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Development and Applications of CRISPR-Cas9 For Genome Engineering
Development and Applications of CRISPR-Cas9 For Genome Engineering
Review
*Correspondence: zhang@broadinstitute.org
http://dx.doi.org/10.1016/j.cell.2014.05.010
RNAs rather than a library of large, bulky proteins. The ease of scribed as a single RNA before subsequent processing into
Cas9 targeting, its high efficiency as a site-specific nuclease, shorter CRISPR RNAs (crRNAs), which direct the nucleolytic
and the possibility for highly multiplexed modifications have activity of certain Cas enzymes to degrade target nucleic acids.
opened up a broad range of biological applications across basic The CRISPR story began in 1987. While studying the iap
research to biotechnology and medicine. enzyme involved in isozyme conversion of alkaline phosphatase
The utility of customizable DNA-binding domains extends far in E. coli, Nakata and colleagues reported a curious set of 29 nt
beyond genome editing with site-specific endonucleases. repeats downstream of the iap gene (Ishino et al., 1987). Unlike
Fusing them to modular, sequence-agnostic functional effector most repetitive elements, which typically take the form of tandem
domains allows flexible recruitment of desired perturbations, repeats like TALE repeat monomers, these 29 nt repeats were
such as transcriptional activation, to a locus of interest (Xu and interspaced by five intervening 32 nt nonrepetitive sequences.
Bestor, 1997; Beerli et al., 2000a; Konermann et al., 2013; Over the next 10 years, as more microbial genomes were
Maeder et al., 2013a; Mendenhall et al., 2013). In fact, any sequenced, additional repeat elements were reported from
modular enzymatic component can, in principle, be substituted, genomes of different bacterial and archaeal strains. Mojica and
allowing facile additions to the genome engineering toolbox. colleagues eventually classified interspaced repeat sequences
Integration of genome- and epigenome-modifying enzymes as a unique family of clustered repeat elements present in
with inducible protein regulation further allows precise temporal >40% of sequenced bacteria and 90% of archaea (Mojica
control of dynamic processes (Beerli et al., 2000b; Konermann et al., 2000).
et al., 2013). These early findings began to stimulate interest in such micro-
bial repeat elements. By 2002, Jansen and Mojica coined the
CRISPR-Cas9: From Yogurt to Genome Editing acronym CRISPR to unify the description of microbial genomic
The recent development of the Cas9 endonuclease for genome loci consisting of an interspaced repeat array (Jansen et al.,
editing draws upon more than a decade of basic research into 2002; Barrangou and van der Oost, 2013). At the same time,
understanding the biological function of the mysterious repetitive several clusters of signature CRISPR-associated (cas) genes
elements now known as CRISPR (Figure 3), which are found were identified to be well conserved and typically adjacent to
throughout the bacterial and archaeal diversity. CRISPR loci the repeat elements (Jansen et al., 2002), serving as a basis for
typically consist of a clustered set of CRISPR-associated (Cas) the eventual classification of three different types of CRISPR
genes and the signature CRISPR array—a series of repeat systems (types I–III) (Haft et al., 2005; Makarova et al., 2011b).
sequences (direct repeats) interspaced by variable sequences Types I and III CRISPR loci contain multiple Cas proteins, now
(spacers) corresponding to sequences within foreign genetic known to form complexes with crRNA (CASCADE complex for
elements (protospacers) (Figure 4). Whereas Cas genes are type I; Cmr or Csm RAMP complexes for type III) to facilitate
translated into proteins, most CRISPR arrays are first tran- the recognition and destruction of target nucleic acids (Brouns
et al., 2008; Hale et al., 2009) (Figure 4). In contrast, the type II degrade viral transcripts in a RNAi-like mechanism (Makarova
system has a significantly reduced number of Cas proteins. et al., 2006) or that CRISPR spacers direct Cas enzymes to
However, despite increasingly detailed mapping and annotation cleave viral DNA at spacer-matching regions (Bolotin et al.,
of CRISPR loci across many microbial species, their biological 2005).
significance remained elusive. Working with the dairy production bacterial strain Strepto-
A key turning point came in 2005, when systematic analysis of coccus thermophilus at the food ingredient company Danisco,
the spacer sequences separating the individual direct repeats Horvath and colleagues uncovered the first experimental
suggested their extrachromosomal and phage-associated ori- evidence for the natural role of a type II CRISPR system as an
gins (Mojica et al., 2005; Pourcel et al., 2005; Bolotin et al., adaptive immunity system, demonstrating a nucleic-acid-based
2005). This insight was tremendously exciting, especially given immune system in which CRISPR spacers dictate target speci-
previous studies showing that CRISPR loci are transcribed ficity while Cas enzymes control spacer acquisition and phage
(Tang et al., 2002) and that viruses are unable to infect archaeal defense (Barrangou et al., 2007). A rapid series of studies illumi-
cells carrying spacers corresponding to their own genomes nating the mechanisms of CRISPR defense followed shortly and
(Mojica et al., 2005). Together, these findings led to the specula- helped to establish the mechanism as well as function of all three
tion that CRISPR arrays serve as an immune memory and types of CRISPR loci in adaptive immunity. By studying the type I
defense mechanism, and individual spacers facilitate defense CRISPR locus of Escherichia coli, van der Oost and colleagues
against bacteriophage infection by exploiting Watson-Crick showed that CRISPR arrays are transcribed and converted into
base-pairing between nucleic acids (Mojica et al., 2005; Pourcel small crRNAs containing individual spacers to guide Cas
et al., 2005). Despite these compelling realizations that CRISPR nuclease activity (Brouns et al., 2008). In the same year,
loci might be involved in microbial immunity, the specific mech- CRISPR-mediated defense by a type III-A CRISPR system
anism of how the spacers act to mediate viral defense remained from Staphylococcus epidermidis was demonstrated to block
a challenging puzzle. Several hypotheses were raised, including plasmid conjugation, establishing the target of Cas enzyme
thoughts that CRISPR spacers act as small RNA guides to activity as DNA rather than RNA (Marraffini and Sontheimer,
2008), although later investigation of a different type III-B system Around this time, two studies characterizing the functional
from Pyrococcus furiosus also revealed crRNA-directed RNA mechanisms of the native type II CRISPR system elucidated
cleavage activity (Hale et al., 2009, 2012). the basic components that proved vital for engineering a simple
As the pace of CRISPR research accelerated, researchers RNA-programmable DNA endonuclease for genome editing.
quickly unraveled many details of each type of CRISPR system First, Moineau and colleagues used genetic studies in Strepto-
(Figure 4). Building on an earlier speculation that protospacer- coccus thermophilus to reveal that Cas9 (formerly called
adjacent motifs (PAMs) may direct the type II Cas9 nuclease to Cas5, Csn1, or Csx12) is the only enzyme within the cas
cleave DNA (Bolotin et al., 2005), Moineau and colleagues high- gene cluster that mediates target DNA cleavage (Garneau
lighted the importance of PAM sequences by demonstrating that et al., 2010). Next, Charpentier and colleagues revealed a
PAM mutations in phage genomes circumvented CRISPR inter- key component in the biogenesis and processing of crRNA
ference (Deveau et al., 2008). Additionally, for types I and II, the in type II CRISPR systems—a noncoding trans-activating
lack of PAM within the direct repeat sequence within the CRISPR crRNA (tracrRNA) that hybridizes with crRNA to facilitate
array prevents self-targeting by the CRISPR system. In type III RNA-guided targeting of Cas9 (Deltcheva et al., 2011). This
systems, however, mismatches between the 50 end of the crRNA dual RNA hybrid, together with Cas9 and endogenous RNase
and the DNA target are required for plasmid interference (Marraf- III, is required for processing the CRISPR array transcript
fini and Sontheimer, 2010). into mature crRNAs (Deltcheva et al., 2011). These two studies
By 2010, just 3 years after the first experimental evidence for suggested that there are at least three components (Cas9,
CRISPR in bacterial immunity, the basic function and mecha- the mature crRNA, and tracrRNA) that are essential for recon-
nisms of CRISPR systems were becoming clear. A variety of stituting the type II CRISPR nuclease system. Given the
groups had begun to harness the natural CRISPR system for increasing importance of programmable site-specific nucleases
various biotechnological applications, including the generation based on ZFs and TALEs for enhancing eukaryotic genome
of phage-resistant dairy cultures (Quiberoni et al., 2010) and editing, it was tantalizing to think that perhaps Cas9 could
phylogenetic classification of bacterial strains (Horvath et al., be developed into an RNA-guided genome editing system.
2008, 2009). However, genome editing applications had not From this point, the race to harness Cas9 for genome editing
yet been explored. was on.
with multiplex nicking to further reduce off-target mutagenesis states, or even rearrange the three-dimensional organization of
(Fu et al., 2014). Future structure-function analyses and Cas9 the genome.
and protein engineering via rational design or directed evolution Rapid Generation of Cellular and Animal Models
may lead to further improvements in Cas9 specificity. Cas9-mediated genome editing has enabled accelerated gener-
ation of transgenic models and expands biological research
Applications of Cas9 in Research, Medicine, and beyond traditional, genetically tractable animal model organisms
Biotechnology (Sander and Joung, 2014). By recapitulating genetic mutations
Cas9 can be used to facilitate a wide variety of targeted genome found in patient populations, CRISPR-based editing could be
engineering applications. The wild-type Cas9 nuclease has used to rapidly model the causal roles of specific genetic varia-
enabled efficient and targeted genome modification in many tions instead of relying on disease models that only phenocopy a
species that have been intractable using traditional genetic particular disorder. This could be applied to develop novel trans-
manipulation techniques. The ease of retargeting Cas9 by simply genic animal models (Wang et al., 2013; Niu et al., 2014), to
designing a short RNA sequence also enables large-scale unbi- engineer isogenic ES and iPS cell disease models with specific
ased genome perturbation experiments to probe gene function mutations introduced or corrected, respectively, or in vivo and
or elucidate causal genetic variants. In addition to facilitating co- ex vivo gene correction (Schwank et al., 2013; Wu et al., 2013).
valent genome modifications, the wild-type Cas9 nuclease can For generation of cellular models, Cas9 can be easily intro-
also be converted into a generic RNA-guided homing device duced into the target cells using transient transfection of plas-
(dCas9) by inactivating the catalytic domains. The use of effector mids carrying Cas9 and the appropriately designed sgRNA
fusions can greatly expand the repertoire of genome engineering (Figure 6C). Additionally, the multiplexing capabilities of Cas9
modalities achievable using Cas9. For example, a variety of pro- offer a promising approach for studying common human
teins or RNAs can be tethered to Cas9 or sgRNA to alter tran- diseases—such as diabetes, heart disease, schizophrenia, and
scription states of specific genomic loci, monitor chromatin autism—that are typically polygenic. Large-scale genome-wide
and efficacious delivery systems to target specific disease Bibikova, M., Carroll, D., Segal, D.J., Trautman, J.K., Smith, J., Kim, Y.G., and
Chandrasegaran, S. (2001). Stimulation of homologous recombination through
tissues. To achieve high levels of therapeutic efficacy and simul-
targeted cleavage by chimeric nucleases. Mol. Cell. Biol. 21, 289–297.
taneously address a broad spectrum of genetic disorders,
Bibikova, M., Golic, M., Golic, K.G., and Carroll, D. (2002). Targeted chromo-
homologous recombination efficiency will need to be signifi-
somal cleavage and mutagenesis in Drosophila using zinc-finger nucleases.
cantly improved. Although permanent genome modification Genetics 161, 1169–1175.
has advantages over monoclonal antibody or siRNA treatments, Bibikova, M., Beumer, K., Trautman, J.K., and Carroll, D. (2003). Enhancing
which require repeated administration of the therapeutic mole- gene targeting with designed zinc finger nucleases. Science 300, 764.
cule, the long-term implications remain unclear. As researchers Boch, J., Scholze, H., Schornack, S., Landgraf, A., Hahn, S., Kay, S., Lahaye,
further develop and test Cas9 toward clinical translation, it will T., Nickstadt, A., and Bonas, U. (2009). Breaking the code of DNA binding
be paramount to thoroughly characterize the safety as well as specificity of TAL-type III effectors. Science 326, 1509–1512.
physiological effects of Cas9 using a variety of preclinical Bolotin, A., Quinquis, B., Sorokin, A., and Ehrlich, S.D. (2005). Clustered regu-
models. larly interspaced short palindrome repeats (CRISPRs) have spacers of extra-
chromosomal origin. Microbiology 151, 2551–2561.
Brouns, S.J., Jore, M.M., Lundgren, M., Westra, E.R., Slijkhuis, R.J., Snijders,
Conclusions
A.P., Dickman, M.J., Makarova, K.S., Koonin, E.V., and van der Oost, J. (2008).
The story of how a mysterious prokaryotic viral defense system Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321,
became one of the most powerful and versatile platforms for 960–964.
engineering biology highlights the importance of basic science Capecchi, M.R. (1989). Altering the genome by homologous recombination.
research. Just as recombinant DNA technology benefited from Science 244, 1288–1292.
basic investigation of the restriction enzymes that are central Chen, B., Gilbert, L.A., Cimini, B.A., Schnitzbauer, J., Zhang, W., Li, G.W.,
to warfare between phage and bacteria, the latest generation Park, J., Blackburn, E.H., Weissman, J.S., Qi, L.S., and Huang, B. (2013).
of Cas9-based genome engineering tools are also based on Dynamic imaging of genomic loci in living human cells by an optimized
components from the microbial antiphage defense system. It is CRISPR/Cas system. Cell 155, 1479–1491.
highly likely that the future solutions for efficient and precise Cho, S.W., Kim, S., Kim, J.M., and Kim, J.S. (2013). Targeted genome engi-
gene modification will be found in as of yet unexplored corners neering in human cells with the Cas9 RNA-guided endonuclease. Nat.
Biotechnol. 31, 230–232.
of the rich biological diversity of nature.
Choulika, A., Perrin, A., Dujon, B., and Nicolas, J.F. (1995). Induction of homo-
logous recombination in mammalian chromosomes by using the I-SceI system
SUPPLEMENTAL INFORMATION of Saccharomyces cerevisiae. Mol. Cell. Biol. 15, 1968–1973.
Christian, M., Cermak, T., Doyle, E.L., Schmidt, C., Zhang, F., Hummel, A.,
Supplemental Information includes one movie and can be found with this
Bogdanove, A.J., and Voytas, D.F. (2010). Targeting DNA double-strand
article at http://dx.doi.org/10.1016/j.cell.2014.05.010.
breaks with TAL effector nucleases. Genetics 186, 757–761.
Chylinski, K., Le Rhun, A., and Charpentier, E. (2013). The tracrRNA and Cas9
ACKNOWLEDGMENTS
families of type II CRISPR-Cas immunity systems. RNA Biol. 10, 726–737.
We gratefully acknowledge Sigrid Knemeyer for help with illustration; Ian Slay- Chylinski, K., Makarova, K.S., Charpentier, E., and Koonin, E.V. (2014).
maker for structural guidance; Chengwei Luo for expertise in phylogenetic Classification and evolution of type II CRISPR-Cas systems. Nucleic Acids
analysis; Emmanuelle Charpentier, Philippe Horvath, Charles Jennings, Ellen Res. Published online Apr 11, 2014. http://dx.doi.org/10.1093/nar/gku241.
Law, Luciano Marraffini, Francisco Mojica, Hiroshi Nishimasu, Virginijus Cohen, J., Pertsemlidis, A., Kotowski, I.K., Graham, R., Garcia, C.K., and
Siksnys, and Alexandro Trevino for discussion and comments; and the Hobbs, H.H. (2005). Low LDL cholesterol in individuals of African descent
Marraffini, L.A., and Sontheimer, E.J. (2010). Self versus non-self discrimina- Rouet, P., Smih, F., and Jasin, M. (1994). Introduction of double-strand breaks
tion during CRISPR RNA-directed immunity. Nature 463, 568–571. into the genome of mouse cells by expression of a rare-cutting endonuclease.
Mol. Cell. Biol. 14, 8096–8106.
Mendenhall, E.M., Williamson, K.E., Reyon, D., Zou, J.Y., Ram, O., Joung, J.K.,
and Bernstein, B.E. (2013). Locus-specific editing of histone modifications at Rudin, N., Sugarman, E., and Haber, J.E. (1989). Genetic and physical analysis
endogenous enhancers. Nat. Biotechnol. 31, 1133–1136. of double-strand break repair and recombination in Saccharomyces cerevi-
siae. Genetics 122, 519–534.
Miller, J.C., Holmes, M.C., Wang, J., Guschin, D.Y., Lee, Y.L., Rupniewski, I.,
Beausejour, C.M., Waite, A.J., Wang, N.S., Kim, K.A., et al. (2007). An Sander, J.D., and Joung, J.K. (2014). CRISPR-Cas systems for editing, regu-
improved zinc-finger nuclease architecture for highly specific genome editing. lating and targeting genomes. Nat. Biotechnol. 32, 347–355.
Nat. Biotechnol. 25, 778–785. Sander, J.D., Dahlborg, E.J., Goodwin, M.J., Cade, L., Zhang, F., Cifuentes,
Miller, J.C., Tan, S., Qiao, G., Barlow, K.A., Wang, J., Xia, D.F., Meng, X., D., Curtin, S.J., Blackburn, J.S., Thibodeau-Beganny, S., Qi, Y., et al. (2011).
Paschon, D.E., Leung, E., Hinkley, S.J., et al. (2011). A TALE nuclease architec- Selection-free zinc-finger-nuclease engineering by context-dependent
ture for efficient genome editing. Nat. Biotechnol. 29, 143–148. assembly (CoDA). Nat. Methods 8, 67–69.
Mojica, F.J., Dı́ez-Villaseñor, C., Soria, E., and Juez, G. (2000). Biological Sapranauskas, R., Gasiunas, G., Fremaux, C., Barrangou, R., Horvath, P., and
significance of a family of regularly spaced repeats in the genomes of Archaea, Siksnys, V. (2011). The Streptococcus thermophilus CRISPR/Cas system
Bacteria and mitochondria. Mol. Microbiol. 36, 244–246. provides immunity in Escherichia coli. Nucleic Acids Res. 39, 9275–9282.
Schwank, G., Koo, B.K., Sasselli, V., Dekkers, J.F., Heo, I., Demircan, T.,
Mojica, F.J., Dı́ez-Villaseñor, C., Garcı́a-Martı́nez, J., and Soria, E. (2005).
Sasaki, N., Boymans, S., Cuppen, E., van der Ent, C.K., et al. (2013). Functional
Intervening sequences of regularly spaced prokaryotic repeats derive from
repair of CFTR by CRISPR/Cas9 in intestinal stem cell organoids of cystic
foreign genetic elements. J. Mol. Evol. 60, 174–182.
fibrosis patients. Cell Stem Cell 13, 653–658.
Moscou, M.J., and Bogdanove, A.J. (2009). A simple cipher governs DNA
Shah, S.A., Erdmann, S., Mojica, F.J., and Garrett, R.A. (2013). Protospacer
recognition by TAL effectors. Science 326, 1501.
recognition motifs: mixed identities and functional diversity. RNA Biol. 10,
Musunuru, K., Pirruccello, J.P., Do, R., Peloso, G.M., Guiducci, C., Sougnez, 891–899.
C., Garimella, K.V., Fisher, S., Abreu, J., Barry, A.J., et al. (2010). Exome
Shalem, O., Sanjana, N.E., Hartenian, E., Shi, X., Scott, D.A., Mikkelsen, T.S.,
sequencing, ANGPTL3 mutations, and familial combined hypolipidemia.
Heckl, D., Ebert, B.L., Root, D.E., Doench, J.G., and Zhang, F. (2014).
N. Engl. J. Med. 363, 2220–2227.
Genome-scale CRISPR-Cas9 knockout screening in human cells. Science
Niewoehner, J., Bohrmann, B., Collin, L., Urich, E., Sade, H., Maier, P., Rueger, 343, 84–87.
P., Stracke, J.O., Lau, W., Tissot, A.C., et al. (2014). Increased brain penetra-
Smith, J., Grizot, S., Arnould, S., Duclert, A., Epinat, J.C., Chames, P., Prieto,
tion and potency of a therapeutic antibody using a monovalent molecular shut-
J., Redondo, P., Blanco, F.J., Bravo, J., et al. (2006). A combinatorial approach
tle. Neuron 81, 49–60.
to create artificial homing endonucleases cleaving chosen sequences. Nucleic
Nishimasu, H., Ran, F.A., Hsu, P.D., Konermann, S., Shehata, S.I., Dohmae, Acids Res. 34, e149.
N., Ishitani, R., Zhang, F., and Nureki, O. (2014). Crystal structure of Cas9 in
Sternberg, S.H., Redding, S., Jinek, M., Greene, E.C., and Doudna, J.A. (2014).
complex with guide RNA and target DNA. Cell 156, 935–949.
DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature
Niu, Y., Shen, B., Cui, Y., Chen, Y., Wang, J., Wang, L., Kang, Y., Zhao, X., Si, 507, 62–67.
W., Li, W., et al. (2014). Generation of gene-modified cynomolgus monkey via
Tang, T.H., Bachellerie, J.P., Rozhdestvensky, T., Bortolin, M.L., Huber, H.,
Cas9/RNA-mediated gene targeting in one-cell embryos. Cell 156, 836–843.
Drungowski, M., Elge, T., Brosius, J., and Hüttenhofer, A. (2002). Identification
Oh, B., Hwang, S., McLaughlin, J., Solter, D., and Knowles, B.B. (2000). Timely of 86 candidates for small non-messenger RNAs from the archaeon Archaeo-
translation during the mouse oocyte-to-embryo transition. Development 127, globus fulgidus. Proc. Natl. Acad. Sci. USA 99, 7536–7541.
3795–3803.
Tebas, P., Stein, D., Tang, W.W., Frank, I., Wang, S.Q., Lee, G., Spratt, S.K.,
Pattanayak, V., Lin, S., Guilinger, J.P., Ma, E., Doudna, J.A., and Liu, D.R. Surosky, R.T., Giedlin, M.A., Nichol, G., et al. (2014). Gene editing of CCR5
(2013). High-throughput profiling of off-target DNA cleavage reveals RNA- in autologous CD4 T cells of persons infected with HIV. N. Engl. J. Med.
programmed Cas9 nuclease specificity. Nat. Biotechnol. 31, 839–843. 370, 901–910.
Perez-Pinera, P., Kocak, D.D., Vockley, C.M., Adler, A.F., Kabadi, A.M., Urnov, F.D., Miller, J.C., Lee, Y.L., Beausejour, C.M., Rock, J.M., Augustus, S.,
Polstein, L.R., Thakore, P.I., Glass, K.A., Ousterout, D.G., Leong, K.W., et al. Jamieson, A.C., Porteus, M.H., Gregory, P.D., and Holmes, M.C. (2005). Highly
(2013). RNA-guided gene activation by CRISPR-Cas9-based transcription efficient endogenous human gene correction using designed zinc-finger
factors. Nat. Methods 10, 973–976. nucleases. Nature 435, 646–651.