Zinc Finger Nuclease
Zinc Finger Nuclease
Zinc Finger Nuclease
2 DNA-binding domain
The DNA-binding domains of individual ZFNs typically
contain between three and six individual zinc nger repeats and can each recognize between 9 and 18 basepairs.
If the zinc nger domains are perfectly specic for their
intended target site then even a pair of 3-nger ZFNs that
recognize a total of 18 basepairs can, in theory, target a
single locus in a mammalian genome.
DNA-cleavage domain
A pair of two ZFNs with three zinc ngers each are shown introducing a double-strand break. Subsequent to this, the double
strand break is being repaired through either homologous recombination or non-homologous end joining.[1]
3 APPLICATIONS
Applications
Similar research of using ZFNs to create specic mutations in zebrash embryo has also been carried out by
other research groups. The kdr gene in zebra sh encodes for the vascular endothelial growth factor-2 receptor. Mutagenic lesions at this target site was induced using ZFN technique by a group of researchers in US. They
suggested that the ZFN technique allows straightforward
generation of a targeted allelic series of mutants; it does
not rely on the existence of species-specic embryonic
stem cell lines and is applicable to other vertebrates, especially those whose embryos are easily available; nally, it
is also feasible to achieve targeted knock-ins in zebrash,
therefore it is possible to create human disease models
that are heretofore inaccessible.
3.1
Disabling an allele
ZFNs can be used to disable dominant mutations in heterozygous individuals by producing double-strand breaks
(DSBs) in the DNA (see Genetic recombination) in the
mutant allele, which will, in the absence of a homologous
template, be repaired by non-homologous end-joining
(NHEJ). NHEJ repairs DSBs by joining the two ends together and usually produces no mutations, provided that
the cut is clean and uncomplicated. In some instances,
however, the repair will be imperfect, resulting in deletion
or insertion of base-pairs, producing frame-shift and preventing the production of the harmful protein.[32] Multiple pairs of ZFNs can also be used to completely remove entire large segments of genomic sequence.[33] To
monitor the editing activity, a PCR of the target area
will amplify both alleles and, if one contains an insertion, deletion, or mutation, it will result in a heterduplex
single-strand bubble that cleavage assays can easily detect. ZFNs have also been used to modify disease-causing
alleles in triplet repeat disorders. Expanded CAG/CTG
repeat tracts are the genetic basis for more than a dozen
inherited neurological disorders including Huntingtons
disease, myotonic dystrophy, and several spinocerebellar ataxias. It has been demonstrated in human cells that
ZFNs can direct double-strand breaks (DSBs) to CAG repeats and shrink the repeat from long pathological lengths
to short, less toxic lengths.[34]
Recently, a group of researchers have successfully applied the ZFN technology to genetically modify the gol
pigment gene and the ntl gene in zebrash embryo. Specic zinc-nger motifs were engineered to recognize dis-
Allele editing
3
based approach has the potential to circumvent all the
problems associated with the viral delivery of therapeutic genes.[35] The rst therapeutic applications of ZFNs
are likely to involve ex vivo therapy using a patients own
stem cells. After editing the stem cell genome, the cells
could be expanded in culture and reinserted into the patient to produce dierentiated cells with corrected functions. The initial targets will likely include the causes of
monogenic diseases such as the IL2R gene and the bglobin gene for gene correction and CCR5 gene for mutagenesis and disablement.[32]
4
4.1
Potential Problems
O-target Cleavage
If the zinc nger domains are not specic enough for their
target site or they do not target a unique site within the
genome of interest, o-target cleavage may occur. Such
o-target cleavage may lead to the production of enough
double-strand breaks to overwhelm the repair machinery and, as a consequence, yield chromosomal rearrangements and/or cell death. O-target cleavage events may
also promote random integration of donor DNA.[32] Two
separate methods have been demonstrated to decrease
o-target cleavage for 3-nger ZFNs that target two adjacent 9-basepair sites.[36] Other groups use ZFNs with
4, 5 or 6 zinc ngers that target longer and presumably
rarer sites and such ZFNs could theoretically yield less
o-target activity. A comparison of a pair of 3-nger
ZFNs and a pair of 4-nger ZFNs detected o-target
cleavage in human cells at 31 loci for the 3-nger ZFNs
and at 9 loci for the 4-nger ZFNs.[37] Whole genome sequencing of C. elegans modied with a pair of 5-nger
ZFNs found only the intended modication and a deletion at a site unrelated to the ZFN site indicating this
pair of ZFNs was capable of targeting a unique site in the
C. elegans genome.[20]
4.2
Immunogenicity
5 Prospects
The ability to precisely manipulate the genomes of plants,
animals and insects has numerous applications in basic research, agriculture, and human therapeutics. Using ZFNs
to modify endogenous genes has traditionally been a difcult task due mainly to the challenge of generating zinc
nger domains that target the desired sequence with sufcient specicity. Improved methods of engineering zinc
nger domains and the availability of ZFNs from a commercial supplier now put this technology in the hands of
increasing numbers of researchers. Several groups are
also developing other types of engineered nucleases including engineered homing endonucleases [40] [41] and nucleases based on engineered TAL eectors. [42] [43] TAL
eector nucleases (TALENs) are particularly interesting
because TAL eectors appear to be very simple to engineer [44] [45] and TALENs can be used to target endogenous loci in human cells.[46] But to date no one has reported the isolation of clonal cell lines or transgenic organisms using such reagents. One type of ZFN, known
as SB-728-T, has been tested for potential application in
the treatment of HIV.[47]
6 Zinc-nger Nickases
Zinc-nger nickases (ZFNickases) are created by inactivating the catalytic activity of one ZFN monomer in
the ZFN dimer required for double-strand cleavage.[48]
ZFNickases demonstrate strand-specic nicking activity
in vitro and thus provide for highly specic single-strand
breaks in DNA.[48] These SSBs undergo the same cellular
mechanisms for DNA that ZFNs exploit, but they show a
signicantly reduced frequency of mutagenic NHEJ repairs at their target nicking site. This reduction provides
a bias for HR-mediated gene modications. ZFNickases
can induce targeted HR in cultured human and livestock
cells, although at lower levels than corresponding ZFNs
from which they were derived because nicks can be repaired without genetic alteration.[49] [38] A major limitation of ZFN-mediated gene modications is the competition between NHEJ and HR repair pathways. Regardless
of the presence of a DNA donor construct, both repair
mechanisms can be activated following DSBs induced by
ZFNs. Thus, ZFNickases is the rst plausible attempt at
engineering a method to favor the HR method of DNA
repair as opposed to the error-prone NHEJ repair. By reducing NHEJ repairs, ZFNickases can thereby reduce the
spectrum of unwanted o-target alterations. The ease by
which ZFNickases can be derive from ZFNs provides a
great platform for further studies regarding the optimization of ZFNickases and possibly increasing their levels
of targeted HR while still maintain their reduced NHEJ
frequency.
specicity (due to their short recognition sequences) unfortunately, rendered them toxic to the host genome. The
latter-potential host-genome toxicity posed by the raw
bacteria-derived REases limited their application to exvivo modalities for HIV prevention, namely synthetic or
live microbicides. Subsequently, however, the unique
specicity oered by ZFNs was quickly recognized and
harnessed, paving way for a novel strategy for attacking HIV in-vivo (through target mutagenesis of proviral
HIV DNA) that is similar to the manner by which bacteria equipped with R-M systems do, to disable the foreign DNAs of in-coming phage-genomes. Because latent proviral HIV DNA resident in resting memory CD4
cells forms the major barrier to the eradication of HIV
by highly active antiviral therapy (HAART), it is speculated that this approach may oer a 'functional cure for
HIV. Both ex-vivo (manipulation of stem or autologous
T cell precursors) and in-vivo delivery platforms are being explored. It is also hoped that, when applied to nonHIV infected persons, this strategy could oer a genomic
vaccine against HIV and other viruses. Similar work is
ongoing for high-risk HPVs (with the intent of reversing cervical neoplasia) [60] as well as with HSV-2 (with
the goal of achieving a complete cure for genital herpes)
7.4
Limitations
7.3
To employ the ZFNs in clinical settings the following criteria need to be met: i) High specicity of DNA-binding
Correlates with better performance and less toxicity
of ZFNs. Engineered ZFNs take into account positional
and context-dependent eects of zinc ngers to increase
specicity.[82] ii) Enable allosteric activation of FokI once
bound to DNA in order for it to produce only the required
DSB.[82] iii) In order to deliver two dierent zinc nger
nuclease subunits and donor DNA to the cell, the vectors
that are used need to be improved to decrease the risk
of mutagenesis.[82] These include adeno-associated virus
vectors, integrase-decient lentiviral vectors and adenovirus type 5 vectors.[82] iv) Transient expression of ZFNs
would be preferred over permanent expression of these
proteins in order to avoid o-target eects.[82] v) During
gene targeting, genotoxicity associated with high expression of ZFNs might lead to cell apoptosis and thus needs
to be thoroughly veried in vitro and in vivo transformation assays.[82]
7.5
Administration of Treatment
See also
Genome editing with engineered nucleases
Zinc nger
Gene targeting
Zinc nger protein
Zinc nger chimera
Protein engineering
Genome engineering
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10
11
10
Further reading
Mandell JG, Barbas CF (July 2006). Zinc Finger Tools: custom DNA-binding domains for
Nucleic
transcription factors and nucleases.
Acids Res. 34 (Web Server issue): W51623.
doi:10.1093/nar/gkl209. PMC 1538883. PMID
16845061.
Porteus MH, Carroll D (August 2005). Gene targeting using zinc nger nucleases. Nat. Biotechnol. 23 (8): 96773. doi:10.1038/nbt1125. PMID
16082368.
Doyon Y, McCammon JM, Miller JC et al.
(June 2008). Heritable Targeted Gene Disruption in Zebrash Using Designed Zinc Finger Nucleases. Nat. Biotechnol. 26 (6): 7028.
doi:10.1038/nbt1409. PMC 2674762. PMID
18500334.
EXTERNAL LINKS
11 External links
Zinc nger selector
Zinc Finger Consortium website
Zinc Finger Consortium materials from Addgene
A commercial supplier of ZFNs
11
12
12.1
12.2
Images
File:Repair_outcomes_of_a_genomic_double-strand_break_for_ZFN_cleavage.jpg
Source:
http://upload.wikimedia.org/
wikipedia/commons/d/de/Repair_outcomes_of_a_genomic_double-strand_break_for_ZFN_cleavage.jpg License: CC BY-SA 3.0
Contributors: Carroll, D. Genome engineering with zinc-nger nucleases. Genetics Society of America, 2011, 188(4), pp 773-782.
Original artist: Dana Carroll
12.3
Content license