Skip to main content

Advertisement

Log in

Abstract

Type II CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR associated proteins) system based on RNA and Cas9 protein is an essential part of adaptive immune systems of bacteria and archaea against invading genetic elements. Both the RNA elements and the protein component of the system can be reprogrammed, making it a powerful and versatile tool for genome engineering in various types of organisms. Compared with other tools in genome editing, the CRISPR/Cas system is characterized by its specificity, simplicity and diversity, and yet the procedure is rapid and cost effective. This review presents the latest developments and methodologies on the applications of Type II CRISPR/Cas system in gene targeted editing. Future prospects of the technology are discussed.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  1. Richter C, Chang J, Fineran P (2012) Function and regulation of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated (Cas) systems. Viruses Basel 4:2291–2311. doi:10.3390/v4102291

    Article  CAS  Google Scholar 

  2. Ishino Y, Shinagawa H, Makino K, Amemura M, Nakata A (1987) Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J Bacteriol 169:5429–5433

    PubMed Central  CAS  PubMed  Google Scholar 

  3. Pourcel C, Salvignol G, Vergnaud G (2005) CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology (Reading, England) 151:653–663. doi:10.1099/mic.0.27437-0

    Article  CAS  Google Scholar 

  4. Bolotin A, Quinquis B, Sorokin A, Ehrlich S (2005) Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology (Reading, England) 151:2551–2561. doi:10.1099/mic.0.28048-0

    Article  CAS  Google Scholar 

  5. Jansen R, Embden J, Gaastra W, Schouls L (2002) Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol 43:1565–1575. doi:10.1046/j.1365-2958.2002.02839.x

    Article  CAS  PubMed  Google Scholar 

  6. Makarova K, Aravind L, Grishin N, Rogozin I, Koonin E (2002) A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. Nucleic Acid Res 30:482–496. doi:10.1093/nar/30.2.482

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  7. Kowalczykowski S (2000) Initiation of genetic recombination and recombination-dependent replication. Trend Biochem Sci 25:156–165. doi:10.1016/S0968-0004(00)01569-3

    Article  CAS  PubMed  Google Scholar 

  8. Brugmans L, Kanaar R, Essers J (2007) Analysis of DNA double-strand break repair pathways in mice. Mutat Res 614:95–108. doi:10.1016/j.mrfmmm.2006.01.022

    Article  CAS  PubMed  Google Scholar 

  9. Sung P, Klein H (2006) Mechanism of homologous recombination: mediators and helicases take on regulatory functions. Nat Rev Mol Cell Biol. doi:10.1038/nrm2008

  10. Bailey S (2008) Telomeres and double-strand breaks—all’s well that “ends” well. Radiat Res 169:1–7. doi:10.1667/RR1197.1

    Article  CAS  PubMed  Google Scholar 

  11. Carlson D, Fahrenkrug S, Hackett P (2012) Targeting DNA with fingers and TALENs. Mol Ther Nucleic Acids 1. doi:10.1038/mtna.2011.5

  12. Lloyd A, Plaisier C, Carroll D (2005) Targeted mutagenesis using zinc-finger nucleases in Arabidopsis. Proc Natl Acad Sci USA. doi:10.1073/pnas.0409339102

  13. Wang J, Friedman G, Doyon Y, Wang N, Li C (2012) Targeted gene addition to a predetermined site in the human genome using a ZFN-based nicking enzyme. Genome Res. doi:10.1101/gr.122879.111

  14. Townsend J, Wright D et al (2009) High-frequency modification of plant genes using engineered zinc-finger nucleases. Nature 459:442–445. doi:10.1038/nature07845

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  15. Carroll D (2011) Zinc-finger nucleases: a panoramic view. Curr Gene Ther 11:2–10

    Article  CAS  PubMed  Google Scholar 

  16. Cathomen T, Joung J (2008) Zinc-finger nucleases: the next generation emerges. Mol Ther. doi:10.1038/mt.2008.114

  17. Hsia KC, Li CL, Yuan HS (2005) Structural and functional insight into sugar-nonspecific nucleases in host defense. Curr Opin Struct Biol 15(1):126–134

    Article  CAS  PubMed  Google Scholar 

  18. Garneau J, Dupuis M et al (2010) The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468:67–71. doi:10.1038/nature09523

    Article  CAS  PubMed  Google Scholar 

  19. Brouns SJ, Jore M et al (2008) Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321:960–964. doi:10.1126/science.1159689

    Article  CAS  PubMed  Google Scholar 

  20. Deltcheva E, Chylinski K et al (2011) CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471:602–607. doi:10.1038/nature09886

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  21. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna J, Charpentier E (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337:816–821. doi:10.1126/science.1225829

    Article  CAS  PubMed  Google Scholar 

  22. Bikard D, Jiang W, Samai P, Hochschild A, Zhang F, Marraffini L (2013) Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acid Res. doi:10.1093/nar/gkt520

  23. Jiang W, Bikard D, Cox D, Zhang F, Marraffini L (2013) RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol 31:233–239. doi:10.1038/nbt.2508

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  24. Mali P, Yang L et al (2013) RNA-guided human genome engineering via Cas9. Science 339:823–826. doi:10.1126/science.1232033

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  25. Cong L, Ran F et al (2013) Multiplex genome engineering using CRISPR/Cas systems. Science 339:819–823. doi:10.1126/science.1231143

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  26. Hsu P, Scott D et al (2013) DNA targeting specificity of RNA-guided Cas9 nucleases. Nat. Biotechnol. doi:10.1038/nbt.2647

  27. Fu Y, Foden J et al. (2013) High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat. Biotechnol. doi:10.1038/nbt.2623

  28. Pattanayak V, Lin S, Guilinger JP, Ma E, Doudna JA, Liu DR (2013) High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat Biotechnol 31(9):839–843

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  29. Hou Z, Y Zhang et al (2013) Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis. P Natl Acad Sci USA 110:15644–15649. doi:10.1073/pnas.1313587110

    Article  CAS  Google Scholar 

  30. Richter H, Randau L, Plagens A (2013) Exploiting CRISPR/Cas: interference mechanisms and applications. Int J Mol Sci 14:14518–14531. doi:10.3390/ijms140714518

    Article  PubMed Central  PubMed  Google Scholar 

  31. Gilbert L, Larson M et al (2013) CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154:442–451. doi:10.1016/j.cell.2013.06.044

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  32. Qi L, Larson M et al (2013) Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152:1173–1183. doi:10.1016/j.cell.2013.02.022

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  33. Certo MT, Ryu B et al (2011) Tracking genome engineering outcome at individual DNA breakpoints. Nat Methods 8:671–676. doi:10.1038/nmeth.1648

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  34. Ran FA, Hsu PD et al (2013) Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 154:1380–1389. doi:10.1016/j.cell.2013.08.021

    Article  CAS  PubMed  Google Scholar 

  35. DiCarlo J, Norville J, Mali P, Rios X, Aach J, Church G (2013) Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acid Res 41:4336–4343. doi:10.1093/nar/gkt135

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  36. Mali P, Aach J et al (2013a) CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat. Biotechnol. doi:10.1038/nbt.2675

  37. Hwang W, Fu Y et al (2013) Efficient genome editing in zebrafish using a CRISP]R-Cas system. Nat Biotechnol 31:227–229. doi:10.1038/nbt.2501

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  38. Cradick T, Fine E, Antico C, Bao G (2013) CRISPR/Cas9 systems targeting β-globin and CCR5 genes have substantial off-target activity. Nucleic acids Res. doi:10.1093/nar/gkt714

  39. Sander JD, Ramirez C et al. (2013) In silico abstraction of zinc finger nuclease cleavage profiles reveals an expanded landscape of off-target sites. Nucleic Acid Res. doi:10.1093/nar/gkt716

  40. Jao L-E, Wente SR, Chen W (2013) Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system. Proc Natl Acad Sci USA 110:13904–13909. doi:10.1073/pnas.1308335110

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  41. Xiao A, Wang Z et al (2013) Chromosomal deletions and inversions mediated by TALENs and CRISPR/Cas in zebrafish. Nucleic Acids Res. doi:10.1093/nar/gkt464

  42. Qiu Z, Liu M et al (2013) High-efficiency and heritable gene targeting in mouse by transcription activator-like effector nucleases. Nucleic Acid Res 41:e120–e120. doi:10.1093/nar/gkt258

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  43. Tzur YB, Friedland AE, Nadarajan S, Church GM, Calarco JA, Colaiácovo MP (2013) Heritable custom genomic modifications in Caenorhabditis elegans via a CRISPR-Cas9 system. Genetics. doi:10.1534/genetics. 113.156075

  44. Gratz SJ, Cummings A et al. (2013) Genome engineering of Drosophila with the CRISPR RNA-guided Cas9 nuclease. Genetics. doi:10.1534/genetics.113.152710

  45. Nekrasov V, Staskawicz B, Weigel D, Jones JD, Kamoun S (2013) Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease. Nat Biotechnol 31:691–693. doi:10.1038/nbt.2655

    Article  CAS  PubMed  Google Scholar 

  46. Shan Q, Wang Y et al (2013) Targeted genome modification of crop plants using a CRISPR-Cas system. Nat Biotechnol 31:686–688

    Article  CAS  PubMed  Google Scholar 

  47. Joung J, Sander J (2013) TALENs: a widely applicable technology for targeted genome editing. Nat Rev Mol Cell Biol 14:49–55. doi:10.1038/nrm3486

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  48. Tzfira T, White C (2005) Towards targeted mutagenesis and gene replacement in plants. Trends Biotechnol 23:567–569. doi:10.1016/j.tibtech.2005.10.002

    Article  CAS  PubMed  Google Scholar 

  49. Miller J, Tan S et al (2011) A TALE nuclease architecture for efficient genome editing. Nat Biotechnol 29:143–148. doi:10.1038/nbt.1755

    Article  CAS  PubMed  Google Scholar 

  50. Petolino J, Worden A et al (2010) Zinc finger nuclease-mediated transgene deletion. Plant Mol Biol 73:617–628. doi:10.1007/s11103-010-9641-4

    Article  CAS  PubMed  Google Scholar 

  51. Carroll D (2012) A CRISPR approach to gene targeting. Mol Ther 20:1658–1660. doi:10.1038/mt.2012.171

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  52. Klug A (2010) The discovery of zinc fingers and their applications in gene regulation and genome manipulation. Annu Rev Biochem 79:213–231. doi:10.1146/annurev-biochem-010909-095056

    Article  CAS  PubMed  Google Scholar 

  53. Beerli R, Barbas C (2002) Engineering polydactyl zinc-finger transcription factors. Nat Biotechnol 20:135–141. doi:10.1038/nbt0202-135

    Article  CAS  PubMed  Google Scholar 

  54. Händel E-M, Alwin S, Cathomen T (2009) Expanding or restricting the target site repertoire of zinc-finger nucleases: the inter-domain linker as a major determinant of target site selectivity. Mol Ther 17:104–111. doi:10.1038/mt.2008.233

    Article  PubMed Central  PubMed  Google Scholar 

  55. Urnov F, Rebar E, Holmes M, Zhang H, Gregory P (2010) Genome editing with engineered zinc finger nucleases. Nat Rev Genet 11:636–646. doi:10.1038/nrg2842

    Article  CAS  PubMed  Google Scholar 

  56. Doyon Y, McCammon J et al (2008) Heritable targeted gene disruption in zebrafish using designed zinc-finger nucleases. Nat Biotechnol 26:702–708. doi:10.1038/nbt1409

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  57. Carbery I, Ji D et al (2010) Targeted genome modification in mice using zinc-finger nucleases. Genetics 186:451–459. doi:10.1534/genetics.110.117002

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  58. Rogers C, Hsu P et al (2008) Disruption of the CFTR gene produces a model of cystic fibrosis in newborn pigs. Science 321:1837–1841. doi:10.1126/science.1163600

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  59. Wood AJ, Lo T et al (2011) Targeted genome editing across species using ZFNs and TALENs. Science 333:307. doi:10.1126/science.1207773

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  60. Takasu Y, Kobayashi I et al (2010) Targeted mutagenesis in the silkworm Bombyx mori using zinc finger nuclease mRNA injection. Insect Biochem Mol Biol 40:759–765. doi:10.1016/j.ibmb.2010.07.012

    Article  CAS  PubMed  Google Scholar 

  61. Takasu Y, Kobayashi I et al (2010) Targeted mutagenesis in the silkworm Bombyx mori using zinc finger nuclease mRNA injection. Insect Biochem Mol Biol 40:759–765. doi:10.1016/j.ibmb.2010.07.012

    Article  CAS  PubMed  Google Scholar 

  62. Perez E, Wang J et al (2008) Establishment of HIV-1 resistance in CD4+ T cells by genome editing using zinc-finger nucleases. Nat Biotechnol 26:808–816. doi:10.1038/nbt1410

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  63. Ramirez CL, Foley J et al (2008) Unexpected failure rates for modular assembly of engineered zinc fingers. Nat Methods 5:374–375. doi:10.1038/nmeth0508-3746

    Article  CAS  PubMed  Google Scholar 

  64. Li T, Huang S et al (2011) Modularly assembled designer TAL effector nucleases for targeted gene knockout and gene replacement in eukaryotes. Nucleic Acid Res 39:6315–6325. doi:10.1093/nar/gkr188

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  65. Doyle EL, Booher N et al (2012) TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction. Nucleic Acid Res 40. doi:10.1093/nar/gks608

  66. Maeder M, Thibodeau-Beganny S et al (2008) Rapid “open-source” engineering of customized zinc-finger nucleases for highly efficient gene modification. Mol Cell 31:294–301. doi:10.1016/j.molcel.2008.06.016

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  67. Sander J, Cade L, Khayter C, Reyon D (2011a) Targeted gene disruption in somatic zebrafish cells using engineered TALENs. Nat. Biotechnol. doi:10.1038/nbt.1934

  68. Sander J, Dahlborg E et al (2011) Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA). Nat Methods 8:67–69. doi:10.1038/nmeth.1542

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  69. Boch J, Bonas U (2010) Xanthomonas Avr Bs3 family-type III effectors: discovery and function. Annu Rev Phytopathol 48:419–436. doi:10.1146/annurev-phyto-080508-081936

    Article  CAS  PubMed  Google Scholar 

  70. Römer P, Hahn S, Jordan T, Strauß T, Bonas U, Lahaye T (2007) Plant pathogen recognition mediated by promoter activation of the pepper Bs3 resistance gene. Science 318:645–648. doi:10.1126/science.1144958

    Article  PubMed  Google Scholar 

  71. Kay S, Bonas U (2009) How Xanthomonas type III effectors manipulate the host plant. Curr Opin Microbiol 12:37–43. doi:10.1016/j.mib.2008.12.006

    Article  CAS  PubMed  Google Scholar 

  72. Moscou M, Bogdanove A (2009) A simple cipher governs DNA recognition by TAL effectors. Science. doi:10.1126/science.1178817

  73. Bogdanove AJ, Voytas DF (2011) TAL effectors: customizable proteins for DNA targeting. Science 333:1843–1846. doi:10.1126/science.1204094

    Article  CAS  PubMed  Google Scholar 

  74. Cui X, Ji D, Fisher D, Wu Y, Briner D, Weinstein E (2011) Targeted integration in rat and mouse embryos with zinc-finger nucleases. Nat Biotechnol 29:64–67. doi:10.1038/nbt.1731

    Article  CAS  PubMed  Google Scholar 

  75. Hauschild J, Petersen B et al (2011) Efficient generation of a biallelic knockout in pigs using zinc-finger nucleases. Proc Natl Acad Sci USA 108:12013–12017. doi:10.1073/pnas.1106422108

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  76. Hockemeyer D, Wang H et al (2011) Genetic engineering of human pluripotent cells using TALE nucleases. Nat Biotechnol 29:731–734. doi:10.1038/nbt.1927

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  77. Li T, Liu B, Spalding M, Weeks D, Yang B (2012) High-efficiency TALEN-based gene editing produces disease-resistant rice. Nat Biotechnol 30:390–392. doi:10.1038/nbt.2199

    Article  CAS  PubMed  Google Scholar 

  78. Stoddard B (2011) Homing endonucleases: from microbial genetic invaders to reagents for targeted DNA modification. Structure 19:7–15. doi:10.1016/j.str.2010.12.003

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  79. Ellis B, Hirsch M, Porter S, Samulski R, Porteus M (2013) Zinc-finger nuclease-mediated gene correction using single AAV vector transduction and enhancement by Food and Drug Administration-approved drugs. Gene Ther 20:35–42. doi:10.1038/gt.2011.211

    Article  CAS  PubMed  Google Scholar 

  80. Chen S, Oikonomou G et al (2013) A large-scale in vivo analysis reveals that TALENs are significantly more mutagenic than ZFNs generated using context-dependent assembly. Nucleic Acid Res 41:2769–2778. doi:10.1093/nar/gks1356

    Article  PubMed Central  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This work was supported by Guangdong Natural Science Foundation of China (S2011010004264, 05003328), Guangdong Science and Technology Program (No. 2008B020100001), National Natural Science Foundation of China (No. 30370799), Open Fund of MOE Key Laboratory of Aquatic Product Safety, Open Fund of Laboratory at Sun Yat-sen University (KF201328), Wen’s Group (wens-kjhz-2007-03-09-01), The Genetics Teaching Group Project of Guangdong Province to Q. Liu, and NSFC(J1310025) to the School of Life Sciences at SYSU. The authors are grateful to Ms. Yan Shi for proofreading and anonymous reviewers for valuable suggestions.

Conflict of interest

The authors declare no conflict of interest.

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Shengchun Guo, Zhining Li or Qiuyun Liu.

Additional information

Ying Lv, Yuxiang Lin, Kaixuan Lin, Peng Peng and Yangxiu Wu have contributed equally to this work.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Guo, S., Lv, Y., Lin, Y. et al. CRISPR/Cas9 Systems: The Next Generation Gene Targeted Editing Tool. Proc. Natl. Acad. Sci., India, Sect. B Biol. Sci. 85, 377–387 (2015). https://doi.org/10.1007/s40011-014-0362-3

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s40011-014-0362-3

Keywords

Navigation