experiments:

DSB initiates non-homologous

end joining (NHEJ)
Indel on Exon 4

Primers for
sequencing

gRNA and Cas9 complex

Figure 8: Sanger sequencing (A) and western blot (B) results for HCT116 KRAS
-/B

HCT116

Kra
s-

/-

16

For each guide RNA you use, isolate multiple, independent clonal cell
populations or founder individuals. The likelihood o-target DSBs occur in the
same place in independent clones is very low.
Use at least two independent gRNA sequences in parallel to derive distinct
clones or founder individuals. Models created through genome editing with
distinct guideRNA that share an on-target locus but do not share o-target loci
are an excellent way to create independent replicates.
Although few labs have the resources to do statistically powerful whole genome
sequencing verication protocols such as gUIDEseq, it is relatively easy to select
the few predicted o-target sequences for each gRNA you use and then sequence
around those loci to ensure that o-target indels have not been introduced.
If you use most or all of these tips in combination, you can have condence that your
experiments will reveal true genotype/phenotype relationships.

Exon2

T1

Whole genome sequencing is often not practical for low frequency events. In
addition, targeted sequencing only of computationally predicted o-target sites
introduces a strong observational bias. Therefore, researchers in Keith Joungs lab
developed a technique called Genome-wide Unbiased Identication of DSBs
Enabled by sequencing (GUIDE-seq) to better quantify o-target activity of Cas9
throughout the genome (Tsai et al., 2015). GUIDE-seq introduces a tag any time a
DSB occurs, and then sequences around the tags to determine all o-target
cleavage locations. They found surprising results, including that the majority of
cleavage sites identied by GUIDE-seq were not of GUIDE-seq OT sites were not
predicted by any algorithm, because they contain up to 6 mismatched nucleotides
and in many cases include non-canonical PAMs.

To knock-out the K-Ras locus, gRNA and Cas9 vectors were encapsulated into a
virus. In this case, exon 4 was targeted by the gRNA-Cas9 complex to generate a
DSB. In the absence of donor DNA, the DSB was repaired by NHEJ to create an
indel. Sanger sequencing (Figure 8A) and a western blot (Figure 8B) were used to
conrm successful knock-out of the KRAS gene.

16

To determine o-target eects, you may sequence around regions that are
predicted to be likely sites for o-target cleavage based on sequence similarity to
the on-target site, particularly in the seed region. A more rigorous measure of
o-target cleavage can be performed using whole-genome sequencing.

Using GenScripts GenCRISPRTM

cell line services, any gene can
be targeted in any mammalian
cell. All clones are target
sequence validated and a
detailed report on clone
generation is provided.

HC

In some cases, such as in populations of primary cells, you may simply want to
show that you achieved high KO or KI eciency, without isolating clones for
conrmation. Genome editing eciency is typically determined via Surveyor assay
(T7E1 assay) or assayed with next-generation sequencing (NGS). Many unique
insertions and deletions will likely be observed.

The KRAS gene encodes for a protein called

K-Ras, which is an important regulator of cell
division. This gene, when mutated, can
cause cells to become cancerous. In this case
study, the K-Ras locus was knocked-out in the
human colon cancer cell line, HCT116 (Figure
7).

T1

To identify successful cases of CRISPR-mediated KO, the target site should be

sequence to conrm a frame-shift mutation has occurred. You should also
conrm that the mRNA and protein are signicantly depleted or absent, such as
by qPCR and Western blot on genome-edited samples versus unedited (parental)
controls.

Case Study 1: Generating K-Ras knock-out cell lines using

CRISPR genome editing

HC

Check for intended KO / KI and o-target eects

K-ras
HCT116 KRAS -/-

beta actin

www.genscript.com

17

Case Study 2: Using CRISPR to generate GLP-1R knock-in cell

lines
Glucagon-like peptide 1 receptor (GLP-1R) is expressed in pancreatic cells and
when stimulated increases insulin synthesis and release (Drucker et al., 1987).
Consequently, it is a common target for the development of therapeutics for
diabetes. In this study, a knock-in cell line was generated using GLP-1R donor DNA
(containing the gene of interest and a puromycin selectable marker) and HEK 293T
cells. The AAVS1 locus was targeted as the knock-in region (Figure 9). The cells
were co-transfected with the donor DNA, Cas9 and gRNA, and positive clones
were selected from the cell pools by Sanger sequencing and PCR.
Figure 9: Integration of GLP-1R into HEK 293T cells
gRNA and Cas9 complex

AAVS1 locus

DNA break stimulates

homologous recombination
Donor Vector

Homologous

Gene edited
locus

Puro

GLP-1R

Homologous

Integration of donor into

AAVS1locus

Case Study 3: Microbial Genome Editing

Microbial genome editing has many
GenScripts Microbial Genome
applications in both pharma and industry
Editing service uses Red
from studying gene function to the
CRISPR/Cas editing technology.
production of recombinant proteins for drug
This technique is the most
discovery and development. CRISPR/Cas can
precise, ecient, and cost
also be used to generate knock-in and
eective recombineering
knock-outs in microbes, such as E. coli. Since
method on the market!
HR frequency is generally lower in microbes
than mammalian cells, CRISPR/Cas can be
combined with other recombination techniques to improve gene editing
eciency (Jiang et al., 2015). In this example, Red recombineering, one of the
most eective recombination techniques in bacteria, is combined with
CRISPR/Cas for ecient, seamless genome editing in E. coli.
In this case study, Red CRISPR/Cas is used to knock-out cadA in the BL21 E. coli
strain. The CasA protein is a component of lysine decarboxylase, an enzyme that
helps bacteria survive in acidic environments (Lee et al., 2007). After the reaction,
Sanger sequencing and colony PCR screening was used to conrm knock-out was
successful (Figure 11).
Figure 11: Seamless knock-out of cadA in BL21 E. coli

Puro-GLP-1R

Sanger sequencing of BL21 cadA

Primers for
sequencing

Figure 10: Immunocytochemistry (left) and western blot (right) analysis of

GLP-1R clones
Negative Control GLP-1R clone

Anti-GLP-1R

Phase contrast

Cell line: NC GLP-1R clone

80 kD
60 kD
50 kD
40 kD

GLP-1R

www.genscript.com

Seq primer R

cadA

30 kD
20 kD

After 2 weeks of maintenance under puromycin selection, surviving cells were

isolated and PCR analyzed for the Puro-GFP insert, which indicated GLP-1R was
successfully inserted into the AAVS1 locus. Along with the Sanger sequencing
results, immunocytochemistry and western blot analysis conrmed that the
transfection was successful (Figure 10).

18

Seq primer F

1 2 3 4 5 6 7 8 M 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24

(bp)
3000
2000
1500
1000
750
500
250
100

KO strain

www.genscript.com

19

CRISPR genome editing powers novel ndings across

disciplines
CRISPR/Cas genome editing has been used to accelerate research in many
dierent arenas of basic life science and biomedical research.
Table 3: Research applications for CRISPR/Cas9 genome editing

Neuroscience

Cancer
Biology

CRISPR/Cas identies novel tumor suppressor genes and new

animal models for brain tumors. Mutations to tumor suppressor
genes are often causes for cancer progression, and developing animal
models for these transformations is a very time-intensive. To address
this, Zimermann et al (2015), used CRISPR/Cas to somatically induce
loss-of-function (LOF) mutations in genes in the Sonic Hedgehog (Shh)
signaling pathway: in previous studies, the authors found that SHH
regulates proliferation of neural cells in the brain that can lead to
malignant brain tumors. The results of this study conrmed that
CRISPR/Cas could successfully induce these LOF mutations for the
development of new, relevant brain tumor models.

Vaccines/
Virology

T cell engineering with CRISPR/Cas reveals a new therapeutic

strategy for HIV. While successful T cell editing has historically
been challenging, Schumann et al (2015) reported that the
CRISPR/Cas editing tool can be used to successfully knock-out
CXCR4, a co-receptor that HIV uses to infect cells. Using this
technology, the authors reported that approximately 40% of CD4+
T-cells are CXCR4- following transfection with Cas9: gRNA
ribonucleases.

Plant Biology

Immunology

20

A novel rat model for muscular dystrophy reveals new treatment

targets. Muscular Dystrophy is a condition associated with a loss of
the protein Dystrophin, which is deadly when it aects the cardiac
muscle. The lack of appropriate animal modes has made therapeutic
discovery challenging; however, in a recent study by Nakamura et al
(2014), CRISPR/Cas was used to knock-out the Dystrophin gene (Dmd)
in rats. These mutations were heritable, thus presenting a new animal
model to study new therapeutic targets for muscular dystrophy.

Successful adaptation of the CRISPR/Cas editing system in rice.

Targeted mutagenesis has many implications for developing new
traits in plants; however, mutation frequencies have varied
signicantly between species and delivery in plants can be
particularly dicult. In an eort to optimize the process in rice,
Mikami et al (2015) tested the eciency of multiple gRNA and Cas9
vectors in rice calli. From this study they identied two Cas9 vectors,
MMCas9 and FFCas9, as being the most eective for rice plants.
Knock-out nasal airway epithelial cells reveal a new
pro-inammatory function of the MUC18 gene. Genome editing in
primary cell lines has been a persistent challenge; however, Chu et
al (2015) demonstrated that CRISPR/Cas could be used to knockout
Muc18, a gene known to promote tumor metastasis, to better
understand its function. In this study, the group showed that MUC18
KO has a pro-inammatory role in the airway epithelium following
exposure to viral and bacterial stimuli.

www.genscript.com

Expanding the Research Applications for CRISPR

CRISPR/Cas9 technology has been adapted for many research applications other
than genome editing, such as:

in situ functional assays in mouse tumor models (Malina et al., 2013),

targeting functional long noncoding RNAs (lncRNA) or ribonucleoprotein

(RNP) complexes to specic genomic loci (Shechner et al., 2015)

Studying genome architecture and long-distance gene-enhancer

interactions by disrupting megabase-scale topological chromatin
domains (Lupiez et al., 2015)

Genome-wide screens using CRISPR libraries

In addition to targeting a single gene or a
few specic genes at a time, CRISPR has
been adapted for genome-wide screening to
discover genes whose inhibition or aberrant
activation can drive phenotypes implicated
in disease, development, or other biological
processes.

GenScript oers amplied, NGS

validated GeCKO and SAM
libraries to accelerate your
genome-wide screening eorts.

Genome-scale CRISPR knock-out libraries (GeCKO v2) libraries for mouse and
human genomes enable rapid screening for loss-of-function mutations, as described
by Sanjana et al (2014). GeCKO libraries are a mixed pool of CRISPR guide RNAs
that target every gene and miRNA in the genome. Each gRNA is cloned into a
lentiviral vector optimized to produce high-titer virus for ecient lentiviral transduction
of primary cells or cultured cell lines. Either a single-vector or dual-vector system may
be used (see Figure 6 on page 11). A cell population should be transduced with
the GeCKO library pool at a low MOI ensuring no more than one gRNA enters any
given cell. After transduction, deep sequencing with NGS should be performed to
assess gRNA representation in the cell pool before beginning a screening protocol.
At the end of the screen, after a second round of NGS, data analysis should be
performed to identify the guides that were lost or enriched over the course of the
screen. In order to identify true positive hits from a GeCKO library screen, you
should identify genes for which multiple guides were enriched. A detailed GeCKO
screening protocol may be found on the Genome Engineering website.
GeCKO libraries were designed to contain 6 single guide RNA (sgRNA) molecules
targeting each gene within the human or mouse genome, as well as 4 sgRNA
targeting each miRNA, and 1000 control (non-targeting) sgRNAs. The gRNA
sequences are distributed over three or four constitutively expressed exons for
each gene and were selected to minimize o-target genome modication.
www.genscript.com

21

Each library was divided into two sublibraries, A and B, containing 3 unique sgRNA
for each gene; only library A contains 4 sgRNA targeting each of 1,864 miRNAs;
both A and B contain the same 1,000 nontargeting control sgRNAs. The use of a
single sublibrary maintains comprehensive genome-scale coverage but reduces
the number of cells required to perform a screen, which is useful when cell
numbers are limiting (for example, with primary cells or in vivo screens);
alternatively, larger screens can be performed by combining both sublibraries.
The GeCKO library can be used in place of RNAi libraries for loss-of-function
screening for any phenotype of interest, for example, to identify genes whose
loss of function enables drug resistance in cancer cells (see box on page 23). As a
complimentary approach, a CRISPR-based gene activation library can be used in
place of a cDNA overexpression library for gain-of-function screening, as
described below.

Adapting CRISPR for Transcriptional Regulation

Several research groups have harnessed the specicity and easy re-programmability
of the CRISPR/Cas9 system to create programmable transcription factors that can
activate or repress transcription of any desired coding region within a genome
(Gilbert et al., 2013; Bikard et al., 2013; Cheng et al., 2013; Perez-Pinera et al., 2013).
These systems use a nucleolytically inactive Cas9 protein (typically denoted as
dead or dCas9) in order to target the Cas9-gRNA complex to the right position
in the genome without cleaving or altering genomic DNA. They fuse the Cas9 to a
well-characterized transcription-regulating domain, and then design guide RNA to
direct the complex to just upstream of the transcription start site. Several light-inducible
CRISPR-based transcription factors have been designed to allow precise spatial and
temporal control of endogenous gene activation
(Polstein et al., 2015; Nihongaki et al., 2015).
MS2 RNA aptmers
dCas9
One CRISPR-based transcriptional activator that
sgRNA
has been used not only to target single genes
VP64
but also for genome-wide gain-of-function
screening is the CRISPR/Cas9 Synergistic
MS2
Activation Mediator (SAM) system developed in
p65
HSF1
the laboratory of Feng Zhang at the Broad
Institute. SAM enables robust transcriptional
activation of endogenous genes targeted by
guide RNA that binds within 200 bp upstream of
the transcription start site. SAM can be used to
activate transcription of a single gene or up to 10
assembled SAM complex

22

www.genscript.com

genes at once in the same cell. They can also be used to interrogate the function of
long intergenic non-coding RNA (lincRNA) transcripts in addition to genes. Stable
expression of SAM components via lentiviral transduction generates cell lines show
stable and robust transcriptional activation, even of genes that are normally
transcriptionally silent. These cell lines can be ideal research tools to characterize the
function of specic candidate genes or groups of genes.
SAM can also be used for discovery research to identify the genes that drive phenotypes
of interest in any disease model or developmental/dierentiation process by using a
genome-wide SAM gRNA library for gain-of-function screening (Konermann et al.,
2015). The screening process is similar to the GeCKO library screening experimental
protocol described above, but the library is designed to activate transcription rather
than edit the genome. The human genome-wide SAM library contains 3 guide RNA
targeting within 200 bp upstream of each of 23,430 coding gene isoform with a
unique transcription start site in the human reference genome, for a total of 70,290
guides. This mixed pool of SAM guide RNAs is delivered along with the other SAM
components using lentiviral vectors.

CRISPR libraries yield insights into Cancer Biology

An oncogenic mutation observed in melanoma cells, BRAF(V600E), makes
cells susceptible to therapeutic treatment with BRAF inhibitors. However,
some melanoma cells are able to develop resistance to these drugs over
time. Genome-wide CRISPR libraries were used to identify genes whose upor down-regulation within melanoma cells could confer resistance to BRAF
inhibiting drugs (Shalem et al., 2014; Konermann et al., 2015)
Both GeCKO and SAM libraries were used to screen A375 (BRAF(V600E))
melanoma cells, by transducing a cell pool with the library and performing
NGS to quantify sgRNA representation before and after a 14-day drug
treatment. After treatment, most gRNA were substantially reduced, while a
small set were highly enriched. The gene expression signature based on the
top screening hits correlated with markers of BRAF inhibitor resistance in
cell lines and patient-derived samples, enhancing condence in the clinical
relevance of these results. Genes for which several unique gRNA were
enriched were considered top hits; these included genes previously known
to confer resistance, such as EGFR and other genes in the ERK pathway, as
well as numerous novel candidate genes, which can be subsequently
validated using individual sgRNA and cDNA overexpression.

www.genscript.com

23

Epigenetic Modications

Stem Cell Dierentiation

Epigenetic modications to genomic DNA and to the histone proteins that help
organize chromosomes are increasingly shown to play critical roles in biological
processes. Epigenetic marks such as methylation or acetylation at specic
genomic loci or histone residues can be inherited or acquired, and can inuence
gene expression. The enzymes that regulate epigenetic state can be targeted via
CRISPR genome editing or order to generate genomewide perturbations in
epigenetic state. This was seen, for example, after CRISPR-mediated KO of all
three active DNA methyltransferases (DNMTs), individually or in combination, in
human embryonic stem cells (ESCs), allowing researchers to characterize viable,
pluripotent cell lines with distinct eects on the DNA methylation landscape (Liao
et al., 2015).

CRISPR technology can be used to guide stem cell dierentiation for both basic
research and therapeutics. Stem cell dierentiation typically requires the robust
activation of specic genes typically transcription factors that control broad
programs of downstream target gene expression in specic combinations and
sequences, over the course of several weeks or months. A catalytically inactive
Cas9 nuclease that is fused to transactivation domains can be used as a
programmable transcription activator to activate genes required for dierentiation.
For example, targeted activation of the endogenous Myod1 gene locus has been
shown to yield stable and sustained reprogramming of mouse embryonic
broblasts into skeletal myocytes (Chakraborty et al., 2014) for the repair of
skeletal muscle tissue.

Researchers increasingly need methods for introducing epigenetic modications

only at desired genomic loci in order to model diseases and test hypotheses
regarding potential therapeutic strategies. For example, specic epigenetic
alterations are often necessary or sucient to drive transformation of normal
cells into cancerous cells, and play roles in later steps of carcinogenesis;
therefore, the enzymes that regulate epigenetic modications to DNA or histone
proteins are candidate targets for cancer therapy (reviewed by Yao et al., 2015).

Induced pluripotent stem cells (iPSCs) have also become popular choices for stem
cell therapy since they can be derived from patient-specic cells, overcoming
ethical issues associated with embryonic stem cells. Similar to embryonic stem
cells, iPSCs must be pre-dierentiated prior to implantation to avoid teratoma
formation; however, dierentiation eciency continues to be a bottleneck.
Recent reports indicate that CRISPR may be an essential tool to improve
dierentiation, and has been used to derive a variety of cell types including
muscle cells for the treatment of muscular dystrophy (Loperdo et al., 2015) and
hematopoietic stem cells for the treatment of sickle cell anemia (Song et al.,
2015). Recently, there have been multiple studies investigating the use of CRISPR
to correct deleterious mutations associated with genetic diseases. For instance,
the inherited blood disease -Thalassemia is caused by deletions to the -globin
(HBB) gene, and by generating iPSCs with this mutation corrected could be a
potential treatment option (Xu et al., 2015). Together these results demonstrate
that CRISPR/Cas can improve the eciency of not only gene targeting, but also
directed dierentiation.

CRISPR technology allows a catalytically inactive Cas9 to serve as a precisely

targeted DNA-binding domain; when fused to epigenetic enzymes such as DNA
methylases, histone acetyltransferases or deacetylases (HATs or HDACs), the
complex can alter the epigenetic state in a precise way at a single precise
location, or at several specic locations simultaneously. For example, a
CRISPR-Cas9-based acetyltransferase consisting of dCas9 fused to the catalytic
core of the human acetyltransferase p300 was shown to acetylate histone H3
lysine 27 specically at its target sites and to robustly activate transcription of
target genes (Hilton et al., 2015).
Similar to the capabilities of the SAM complex for transcription activation, Cas9
epigenetic eectors (epiCas9s) could also be used for genome-wide screening to
discover novel relationships between DNA methylation or chromatin states and
phenotypes such as cellular dierentiation or disease progression (Hsu et al.,
2014).

24

www.genscript.com

Therapeutics
Both well-established pharmaceutical companies and new start-up biotech
companies are racing to create CRISPR-based therapeutics. Compared to other
strategies for gene therapy, CRISPR genome editing is thought to be faster, less
expensive, and potentially far safer. CRISPR-based therapeutics are already in
development for treating blood cancers by modifying patients T cells; eliminating
disease-causing viruses in patients; and correcting single nucleotide mutations
that cause many inherited diseases such as sickle-cell anemia.

www.genscript.com

25

CRISPR genome editing is especially promising for diseases that can be tackled by
modifying cells that can easily be removed from a patient, genome-edited,
screened to ensure no o-target genome modications, and then infused back
into the same patient. Autologous cell therapies that use genome editing to
correct a mutation in the patients own cells could be far safer than current
therapies that use transplants from healthy donors. For example, combining
CRISPR-mediated genome engineering with autologous T-cell therapies holds
great promise for many diseases including cancer, HIV, primary immune
deciencies, and autoimmune diseases. It has already been demonstrated that
primary human CD4+ T cells can be genome-edited with high eciency and
specicity using Cas9 protein in complex with guide RNA (Cas9 RNPs) (Schumann
et al., 2015). Fusing GFP to Cas9 allows FACS-based enrichment of transfected
T-cells (Meissner et al., 2014), and other improvements to CRISPR-based T-cell
therapy protocols are doubtless underway. While there are many examples of in
vitro or animal studies in which CRISPR-mediated gene knockout corrects a
disease phenotype, signicant challenges nonetheless remain to translate these
into safe, ecacious therapies for human patients.
In order to address safety concerns prior to bringing CRISPR technology in to the
clinic, a great deal of attention has already been paid to developing nonviral
vectors such as lipid- or polymer-based nanocarriers, and several are already in
clinical trials (Li et al., 2015). Non-viral CRISPR-mediated gene therapy may bypass
some of the risks of prior viral-based gene therapy strategies, including the risk
that a viral vector might recombine in vivo and become replication-competent; the
risk that randomly integrating viruses will induce insertional mutagenesis, inaccurate
gene dosage; the risk that genetic modications could be made at unintended
genomic loci or in unintended tissues; or the chance that the gene therapy will
simply be ineective due to immune responses directed against the viral vector.
However, even non-viral Cas9 delivery may not completely avoid unwanted immune
responses; a study delivering SpCas9 in vivo in mouse liver detected Cas9-specic
humoral immune responses, highlighting the need for caution in future translational
studies, and reinforcing the idea that ex vivo genome modication of autologous
cells may be a safer route than in vivo delivery of Cas9 (Wang et al., 2015).

26

www.genscript.com

Table 4: Lead Prospects for CRISPR-based Therapeutics

Cancer

CRISPR-mediated knockout of NANOG and NANOGP8 decreases

the in vivo tumorigenic potential of DU145 prostate cancer cell
lines as well as in vitro phenotypes associated with malignancy
such as sphere formation, anchorage-independent growth,
migration capability, and drug resistance, suggesting that
CRISPR-mediated gene knockout may be a viable addition to the
therapeutic arsenal for prostate cancer patients (Kawamura et al.,
2015).

Cardiovascular
Disease

CRISPR/Cas9-mediated gene therapies could be used to correct

inherited or acquired mutations that underlie cardiac disease, or
to introduce therapeutic genes such as SERCA2a, S100A1, and
adenylate cyclase 6 (Rincon et al., 2015)

HIV

HIV has been eectively eliminated in some patients via gene

therapy to delete CCR5, which could be accomplished more
eciently in the future using CRISPR technology. In addition,
CRISPR could be used in stem cell-based gene therapies to treat
chronic HIV infection; hematopoietic stem/progenitor cells have
been engineered to express a chimeric antigen receptor (CAR), so
that they dierentiate into functional cytotoxic T lymphocytes and
natural killer cells that are resistant to HIV infection and suppress
HIV replication (Zhen et al., 2015).

Viral Diseases

CRISPR genome editing may be used to prevent, control, or cure

viral diseases by targeting viral genes essential for replication or
virulence. For example, persistent infection with HPV strains that
cause genital warts, which have a high rate of recurrence after
treatment, could be tackled through CRISPR-mediated inactivation
of viral E 7 gene, as has already been demonstrated in transformed
keratinocytes in vitro (Liu et al. 2015). CRISPR could also be used
to target human genes that could enhance host immune
responses against the virus.

Immunodeciences

Immunodeciencies such as SCID are typically treated by

allogeneic hematopoietic stem cell (HSC) transplantation, which
carry a signicant risk of incompatibility between donor and
patient (Ott de Bruin et al., 2015).

Genetic
Diseases

CRISPR genome editing could enable treatments for a number of

genetic diseases, such as Chronic granulomatous disease (CGD)
(Flynn et al., 2015) and replacing dysfunctional proteins in
photoreceptor cells to restore sight in patients with a genetic
retinal disease.

www.genscript.com

27

Future of CRISPR

References

CRISPR/Cas has revolutionized genome editing for its ease of use and broad
applicability to mammalian cells, microbes, and animal models. Not only does
CRISPR have the potential to enhance our ability to analyze and understand gene
function, but this new tool can also reform the medical industry. Accessible
genome editing techniques can be used to correct genetic mutations that are
responsible for inherited disorders or diseases, and also for large-scale production
and screening of new drugs (Doudna et al., 2014). In addition, the ability of
CRISPR/Cas to both activate and repress gene function in both coding and
non-coding regions of the genome expands its potential even further.

The references cited in this handbook are not intended to be exhaustive.

We apologize for omitting, due to space constraints, many important
contributions from other researchers.

Considering how recently the CRISPR system has been applied to mammalian and
microbial gene editing, there is still room for improvement. As the mechanism
for how Cas9 binds to DNA is revealed, more eective Cas9-gRNA constructs can
be designed (Sternberg and Doudna, 2015). Along the same vein, delivery of
Cas9 into mammalian cells continues to be a bottleneck for some cell types.
Designing smaller Cas9 variants that can be transfected into cells more easily will
expand its applications and uses.
Regardless of these improvements, the signicant role that CRISPR/Cas plays in
the biological sciences is apparent. CRISPR/Cas gene editing remains the easiest
and most exciting technology in genome engineering. There is no doubt that this
is just the beginning of a revolutionary technology that can be used by generations
of scientists to come.

Ablain J et al. A CRISPR/Cas9 vector

system for tissue-specic gene disruption
in zebrash. Dev Cell. 2015 Mar
23;32(6):756.
Bolotin A et al. Clustered regularly spaced
short palindromic repeats (CRISPRs) have
spacers of extrachromosomal origin.
Microbiology. 2005; 151: 2551.
Brouns et al. Small CRISPR RNAs guide
antiviral defense in prokaryotes. Science.
2008; 321 (5891): 960.
Capecchi M. Altering the genome by
homologous recombination. Science.
1989: 244; 1288.
Chakraborty S et al. A CRISPR/Cas9-based
system for reprogramming cell lineage
specication. Stem Cell Rep. 2014 Dec
9;3(6):940.
Chari R et al. Unraveling CRISPR-Cas9
genome engineering parameters via a
library-on-library approach. Nat Methods.
2015 Jul 13.

Want to keep up with advances in CRISPR technology?

Visit www.genscript.com/crispr.html to learn
about the most recent CRISPR-based tools
and research ndings

28

www.genscript.com

Chu VT et al. Increasing the eciency of

homology-directed repair for
CRISPR-Cas9-induced precise gene editing
in mammalian cells. Nat Biotechnol. 2015
May;33(5):543.
Cong L et al. Multiplex genome
engineering using CRISPR/Cas systems.
Science. 2013; 339: 819.
Deveau H et al. Phage response to
CRISPR-encoded resistance in
Streptococcus thermophilus. J. Bacteriol.
2008: 190; 1390.
DiCarlo J. et al. Genome engineering in
Saccharomyces cerevisiae using
CRISPR-Cas systems. Nucleic Acids Res.
2013 Apr;41(7):4336-43.
Doench JG et al. Rational design of highly
active sgRNAs for CRISPR-Cas9-mediated
gene inactivation. Nat Biotechnol. 2014
Dec;32(12):1262.
Drucker DJ et al. Glucagon-like peptide 1
stimulates insulin gene expression and
increases cyclic AMP levels in a rat islet
cell line. PNAS. 1987; 84 (10): 3434.

Choulika A et al. Introduction of homologous

recombination in mammalian
chromosomes by using the I-SceI system
of Saccharomyces cerevisiae. Mol. Cell.
Biol. 1995; 15: 1968.

Friedland AE. et al. Heritable genome

editing in C. elegans via a CRISPR-Cas9
system. Nat Methods. 2013 Aug;10(8):741.

Cheng R et al. Ecient gene editing in

adult mouse livers via adenoviral delivery
of CRISPR/Cas9. FEBS Lett. 2014 Nov
3;588(21):3954.

Fu Y et al. Targeted genome editing in

human cells using CRISPR/Cas nucleases
and truncated guide RNAs. Methods
Enzymol. 2014;546:21.

Chu HW et al. CRISPR-Cas9-mediated

gene knockout in primary human airway
epithelial cells reveals a proinammatory
role for MUC18. Gene ther. June 2015.

Gao J et al. CRISPR/Cas9-mediated

targeted mutagenesis in Nicotiana
tabacum. Plant Mol Biol. 2015 Jan;
87(1-2): 99.

www.genscript.com

29

Guilinger JP et al. Fusion of catalytically

inactive Cas9 to FokI nuclease improves
the specicity of genome modication.
Nat Biotechnol. 2014;32(6):577.
Guo X et al. Ecient RNA/Cas9-mediated
genome editing in Xenopus tropicalis.
Development. 2014 Feb;141(3):707.
Hermann M et al. Binary recombinase
systems for high-resolution conditional
mutagenesis. Nucleic Acids Res. 2014
Apr;42(6):3894.
Hilton IB et al. Epigenome editing by a
CRISPR-Cas9-based acetyltransferase
activates genes from promoters and
enhancers. Nat Biotechnol. 2015
May;33(5):510.
Horvath P and Barrangou R. CRISPR/Cas,
the immune system of bacteria and
archaea. Science. 2010; 327: 167.
Horvath P et al. Diversity, activity, and
evolution of CRISPR loci in Streptococcus
thermophilus. J. Bacteriol. 2008: 190:
1401.
Hsu PD et al. DNA targeting specicity of
RNA-guided Cas9 nucleases. Nat
Biotechnol. 2013; 31: 827.
Hsu PD et al. Development and
Applications of CRISPR-Cas9 for Genome
Engineering. Cell. 2014 Jun 157:1262.
Ishino Y et al. Nucleotide sequence of the
iap gene, responsible for alkaline
phosphatase isozyme conversion in
Escherichia coli and identication of the
gene product. J Bacteriol. 1987: 169; 5429.
Jansen R et al. Identication of genes that
are associated with DNA repeats in
prokaryotes. Mol. Microbiol. 2002; 43:
1565.
Jiang W et al. Demonstration of
CRISPR/Cas9/sgRNA-mediated targeted
gene modication in Arabidopsis,
tobacco, sorghum and rice. Nucleic Acids

30

www.genscript.com

Res. 2013 Nov 1;41(20):e188.

Jiang Y et al. Multigene editing in the
Escherichia coli genome via the
CRISPR/Cas system. Appl. Environ. Microb.
2015; 81(7): 2506.
Jinek M. et al. A programmable
dual-RNA-guided DNA nuclease in
adaptive bacterial immunity. Science.
2012 337:816.
Kearns NA et al. Cas9 eector-mediated
regulation of transcription and
dierentiation in human pluripotent stem
cells. Development. 2014 Jan;141(1):219.
Kim S et al. Highly ecient RNA-guided
genome editing in human cells via
delivery of puried Cas9 ribonucleoproteins.
Genome Res. 2014 Jun;24(6):1012.
Konermann S et al. Genome-scale
transcriptional activation by an
engineered CRISPR-Cas9 complex. Nature.
2015 Jan 29;517(7536):583.
Korge S et al. Highly Ecient Genome
Editing via CRISPR/Cas9 to Create Clock
Gene Knockout Cells. J Biol Rhythms. 2015
Aug 4.
Kuscu C et al. Genome-wide analysis
reveals characteristics of o-target sites
bound by the Cas9 endonuclease. Nat
Biotechnol. 2014 Jul; 32(7):677.
Lee YH et al. CadC has a global
translational eect during acid adaptation
in Salmonella enterica Serovar
Typhimurium. J Bacteriol. 2007; 189(6): 2417.
Liao J et al. Targeted disruption of
DNMT1, DNMT3A and DNMT3B in human
embryonic stem cells. Nat Genet. 2015
May;47(5):469.
Liu YC et al. Reprogrammed CRISPR-Cas9
targeting the conserved regions of
HPV6/11 E7 genes inhibits proliferation
and induces apoptosis in E7-transformed
keratinocytes. Asian J Androl. 2015 Jul 31.

Lupiez DG et al. Disruptions of

topological chromatin domains cause
pathogenic rewiring of gene-enhancer
interactions. Cell. 2015 May 21; 161(5):
1012.
Maddalo D et al. In vivo engineering of
oncogenic chromosomal rearrangements
with the CRISPR/Cas9 system. Nature.
2014 Dec; 516(7531): 423.
Mali P et al. RNA-guided human genome
engineering via Cas9. Science. 2013; 339:
823.
Mali P et al. Cas 9 as a versatile tool for
engineering biology. Nat. Methods. 2013
Oct; 10(10): 957.
Malina A et al. Repurposing CRISPR/Cas9
for in situ functional assays. Genes Dev.
2013 Dec; 27 (23); 2602.
Maruyama T et al. Increasing the
eciency of precise genome editing with
CRISPR-Cas9 by inhibition of
nonhomologous end joining. Nat
Biotechnol. 2015 May; 33(5): 538.
Mikami M et al. Comparison of
crispr/cas9 expression constructs for
ecient targeted mutagenesis in rice.
Plant mol bio. 2015: 88(6); 561.
Mojica F et al. Intervening sequences of
regularly spaced prokaryotic repeats
derive from foreign genomic elements. J.
Mol. Evol. 2005; 60: 174.
Moscou M and Bogdanove A. A simple
cipher governs DNA recognition by TAL
eectors. Science. 2009: 326; 1501.
Nakamura K et al. Generation of muscular
dystrophy model rats with a crispr/cas
system. Sci Rep. 2014 Jul; 4: 5635.
Niu Y. et al. Generation of Gene-Modied
Cynomolgus Monkey via
Cas9/RNA-Mediated Gene Targeting in
One-Cell Embryos. Cell. 2014 Feb
13;156(4):836.

Orban PC et al. Tissue- and site-specic

DNA recombination in transgenic mice.
PNAS. 1992; 89(15): 6861.
Ott de Bruin LM et al. Novel
Genome-Editing Tools to Model and
Correct Primary Immunodeciencies.
Front Immunol. 2015 May; 6:250.
Perez-Pinera P et al. RNA-guided gene
activation by CRISPR-Cas9-based
transcription factors. Nat Methods. 2013
Oct; 10:973.
Pyne M et al. Coupling the CRISPR/Cas9
system with lambda red recombineering
enables simplied chromosomal gene
replacement in Escherichia coli. Appl Envir
Microbiol. 2015; 81(15): 5103.
Qin W et al. Ecient
CRISPR/Cas9-Mediated Genome Editing
in Mice by Zygote Electroporation of
Nuclease. Genetics. 2015 Jun; 200(2): 423.
Ranganathan V et al. Expansion of the
CRISPRCas9 genome targeting space
through the use of H1
promoter-expressed guide RNAs. Nat
Commun. 2014 Aug 8; 5: 4516.
Rincon MY et al. Gene therapy FOR
cardiovascular disease: advances in
vector development, targeting and
delivery for clinical translation.
Cardiovasc Res. 2015 Aug 3.
Sanjana NE et al. Improved vectors and
genome-wide libraries for CRISPR
screening. Nat Methods. 2014 Aug; 11(8):
783.
Sapranauskas R et al. The Streptococcus
thermophilus CRISPR/Cas system
provides immunity in Escherichia coli.
Nucleic Acid Res. 2011: 39; 9275.
Schumann R et al. Generation of knock-in
primary human T cells using Cas9
ribonucleoproteins. PNAS. 2015 Aug
18;112(33):10437-42.

www.genscript.com

31

Shalem O et al. Genome-scale

CRISPR-Cas9 knockout screening in
human cells. Science. 2014 Jan 3;
343(6166): 84.
Shechner DM et al. Multiplexable,
locus-specic targeting of long RNAs with
CRISPR-Display. Nat Methods. 2015 Jul;
12(7): 664.
Song B et al. Improved hematopoietic
dierentiation eciency of
gene-corrected beta-thalassemia induced
pluripotent stem cells by CRISPR/Cas9
system. Stem Cells Dev. May 1, 2015,
24(9): 1053.

Wyvekens N et al. Dimeric CRISPR

RNA-Guided FokI-dCas9 Nucleases
Directed by Truncated gRNAs for Highly
Specic Genome Editing. Hum Gene Ther.
2015 Jul; 26(7): 425.
Xu P et al. Both TALENs and CRISPR/Cas9
directly target to HBB IVS2-654 (C>T)
mutation in -Thalassemia-derived iPSCs.
Sci Rep. 2015; 5: 12065.
Xue Z et al. CRISPR/Cas9 mediates
ecient conditional mutagenesis in
Drosophila. G3 (Bethesda). 2014 Sep
5;4(11):2167.

Sternberg S and Doudna J. Expanding the

Biologists Toolkit with CRISPR-Cas9.
Molecular Cell. 2015; 58; 568.

Yao S et al. CRISPR/Cas9-Mediated

Genome Editing of Epigenetic Factors for
Cancer Therapy. Hum Gene Ther. 2015 Jul;
26(7): 463.

Tsai SQ et al. GUIDE-seq enables

genome-wide proling of o-target
cleavage by CRISPR-Cas nucleases. Nat
Biotechnol. 2015 Feb; 33(2): 187.

Yin L et al. Multiplex Conditional

Mutagenesis Using Transgenic Expression
of Cas9 and sgRNAs. Genetics. 2015
Jun;200(2):431.

Tsai SQ et al. Dimeric CRISPR RNA-guided

FokI nucleases for highly specic genome
editing. Nat Biotechnol. 2014; 32(6): 569.

Zimmerman M et al. Somatic

CRISPR/Cas9-mediated tumour
suppressor disruption enables versatile
brain tumour modelling. Nat Commun.
2015; 6: 7391.

Voit RA et al. Nuclease-mediated gene

editing by homologous recombination of
the human globin locus. Nucleic Acids Res.
2014 Jan; 42(2): 1365.
Waaijers S et al. CRISPR/Cas9-Targeted
Mutagenesis in Caenorhabditis elegans.
Genetics. 2013 Nov;195(3):1187.
Wang D et al. Adenovirus-Mediated
Somatic Genome Editing of Pten by
CRISPR/Cas9 in Mouse Liver in Spite of
Cas9-Specic Immune Responses. Hum
Gene Ther. 2015 Jul; 26(7): 432.
Wang H et al. One step generation of mice
carrying mutations in multiple genes by
CRISPR/Cas-mediated genome
engineering. Cell. 2013 May 9;153(4):910.

32

www.genscript.com

To learn more about GenScripts CRISPR services, visit

www.genscript.com/CRISPR.html
CRISPR/Cas9 FAQs

CRISPR Research Applications

CRISPR Webinars

CRISPR References

Experimental Protocols

Case Studies: KO/KI cell lines

Legal Statement of GenCRISPR Services and Products (Updated on July 28, 2015):
GenCRISPR services and products are covered under US 8,697,359, US 8,771,945, US 8,795,965, US
8,865,406, US 8,871,445, US 8,889,356, US 8,889,418, US 8,895,308, US 8,906,616 and foreign
equivalents and licensed from Broad Institute, Inc. Cambridge, Massachusetts.
The products and the reagents generated from these services shall be used as tools for research
purposes, and shall exclude (a) any human or clinical use, including, without limitation, any
administration into humans or any diagnostic or prognostic use, (b) any human germline modication,
including modifying the DNA of human embryos or human reproductive cells, (c) any in vivo
veterinary or livestock use, or (d) the manufacture, distribution, importation, exportation,
transportation, sale, oer for sale, marketing, promotion or other exploitation or use of, or as, a
testing service, therapeutic or diagnostic for humans or animals.
The purchase of the GenCRISPR Services and Products coveys to the purchaser the limited,
non-transferable right to use the products purchased and the reagents generated from GenCRISPR
services and any related material solely for Research Purposes only, not for any Commercial Purposes.