Creating and evaluating accurate CRISPR-Cas9 scalpels for genomic surgery (original) (raw)
Chylinski, K., Makarova, K.S., Charpentier, E. & Koonin, E.V. Classification and evolution of type II CRISPR-Cas systems. Nucleic Acids Res.42, 6091–6105 (2014). CASPubMedPubMed Central Google Scholar
Makarova, K.S. et al. An updated evolutionary classification of CRISPR-Cas systems. Nat. Rev. Microbiol.13, 722–736 (2015). CASPubMedPubMed Central Google Scholar
Sontheimer, E.J. & Barrangou, R. The bacterial origins of the CRISPR genome-editing revolution. Hum. Gene Ther.26, 413–424 (2015). CASPubMed Google Scholar
Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science337, 816–821 (2012).This study describes the minimal components required to program a type II CRISPR-Cas9 system for targeted DNA cleavagein vitroand demonstrates that crRNA and tracrRNA can be joined into an sgRNA to generate a two-component system for site-specific editing. ArticleCASPubMedPubMed Central Google Scholar
Joung, J.K. & Sander, J.D. TALENs: a widely applicable technology for targeted genome editing. Nat. Rev. Mol. Cell Biol.14, 49–55 (2013). CASPubMed Google Scholar
Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science339, 819–823 (2013).This is one of the first studies to demonstrate that the type II CRISPR-Cas9 system can be programmed to generate DSBs in mammalian cells. This study demonstrated that multiple guides can be used to program cleavage or nicking at more than one sequence in a genome within a cell. CASPubMedPubMed Central Google Scholar
Mali, P. et al. RNA-guided human genome engineering via Cas9. Science339, 823–826 (2013).This is one of the first studies to demonstrate that the type II CRISPR-Cas9 system can be programmed to generate DSBs in a variety of mammalian cell types, including induced pluripotent stem cells. This study also demonstrated HDR-mediated insertion of exogenous DNA sequences using Cas9-induced DSBs or nicks. CASPubMedPubMed Central Google Scholar
Cho, S.W., Kim, S., Kim, J.M. & Kim, J.-S. Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat. Biotechnol.31, 230–232 (2013).This is one of the first studies to demonstrate that the type II CRISPR-Cas9 system can be programmed to generate DSBs in a variety of mammalian cell types. CASPubMed Google Scholar
Jinek, M. et al. RNA-programmed genome editing in human cells. Elife2, e00471 (2013).This is one of the first studies to demonstrate that the type II CRISPR-Cas9 system can be programmed to generate DSBs in mammalian cells. ArticlePubMedPubMed Central Google Scholar
Wang, H. et al. One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell153, 910–918 (2013).This study reports a rapid strategy for generating knockout mouse models using multiplex gene editing, in which two genes can be targeted simultaneously to generate carriers containing dual gene disruptions or ssODNs can be included to create HDR-mediated knock-ins at two different loci. CASPubMedPubMed Central Google Scholar
Hwang, W.Y. et al. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat. Biotechnol.31, 227–229 (2013).This study demonstrated that the type II CRISPR-Cas9 system can be used in a vertebrate organism to successfully inactivate target genes. CASPubMedPubMed Central Google Scholar
Chen, B. et al. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell155, 1479–1491 (2013). CASPubMedPubMed Central Google Scholar
Doudna, J.A. & Charpentier, E. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science346, 1258096 (2014). PubMed Google Scholar
Cox, D.B.T., Platt, R.J. & Zhang, F. Therapeutic genome editing: prospects and challenges. Nat. Med.21, 121–131 (2015). CASPubMedPubMed Central Google Scholar
Jao, L.-E., Wente, S.R. & Chen, W. Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system. Proc. Natl. Acad. Sci. USA110, 13904–13909 (2013). CASPubMedPubMed Central Google Scholar
Swiech, L. et al. In vivo interrogation of gene function in the mammalian brain using CRISPR-Cas9. Nat. Biotechnol.33, 102–106 (2015). CASPubMed Google Scholar
Kabadi, A.M., Ousterout, D.G., Hilton, I.B. & Gersbach, C.A. Multiplex CRISPR/Cas9-based genome engineering from a single lentiviral vector. Nucleic Acids Res.42, e147 (2014). PubMedPubMed Central Google Scholar
Mandal, P.K. et al. Efficient ablation of genes in human hematopoietic stem and effector cells using CRISPR/Cas9. Cell Stem Cell15, 643–652 (2014). CASPubMedPubMed Central Google Scholar
Tsai, S.Q. et al. Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing. Nat. Biotechnol.32, 569–576 (2014). CASPubMedPubMed Central Google Scholar
Hendel, A. et al. Chemically modified guide RNAs enhance CRISPR-Cas genome editing in human primary cells. Nat. Biotechnol.33, 985–989 (2015). CASPubMedPubMed Central Google Scholar
Yang, H. et al. One-step generation of mice carrying reporter and conditional alleles by CRISPR/Cas-mediated genome engineering. Cell154, 1370–1379 (2013). CASPubMedPubMed Central Google Scholar
Canver, M.C. et al. Characterization of genomic deletion efficiency mediated by clustered regularly interspaced palindromic repeats (CRISPR)/Cas9 nuclease system in mammalian cells. J. Biol. Chem.289, 21312–21324 (2014). PubMedPubMed Central Google Scholar
Lupiáñez, D.G. et al. Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell161, 1012–1025 (2015). PubMedPubMed Central Google Scholar
Torres, R. et al. Engineering human tumour-associated chromosomal translocations with the RNA-guided CRISPR-Cas9 system. Nat. Commun.5, 3964 (2014). CASPubMed Google Scholar
Choi, P.S. & Meyerson, M. Targeted genomic rearrangements using CRISPR/Cas technology. Nat. Commun.5, 3728 (2014). CASPubMed Google Scholar
Ghezraoui, H. et al. Chromosomal translocations in human cells are generated by canonical nonhomologous end-joining. Mol. Cell55, 829–842 (2014). CASPubMedPubMed Central Google Scholar
Cho, S.W. et al. Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Res.24, 132–141 (2014). CASPubMedPubMed Central Google Scholar
Wang, T., Wei, J.J., Sabatini, D.M. & Lander, E.S. Genetic screens in human cells using the CRISPR-Cas9 system. Science343, 80–84 (2014). CASPubMed Google Scholar
Shalem, O. et al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science343, 84–87 (2014). CASPubMed Google Scholar
Koike-Yusa, H., Li, Y., Tan, E.-P., Velasco-Herrera, M.D.C. & Yusa, K. Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library. Nat. Biotechnol.32, 267–273 (2014). CASPubMed Google Scholar
Zhou, Y. et al. High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells. Nature509, 487–491 (2014). CASPubMed Google Scholar
Parnas, O. et al. A genome-wide CRISPR screen in primary immune cells to dissect regulatory networks. Cell162, 675–686 (2015). CASPubMedPubMed Central Google Scholar
Byrne, S.M., Ortiz, L., Mali, P., Aach, J. & Church, G.M. Multi-kilobase homozygous targeted gene replacement in human induced pluripotent stem cells. Nucleic Acids Res.43, e21 (2015). PubMed Google Scholar
Yin, H. et al. Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype. Nat. Biotechnol.32, 551–553 (2014). CASPubMedPubMed Central Google Scholar
Schumann, K. et al. Generation of knock-in primary human T cells using Cas9 ribonucleoproteins. Proc. Natl. Acad. Sci. USA112, 10437–10442 (2015). CASPubMedPubMed Central Google Scholar
Lin, S., Staahl, B.T., Alla, R.K. & Doudna, J.A. Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery. Elife3, e04766 (2014). PubMedPubMed Central Google Scholar
Holkers, M. et al. Adenoviral vector DNA for accurate genome editing with engineered nucleases. Nat. Methods11, 1051–1057 (2014). CASPubMed Google Scholar
Kaulich, M. et al. Efficient CRISPR-rAAV engineering of endogenous genes to study protein function by allele-specific RNAi. Nucleic Acids Res.43, e45 (2015). PubMedPubMed Central Google Scholar
Hendel, A. et al. Quantifying genome-editing outcomes at endogenous loci with SMRT sequencing. Cell Rep.7, 293–305 (2014). CASPubMedPubMed Central Google Scholar
Chu, V.T. et al. Increasing the efficiency of homology-directed repair for CRISPR-Cas9–induced precise gene editing in mammalian cells. Nat. Biotechnol.33, 543–548 (2015). CASPubMed Google Scholar
Maruyama, T. et al. Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining. Nat. Biotechnol.33, 538–542 (2015). CASPubMedPubMed Central Google Scholar
Sánchez-Rivera, F.J. et al. Rapid modelling of cooperating genetic events in cancer through somatic genome editing. Nature516, 428–431 (2014). PubMedPubMed Central Google Scholar
Chen, Y. et al. Functional disruption of the dystrophin gene in rhesus monkey using CRISPR/Cas9. Hum. Mol. Genet.24, 3764–3774 (2015). CASPubMedPubMed Central Google Scholar
Ablain, J., Durand, E.M., Yang, S., Zhou, Y. & Zon, L.I.A. CRISPR/Cas9 vector system for tissue-specific gene disruption in zebrafish. Dev. Cell32, 756–764 (2015). CASPubMedPubMed Central Google Scholar
Wang, D. et al. Adenovirus-mediated somatic genome editing of Pten by CRISPR/Cas9 in mouse liver in spite of Cas9-specific immune responses. Hum. Gene Ther.26, 432–442 (2015). CASPubMedPubMed Central Google Scholar
Zuckermann, M. et al. Somatic CRISPR/Cas9-mediated tumour suppressor disruption enables versatile brain tumour modelling. Nat. Commun.6, 7391 (2015). CASPubMed Google Scholar
Sánchez-Rivera, F.J. & Jacks, T. Applications of the CRISPR-Cas9 system in cancer biology. Nat. Rev. Cancer15, 387–395 (2015). PubMedPubMed Central Google Scholar
Wang, G. et al. Modeling the mitochondrial cardiomyopathy of Barth syndrome with induced pluripotent stem cell and heart-on-chip technologies. Nat. Med.20, 616–623 (2014). CASPubMedPubMed Central Google Scholar
Chen, S. et al. Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis. Cell160, 1246–1260 (2015). CASPubMedPubMed Central Google Scholar
Maddalo, D. et al. In vivo engineering of oncogenic chromosomal rearrangements with the CRISPR/Cas9 system. Nature516, 423–427 (2014). CASPubMedPubMed Central Google Scholar
Blasco, R.B. et al. Simple and rapid in vivo generation of chromosomal rearrangements using CRISPR/Cas9 technology. Cell Rep.9, 1219–1227 (2014). CASPubMed Google Scholar
Gersbach, C.A. Technologies and applications for programmable gene regulation and epigenome editing. Nat. Methods (in the press).
Li, H.L. et al. Precise correction of the dystrophin gene in Duchenne muscular dystrophy patient induced pluripotent stem cells by TALEN and CRISPR-Cas9. Stem Cell Reports4, 143–154 (2015). CASPubMed Google Scholar
Park, C.-Y. et al. Functional correction of large factor VIII gene chromosomal inversions in hemophilia A patient-derived iPSCs using CRISPR-Cas9. Cell Stem Cell17, 213–220 (2015). CASPubMed Google Scholar
Gori, J.L. et al. Delivery and specificity of CRISPR-Cas9 genome editing technologies for human gene therapy. Hum. Gene Ther.26, 443–451 (2015). CASPubMed Google Scholar
Wu, Z., Yang, H. & Colosi, P. Effect of genome size on AAV vector packaging. Mol. Ther.18, 80–86 (2010). CASPubMed Google Scholar
Hou, Z. et al. Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis. Proc. Natl. Acad. Sci. USA110, 15644–15649 (2013). CASPubMedPubMed Central Google Scholar
Zhang, Y. et al. Processing-independent CRISPR RNAs limit natural transformation in Neisseria meningitidis. Mol. Cell50, 488–503 (2013). CASPubMedPubMed Central Google Scholar
Ran, F.A. et al. In vivo genome editing using Staphylococcus aureus Cas9. Nature520, 186–191 (2015).This study defined the critical components required for efficient DSB formation by the compact type II-AS. aureusCas9.S. aureusCas9 and its sgRNA were packaged in a single AAV, which permitted efficientin vivogenome editing in mouse liver. CASPubMedPubMed Central Google Scholar
Hacein-Bey-Abina, S. et al. Insertional oncogenesis in 4 patients after retrovirus-mediated gene therapy of SCID-X1. J. Clin. Invest.118, 3132–3142 (2008). CASPubMedPubMed Central Google Scholar
Stein, S. et al. Genomic instability and myelodysplasia with monosomy 7 consequent to EVI1 activation after gene therapy for chronic granulomatous disease. Nat. Med.16, 198–204 (2010). CASPubMed Google Scholar
Sternberg, S.H., Redding, S., Jinek, M., Greene, E.C. & Doudna, J.A. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature507, 62–67 (2014).Thisin vitrostudy combined single-molecule analysis and biochemical assays to provide mechanistic insights into Cas9-sgRNA–mediated DNA recognition and cleavage. CASPubMedPubMed Central Google Scholar
Szczelkun, M.D. et al. Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes. Proc. Natl. Acad. Sci. USA111, 9798–9803 (2014). CASPubMedPubMed Central Google Scholar
Wu, X. et al. Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat. Biotechnol.32, 670–676 (2014). CASPubMedPubMed Central Google Scholar
Anders, C., Niewoehner, O., Duerst, A. & Jinek, M. Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature513, 569–573 (2014).This co-crystal structure of the SpCas9-sgRNA-target DNA complex defined the critical residues involved in PAM recognition by SpCas9. CASPubMedPubMed Central Google Scholar
Jinek, M. et al. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science343, 1247997 (2014). PubMedPubMed Central Google Scholar
Nishimasu, H. et al. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell156, 935–949 (2014).This co-crystal structure of the SpCas9-sgRNA-target DNA complex provided the first high-resolution picture of guide-target heteroduplex formation in the context of SpCas9 recognition. CASPubMedPubMed Central Google Scholar
Jiang, F., Zhou, K., Ma, L., Gressel, S. & Doudna, J.A. A Cas9–guide RNA complex preorganized for target DNA recognition. Science348, 1477–1481 (2015). CASPubMed Google Scholar
Hsu, P.D. et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat. Biotechnol.31, 827–832 (2013).This study was one of the first to systematically evaluate the potential for SpCas9 to tolerate mismatches between the guide sequence and near-cognate genomic sequences. It demonstrated that multiple mismatches can be tolerated at some loci. CASPubMedPubMed Central Google Scholar
Fu, Y. et al. High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat. Biotechnol.31, 822–826 (2013).This study was one of the first to systematically evaluate the potential for SpCas9 to tolerate mismatches between the guide sequence and near-cognate genomic sequences. It demonstrated that for some guides, up to five mismatches can be tolerated. CASPubMedPubMed Central Google Scholar
Chari, R., Mali, P., Moosburner, M. & Church, G.M. Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach. Nat. Methods12, 823–826 (2015). CASPubMedPubMed Central Google Scholar
Kuscu, C., Arslan, S., Singh, R., Thorpe, J. & Adli, M. Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease. Nat. Biotechnol.32, 677–683 (2014). CASPubMed Google Scholar
Zhang, Y. et al. Comparison of non-canonical PAMs for CRISPR/Cas9-mediated DNA cleavage in human cells. Sci. Rep.4, 5405 (2014). PubMedPubMed Central Google Scholar
Mali, P. et al. CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat. Biotechnol.31, 833–838 (2013). CASPubMedPubMed Central Google Scholar
Gasiunas, G., Barrangou, R., Horvath, P. & Siksnys, V. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc. Natl. Acad. Sci. USA109, E2579–E2586 (2012). CASPubMedPubMed Central Google Scholar
Gagnon, J.A. et al. Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs. PLoS ONE9, e98186 (2014). PubMedPubMed Central Google Scholar
Doench, J.G. et al. Rational design of highly active sgRNAs for CRISPR-Cas9–mediated gene inactivation. Nat. Biotechnol.32, 1262–1267 (2014). CASPubMedPubMed Central Google Scholar
Farboud, B. & Meyer, B.J. Dramatic enhancement of genome editing by CRISPR/Cas9 through improved guide RNA design. Genetics199, 959–971 (2015). CASPubMedPubMed Central Google Scholar
Montague, T.G., Cruz, J.M., Gagnon, J.A., Church, G.M. & Valen, E. CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic Acids Res.42, W401–W407 (2014). CASPubMedPubMed Central Google Scholar
Moreno-Mateos, M.A. et al. CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nat. Methods12, 982–988 (2015). CASPubMedPubMed Central Google Scholar
Pattanayak, V. et al. High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat. Biotechnol.31, 839–843 (2013). CASPubMedPubMed Central Google Scholar
Lin, Y. et al. CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences. Nucleic Acids Res.42, 7473–7485 (2014). CASPubMedPubMed Central Google Scholar
Smith, C. et al. Whole-genome sequencing analysis reveals high specificity of CRISPR/Cas9 and TALEN-based genome editing in human iPSCs. Cell Stem Cell15, 12–13 (2014). CASPubMedPubMed Central Google Scholar
Veres, A. et al. Low incidence of off-target mutations in individual CRISPR-Cas9 and TALEN targeted human stem cell clones detected by whole-genome sequencing. Cell Stem Cell15, 27–30 (2014). CASPubMedPubMed Central Google Scholar
Kim, D. et al. Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells. Nat. Methods12, 237–243 (2015). CASPubMed Google Scholar
Tsai, S.Q. & Joung, J.K. What's changed with genome editing? Cell Stem Cell15, 3–4 (2014). CASPubMed Google Scholar
Iyer, V. et al. Off-target mutations are rare in Cas9-modified mice. Nat. Methods12, 479 (2015). CASPubMed Google Scholar
Shen, B. et al. Efficient genome modification by CRISPR-Cas9 nickase with minimal off-target effects. Nat. Methods11, 399–402 (2014). CASPubMed Google Scholar
Varshney, G.K. et al. High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9. Genome Res.25, 1030–1042 (2015). CASPubMedPubMed Central Google Scholar
Zhu, L.J., Holmes, B.R., Aronin, N. & Brodsky, M.H. CRISPRseek: a Bioconductor package to identify target-specific guide RNAs for CRISPR-Cas9 genome-editing systems. PLoS ONE9, e108424 (2014). PubMedPubMed Central Google Scholar
Bae, S., Park, J. & Kim, J.-S. Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics30, 1473–1475 (2014). CASPubMedPubMed Central Google Scholar
Cradick, T.J., Qiu, P., Lee, C.M., Fine, E.J. & Bao, G. COSMID: a web-based tool for identifying and validating CRISPR/Cas off-target sites. Mol. Ther. Nucleic Acids3, e214 (2014). CASPubMedPubMed Central Google Scholar
Singh, R., Kuscu, C., Quinlan, A., Qi, Y. & Adli, M. Cas9-chromatin binding information enables more accurate CRISPR off-target prediction. Nucleic Acids Res.43, e118 (2015). PubMedPubMed Central Google Scholar
Aach, J., Mali, P. & Church, G.M. CasFinder: flexible algorithm for identifying specific Cas9 targets in genomes. bioRxiv doi:10.1101/005074 (2014).
Heigwer, F., Kerr, G. & Boutros, M. E-CRISP: fast CRISPR target site identification. Nat. Methods11, 122–123 (2014). CASPubMed Google Scholar
Sander, J.D. et al. ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool. Nucleic Acids Res.38, W462–W468 (2010). CASPubMedPubMed Central Google Scholar
Xiao, A. et al. CasOT: a genome-wide Cas9/gRNA off-target searching tool. Bioinformatics30, 1180–1182 (2014). CASPubMed Google Scholar
Tsai, S.Q. et al. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat. Biotechnol.33, 187–197 (2015). CASPubMed Google Scholar
Frock, R.L. et al. Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases. Nat. Biotechnol.33, 179–186 (2015). CASPubMed Google Scholar
Wang, X. et al. Unbiased detection of off-target cleavage by CRISPR-Cas9 and TALENs using integrase-defective lentiviral vectors. Nat. Biotechnol.33, 175–178 (2015). CASPubMed Google Scholar
Crosetto, N. et al. Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing. Nat. Methods10, 361–365 (2013). CASPubMedPubMed Central Google Scholar
Gabriel, R. et al. An unbiased genome-wide analysis of zinc-finger nuclease specificity. Nat. Biotechnol.29, 816–823 (2011). CASPubMed Google Scholar
Fu, Y., Sander, J.D., Reyon, D., Cascio, V.M. & Joung, J.K. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat. Biotechnol.32, 279–284 (2014). CASPubMedPubMed Central Google Scholar
Kim, S., Kim, D., Cho, S.W., Kim, J. & Kim, J.-S. Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins. Genome Res.24, 1012–1019 (2014). CASPubMedPubMed Central Google Scholar
Ramakrishna, S. et al. Gene disruption by cell-penetrating peptide-mediated delivery of Cas9 protein and guide RNA. Genome Res.24, 1020–1027 (2014). CASPubMedPubMed Central Google Scholar
D'Astolfo, D.S. et al. Efficient intracellular delivery of native proteins. Cell161, 674–690 (2015). CASPubMed Google Scholar
Zuris, J.A. et al. Cationic lipid-mediated delivery of proteins enables efficient protein-based genome editing in vitro and in vivo. Nat. Biotechnol.33, 73–80 (2015). CASPubMed Google Scholar
Ran, F.A. et al. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell154, 1380–1389 (2013). CASPubMedPubMed Central Google Scholar
Wyvekens, N., Topkar, V.V., Khayter, C., Joung, J.K. & Tsai, S.Q. Dimeric CRISPR RNA-guided FokI-dCas9 nucleases directed by truncated gRNAs for highly specific genome editing. Hum. Gene Ther.26, 425–431 (2015). CASPubMedPubMed Central Google Scholar
Guilinger, J.P., Thompson, D.B. & Liu, D.R. Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification. Nat. Biotechnol.32, 577–582 (2014). CASPubMedPubMed Central Google Scholar
Kleinstiver, B.P. et al. Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature523, 481–485 (2015). PubMedPubMed Central Google Scholar
Bolukbasi, M.F. et al. DNA-binding-domain fusions enhance the targeting range and precision of Cas9. Nat. Methods doi:10.1038/nmeth.3624 (19 October 2015).
Wright, A.V. et al. Rational design of a split-Cas9 enzyme complex. Proc. Natl. Acad. Sci. USA112, 2984–2989 (2015). CASPubMedPubMed Central Google Scholar
Zetsche, B., Volz, S.E. & Zhang, F. A split-Cas9 architecture for inducible genome editing and transcription modulation. Nat. Biotechnol.33, 139–142 (2015). CASPubMed Google Scholar
Nihongaki, Y., Kawano, F., Nakajima, T. & Sato, M. Photoactivatable CRISPR-Cas9 for optogenetic genome editing. Nat. Biotechnol.33, 755–760 (2015). CASPubMed Google Scholar
Truong, D.-J.J. et al. Development of an intein-mediated split-Cas9 system for gene therapy. Nucleic Acids Res.43, 6450–6458 (2015). CASPubMedPubMed Central Google Scholar
Davis, K.M., Pattanayak, V., Thompson, D.B., Zuris, J.A. & Liu, D.R. Small molecule-triggered Cas9 protein with improved genome-editing specificity. Nat. Chem. Biol.11, 316–318 (2015). CASPubMedPubMed Central Google Scholar
Fonfara, I. et al. Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems. Nucleic Acids Res.42, 2577–2590 (2014). CASPubMed Google Scholar
Esvelt, K.M. et al. Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat. Methods10, 1116–1121 (2013). CASPubMedPubMed Central Google Scholar
Zetsche, B. et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell163, 759–771 (2015). CASPubMedPubMed Central Google Scholar
Hendel, A., Fine, E.J., Bao, G. & Porteus, M.H. Quantifying on- and off-target genome editing. Trends Biotechnol.33, 132–140 (2015). CASPubMedPubMed Central Google Scholar
Shi, J. et al. Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains. Nat. Biotechnol.33, 661–667 (2015). CASPubMedPubMed Central Google Scholar
Kok, F.O. et al. Reverse genetic screening reveals poor correlation between morpholino-induced and mutant phenotypes in zebrafish. Dev. Cell32, 97–108 (2015). CASPubMed Google Scholar
Xiao, A. et al. Chromosomal deletions and inversions mediated by TALENs and CRISPR/Cas in zebrafish. Nucleic Acids Res.41, e141 (2013). CASPubMedPubMed Central Google Scholar
Han, J. et al. Efficient in vivo deletion of a large imprinted lncRNA by CRISPR/Cas9. RNA Biol.11, 829–835 (2014). CASPubMedPubMed Central Google Scholar
Wang, S., Sengel, C., Emerson, M.M. & Cepko, C.L. A gene regulatory network controls the binary fate decision of rod and bipolar cells in the vertebrate retina. Dev. Cell30, 513–527 (2014). PubMedPubMed Central Google Scholar
Hnisz, D. et al. Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers. Mol. Cell58, 362–370 (2015). CASPubMedPubMed Central Google Scholar
Hwang, W.Y. et al. Heritable and precise zebrafish genome editing using a CRISPR-Cas system. PLoS ONE8, e68708 (2013). CASPubMedPubMed Central Google Scholar
Sharma, R. et al. In vivo genome editing of the albumin locus as a platform for protein replacement therapy. Blood126, 1777–1784 (2015). CASPubMedPubMed Central Google Scholar
Schmidt, M. et al. Polyclonal long-term repopulating stem cell clones in a primate model. Blood100, 2737–2743 (2002). CASPubMed Google Scholar
Chiarle, R. et al. Genome-wide translocation sequencing reveals mechanisms of chromosome breaks and rearrangements in B cells. Cell147, 107–119 (2011). CASPubMedPubMed Central Google Scholar
Josephs, E.A. et al. Structure and specificity of the RNA-guided endonuclease Cas9 during DNA interrogation, target binding and cleavage. Nucleic Acids Res.43, 8924–8941 (2015). CASPubMedPubMed Central Google Scholar