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Creating and evaluating accurate CRISPR-Cas9 scalpels for genomic surgery

Abstract

The simplicity of site-specific genome targeting by type II clustered, regularly interspaced, short palindromic repeat (CRISPR)-Cas9 nucleases, along with their robust activity profile, has changed the landscape of genome editing. These favorable properties have made the CRISPR-Cas9 system the technology of choice for sequence-specific modifications in vertebrate systems. For many applications, whether the focus is on basic science investigations or therapeutic efficacy, activity and precision are important considerations when one is choosing a nuclease platform, target site and delivery method. Here we review recent methods for increasing the activity and accuracy of Cas9 and assessing the extent of off-target cleavage events.

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Figure 1: Structural overview of SpCas9.
Figure 2: Stages of target-site recognition by Cas9.
Figure 3: Schematic of SpCas9-sgRNA variants with improved precision.

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References

  1. 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).

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Makarova, K.S. et al. An updated evolutionary classification of CRISPR-Cas systems. Nat. Rev. Microbiol. 13, 722–736 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  3. Sontheimer, E.J. & Barrangou, R. The bacterial origins of the CRISPR genome-editing revolution. Hum. Gene Ther. 26, 413–424 (2015).

    CAS  PubMed  Google Scholar 

  4. Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012).This study describes the minimal components required to program a type II CRISPR-Cas9 system for targeted DNA cleavage in vitro and demonstrates that crRNA and tracrRNA can be joined into an sgRNA to generate a two-component system for site-specific editing.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Urnov, F.D., Rebar, E.J., Holmes, M.C., Zhang, H.S. & Gregory, P.D. Genome editing with engineered zinc finger nucleases. Nat. Rev. Genet. 11, 636–646 (2010).

    CAS  PubMed  Google Scholar 

  6. Joung, J.K. & Sander, J.D. TALENs: a widely applicable technology for targeted genome editing. Nat. Rev. Mol. Cell Biol. 14, 49–55 (2013).

    CAS  PubMed  Google Scholar 

  7. Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 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.

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Mali, P. et al. RNA-guided human genome engineering via Cas9. Science 339, 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.

    CAS  PubMed  PubMed Central  Google Scholar 

  9. 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.

    CAS  PubMed  Google Scholar 

  10. Jinek, M. et al. RNA-programmed genome editing in human cells. Elife 2, 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.

    Article  PubMed  PubMed Central  Google Scholar 

  11. Wang, H. et al. One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell 153, 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.

    CAS  PubMed  PubMed Central  Google Scholar 

  12. 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.

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Chen, B. et al. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 155, 1479–1491 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Ledford, H. CRISPR, the disruptor. Nature 522, 20–24 (2015).

    CAS  PubMed  Google Scholar 

  15. Doudna, J.A. & Charpentier, E. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science 346, 1258096 (2014).

    PubMed  Google Scholar 

  16. Cox, D.B.T., Platt, R.J. & Zhang, F. Therapeutic genome editing: prospects and challenges. Nat. Med. 21, 121–131 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Jao, L.-E., Wente, S.R. & Chen, W. Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system. Proc. Natl. Acad. Sci. USA 110, 13904–13909 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Swiech, L. et al. In vivo interrogation of gene function in the mammalian brain using CRISPR-Cas9. Nat. Biotechnol. 33, 102–106 (2015).

    CAS  PubMed  Google Scholar 

  19. 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).

    PubMed  PubMed Central  Google Scholar 

  20. Mandal, P.K. et al. Efficient ablation of genes in human hematopoietic stem and effector cells using CRISPR/Cas9. Cell Stem Cell 15, 643–652 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Tsai, S.Q. et al. Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing. Nat. Biotechnol. 32, 569–576 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Hendel, A. et al. Chemically modified guide RNAs enhance CRISPR-Cas genome editing in human primary cells. Nat. Biotechnol. 33, 985–989 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Yang, H. et al. One-step generation of mice carrying reporter and conditional alleles by CRISPR/Cas-mediated genome engineering. Cell 154, 1370–1379 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  24. 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).

    PubMed  PubMed Central  Google Scholar 

  25. Lupiáñez, D.G. et al. Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell 161, 1012–1025 (2015).

    PubMed  PubMed Central  Google Scholar 

  26. Torres, R. et al. Engineering human tumour-associated chromosomal translocations with the RNA-guided CRISPR-Cas9 system. Nat. Commun. 5, 3964 (2014).

    CAS  PubMed  Google Scholar 

  27. Choi, P.S. & Meyerson, M. Targeted genomic rearrangements using CRISPR/Cas technology. Nat. Commun. 5, 3728 (2014).

    CAS  PubMed  Google Scholar 

  28. Ghezraoui, H. et al. Chromosomal translocations in human cells are generated by canonical nonhomologous end-joining. Mol. Cell 55, 829–842 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  29. 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).

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Wang, T., Wei, J.J., Sabatini, D.M. & Lander, E.S. Genetic screens in human cells using the CRISPR-Cas9 system. Science 343, 80–84 (2014).

    CAS  PubMed  Google Scholar 

  31. Shalem, O. et al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 343, 84–87 (2014).

    CAS  PubMed  Google Scholar 

  32. 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).

    CAS  PubMed  Google Scholar 

  33. Zhou, Y. et al. High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells. Nature 509, 487–491 (2014).

    CAS  PubMed  Google Scholar 

  34. Platt, R.J. et al. CRISPR-Cas9 knockin mice for genome editing and cancer modeling. Cell 159, 440–455 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Parnas, O. et al. A genome-wide CRISPR screen in primary immune cells to dissect regulatory networks. Cell 162, 675–686 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  36. 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 

  37. Yang, L. et al. Optimization of scarless human stem cell genome editing. Nucleic Acids Res. 41, 9049–9061 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Yin, H. et al. Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype. Nat. Biotechnol. 32, 551–553 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  39. Schumann, K. et al. Generation of knock-in primary human T cells using Cas9 ribonucleoproteins. Proc. Natl. Acad. Sci. USA 112, 10437–10442 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Lin, S., Staahl, B.T., Alla, R.K. & Doudna, J.A. Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery. Elife 3, e04766 (2014).

    PubMed  PubMed Central  Google Scholar 

  41. Holkers, M. et al. Adenoviral vector DNA for accurate genome editing with engineered nucleases. Nat. Methods 11, 1051–1057 (2014).

    CAS  PubMed  Google Scholar 

  42. 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).

    PubMed  PubMed Central  Google Scholar 

  43. Hendel, A. et al. Quantifying genome-editing outcomes at endogenous loci with SMRT sequencing. Cell Rep. 7, 293–305 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. 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).

    CAS  PubMed  Google Scholar 

  45. 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).

    CAS  PubMed  PubMed Central  Google Scholar 

  46. Sánchez-Rivera, F.J. et al. Rapid modelling of cooperating genetic events in cancer through somatic genome editing. Nature 516, 428–431 (2014).

    PubMed  PubMed Central  Google Scholar 

  47. Xue, W. et al. CRISPR-mediated direct mutation of cancer genes in the mouse liver. Nature 514, 380–384 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  48. Chen, Y. et al. Functional disruption of the dystrophin gene in rhesus monkey using CRISPR/Cas9. Hum. Mol. Genet. 24, 3764–3774 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  49. 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. Cell 32, 756–764 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  50. 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).

    CAS  PubMed  PubMed Central  Google Scholar 

  51. Zuckermann, M. et al. Somatic CRISPR/Cas9-mediated tumour suppressor disruption enables versatile brain tumour modelling. Nat. Commun. 6, 7391 (2015).

    CAS  PubMed  Google Scholar 

  52. Sánchez-Rivera, F.J. & Jacks, T. Applications of the CRISPR-Cas9 system in cancer biology. Nat. Rev. Cancer 15, 387–395 (2015).

    PubMed  PubMed Central  Google Scholar 

  53. 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).

    CAS  PubMed  PubMed Central  Google Scholar 

  54. Chen, S. et al. Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis. Cell 160, 1246–1260 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  55. Maddalo, D. et al. In vivo engineering of oncogenic chromosomal rearrangements with the CRISPR/Cas9 system. Nature 516, 423–427 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  56. Blasco, R.B. et al. Simple and rapid in vivo generation of chromosomal rearrangements using CRISPR/Cas9 technology. Cell Rep. 9, 1219–1227 (2014).

    CAS  PubMed  Google Scholar 

  57. Gersbach, C.A. Technologies and applications for programmable gene regulation and epigenome editing. Nat. Methods (in the press).

  58. 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 Reports 4, 143–154 (2015).

    CAS  PubMed  Google Scholar 

  59. 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 Cell 17, 213–220 (2015).

    CAS  PubMed  Google Scholar 

  60. 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).

    CAS  PubMed  Google Scholar 

  61. Wu, Z., Yang, H. & Colosi, P. Effect of genome size on AAV vector packaging. Mol. Ther. 18, 80–86 (2010).

    CAS  PubMed  Google Scholar 

  62. Hou, Z. et al. Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis. Proc. Natl. Acad. Sci. USA 110, 15644–15649 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  63. Zhang, Y. et al. Processing-independent CRISPR RNAs limit natural transformation in Neisseria meningitidis. Mol. Cell 50, 488–503 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  64. Ran, F.A. et al. In vivo genome editing using Staphylococcus aureus Cas9. Nature 520, 186–191 (2015).This study defined the critical components required for efficient DSB formation by the compact type II-A S. aureus Cas9. S. aureus Cas9 and its sgRNA were packaged in a single AAV, which permitted efficient in vivo genome editing in mouse liver.

    CAS  PubMed  PubMed Central  Google Scholar 

  65. 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).

    CAS  PubMed  PubMed Central  Google Scholar 

  66. 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).

    CAS  PubMed  Google Scholar 

  67. Sternberg, S.H., Redding, S., Jinek, M., Greene, E.C. & Doudna, J.A. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 507, 62–67 (2014).This in vitro study combined single-molecule analysis and biochemical assays to provide mechanistic insights into Cas9-sgRNA–mediated DNA recognition and cleavage.

    CAS  PubMed  PubMed Central  Google Scholar 

  68. Szczelkun, M.D. et al. Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes. Proc. Natl. Acad. Sci. USA 111, 9798–9803 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  69. Wu, X. et al. Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat. Biotechnol. 32, 670–676 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  70. Anders, C., Niewoehner, O., Duerst, A. & Jinek, M. Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature 513, 569–573 (2014).This co-crystal structure of the SpCas9-sgRNA-target DNA complex defined the critical residues involved in PAM recognition by SpCas9.

    CAS  PubMed  PubMed Central  Google Scholar 

  71. Jinek, M. et al. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science 343, 1247997 (2014).

    PubMed  PubMed Central  Google Scholar 

  72. Nishimasu, H. et al. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell 156, 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.

    CAS  PubMed  PubMed Central  Google Scholar 

  73. Jiang, F., Zhou, K., Ma, L., Gressel, S. & Doudna, J.A. A Cas9–guide RNA complex preorganized for target DNA recognition. Science 348, 1477–1481 (2015).

    CAS  PubMed  Google Scholar 

  74. 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.

    CAS  PubMed  PubMed Central  Google Scholar 

  75. 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.

    CAS  PubMed  PubMed Central  Google Scholar 

  76. Chari, R., Mali, P., Moosburner, M. & Church, G.M. Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach. Nat. Methods 12, 823–826 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  77. 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).

    CAS  PubMed  Google Scholar 

  78. Zhang, Y. et al. Comparison of non-canonical PAMs for CRISPR/Cas9-mediated DNA cleavage in human cells. Sci. Rep. 4, 5405 (2014).

    PubMed  PubMed Central  Google Scholar 

  79. Mali, P. et al. CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat. Biotechnol. 31, 833–838 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  80. 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. USA 109, E2579–E2586 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  81. Gagnon, J.A. et al. Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs. PLoS ONE 9, e98186 (2014).

    PubMed  PubMed Central  Google Scholar 

  82. Doench, J.G. et al. Rational design of highly active sgRNAs for CRISPR-Cas9–mediated gene inactivation. Nat. Biotechnol. 32, 1262–1267 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  83. Farboud, B. & Meyer, B.J. Dramatic enhancement of genome editing by CRISPR/Cas9 through improved guide RNA design. Genetics 199, 959–971 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  84. Xu, H. et al. Sequence determinants of improved CRISPR sgRNA design. Genome Res. 25, 1147–1157 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  85. 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).

    CAS  PubMed  PubMed Central  Google Scholar 

  86. Moreno-Mateos, M.A. et al. CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nat. Methods 12, 982–988 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  87. Pattanayak, V. et al. High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat. Biotechnol. 31, 839–843 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  88. 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).

    CAS  PubMed  PubMed Central  Google Scholar 

  89. Smith, C. et al. Whole-genome sequencing analysis reveals high specificity of CRISPR/Cas9 and TALEN-based genome editing in human iPSCs. Cell Stem Cell 15, 12–13 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  90. 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 Cell 15, 27–30 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  91. Kim, D. et al. Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells. Nat. Methods 12, 237–243 (2015).

    CAS  PubMed  Google Scholar 

  92. Tsai, S.Q. & Joung, J.K. What's changed with genome editing? Cell Stem Cell 15, 3–4 (2014).

    CAS  PubMed  Google Scholar 

  93. Iyer, V. et al. Off-target mutations are rare in Cas9-modified mice. Nat. Methods 12, 479 (2015).

    CAS  PubMed  Google Scholar 

  94. Shen, B. et al. Efficient genome modification by CRISPR-Cas9 nickase with minimal off-target effects. Nat. Methods 11, 399–402 (2014).

    CAS  PubMed  Google Scholar 

  95. Varshney, G.K. et al. High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9. Genome Res. 25, 1030–1042 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  96. 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 ONE 9, e108424 (2014).

    PubMed  PubMed Central  Google Scholar 

  97. 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. Bioinformatics 30, 1473–1475 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  98. 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 Acids 3, e214 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  99. 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).

    PubMed  PubMed Central  Google Scholar 

  100. Aach, J., Mali, P. & Church, G.M. CasFinder: flexible algorithm for identifying specific Cas9 targets in genomes. bioRxiv doi:10.1101/005074 (2014).

  101. Heigwer, F., Kerr, G. & Boutros, M. E-CRISP: fast CRISPR target site identification. Nat. Methods 11, 122–123 (2014).

    CAS  PubMed  Google Scholar 

  102. Sander, J.D. et al. ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool. Nucleic Acids Res. 38, W462–W468 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  103. Xiao, A. et al. CasOT: a genome-wide Cas9/gRNA off-target searching tool. Bioinformatics 30, 1180–1182 (2014).

    CAS  PubMed  Google Scholar 

  104. 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).

    CAS  PubMed  Google Scholar 

  105. Frock, R.L. et al. Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases. Nat. Biotechnol. 33, 179–186 (2015).

    CAS  PubMed  Google Scholar 

  106. 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).

    CAS  PubMed  Google Scholar 

  107. Crosetto, N. et al. Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing. Nat. Methods 10, 361–365 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  108. Gabriel, R. et al. An unbiased genome-wide analysis of zinc-finger nuclease specificity. Nat. Biotechnol. 29, 816–823 (2011).

    CAS  PubMed  Google Scholar 

  109. 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).

    CAS  PubMed  PubMed Central  Google Scholar 

  110. 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).

    CAS  PubMed  PubMed Central  Google Scholar 

  111. Ramakrishna, S. et al. Gene disruption by cell-penetrating peptide-mediated delivery of Cas9 protein and guide RNA. Genome Res. 24, 1020–1027 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  112. D'Astolfo, D.S. et al. Efficient intracellular delivery of native proteins. Cell 161, 674–690 (2015).

    CAS  PubMed  Google Scholar 

  113. 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).

    CAS  PubMed  Google Scholar 

  114. Ran, F.A. et al. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 154, 1380–1389 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  115. 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).

    CAS  PubMed  PubMed Central  Google Scholar 

  116. 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).

    CAS  PubMed  PubMed Central  Google Scholar 

  117. Kleinstiver, B.P. et al. Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature 523, 481–485 (2015).

    PubMed  PubMed Central  Google Scholar 

  118. 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).

  119. Wright, A.V. et al. Rational design of a split-Cas9 enzyme complex. Proc. Natl. Acad. Sci. USA 112, 2984–2989 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  120. Zetsche, B., Volz, S.E. & Zhang, F. A split-Cas9 architecture for inducible genome editing and transcription modulation. Nat. Biotechnol. 33, 139–142 (2015).

    CAS  PubMed  Google Scholar 

  121. Nihongaki, Y., Kawano, F., Nakajima, T. & Sato, M. Photoactivatable CRISPR-Cas9 for optogenetic genome editing. Nat. Biotechnol. 33, 755–760 (2015).

    CAS  PubMed  Google Scholar 

  122. Truong, D.-J.J. et al. Development of an intein-mediated split-Cas9 system for gene therapy. Nucleic Acids Res. 43, 6450–6458 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  123. 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).

    CAS  PubMed  PubMed Central  Google Scholar 

  124. 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).

    CAS  PubMed  Google Scholar 

  125. Esvelt, K.M. et al. Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat. Methods 10, 1116–1121 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  126. Zetsche, B. et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163, 759–771 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  127. Hendel, A., Fine, E.J., Bao, G. & Porteus, M.H. Quantifying on- and off-target genome editing. Trends Biotechnol. 33, 132–140 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  128. Shi, J. et al. Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains. Nat. Biotechnol. 33, 661–667 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  129. Kok, F.O. et al. Reverse genetic screening reveals poor correlation between morpholino-induced and mutant phenotypes in zebrafish. Dev. Cell 32, 97–108 (2015).

    CAS  PubMed  Google Scholar 

  130. Xiao, A. et al. Chromosomal deletions and inversions mediated by TALENs and CRISPR/Cas in zebrafish. Nucleic Acids Res. 41, e141 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  131. Han, J. et al. Efficient in vivo deletion of a large imprinted lncRNA by CRISPR/Cas9. RNA Biol. 11, 829–835 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  132. 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. Cell 30, 513–527 (2014).

    PubMed  PubMed Central  Google Scholar 

  133. Chen, S. et al. Global microRNA depletion suppresses tumor angiogenesis. Genes Dev. 28, 1054–1067 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  134. Hnisz, D. et al. Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers. Mol. Cell 58, 362–370 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  135. Bedell, V.M. et al. In vivo genome editing using a high-efficiency TALEN system. Nature 491, 114–118 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  136. Hwang, W.Y. et al. Heritable and precise zebrafish genome editing using a CRISPR-Cas system. PLoS ONE 8, e68708 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  137. Sharma, R. et al. In vivo genome editing of the albumin locus as a platform for protein replacement therapy. Blood 126, 1777–1784 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  138. Schmidt, M. et al. Polyclonal long-term repopulating stem cell clones in a primate model. Blood 100, 2737–2743 (2002).

    CAS  PubMed  Google Scholar 

  139. Chiarle, R. et al. Genome-wide translocation sequencing reveals mechanisms of chromosome breaks and rearrangements in B cells. Cell 147, 107–119 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  140. 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).

    CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We apologize for the omission of references that could not be included in this review because of space constraints. We thank L.J. Zhu for assistance with the calculation of mismatched off-target sites in the genome for a population of sgRNAs. This work was supported by the US National Institutes of Health (grant R01AI117839 to S.A.W. and J. Luban, and grant R01HL093766 to S.A.W. and N. Lawson).

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Correspondence to Scot A Wolfe.

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The authors have filed patent applications related to genome engineering technologies. S.A.W. is a consultant for Editas Medicine.

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Bolukbasi, M., Gupta, A. & Wolfe, S. Creating and evaluating accurate CRISPR-Cas9 scalpels for genomic surgery. Nat Methods 13, 41–50 (2016). https://doi.org/10.1038/nmeth.3684

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