Transgenic Research

, Volume 25, Issue 5, pp 561–573 | Cite as

CRISPR/Cas9: an advanced tool for editing plant genomes

  • Milan Kumar Samanta
  • Avishek Dey
  • Srimonta Gayen
Review

Abstract

To meet current challenges in agriculture, genome editing using sequence-specific nucleases (SSNs) is a powerful tool for basic and applied plant biology research. Here, we describe the principle and application of available genome editing tools, including zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeat associated CRISPR/Cas9 system. Among these SSNs, CRISPR/Cas9 is the most recently characterized and rapidly developing genome editing technology, and has been successfully utilized in a wide variety of organisms. This review specifically illustrates the power of CRISPR/Cas9 as a tool for plant genome engineering, and describes the strengths and weaknesses of the CRISPR/Cas9 technology compared to two well-established genome editing tools, ZFNs and TALENs.

Keywords

Sequence-specific nucleases Genome editing CRISPR/Cas9 TALENs ZFNs Plants 

References

  1. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P (2007) CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:1709–1712CrossRefPubMedGoogle Scholar
  2. Belhaj K, Chaparro-Garcia A, Kamoun S, Patron NJ, Nekrasov V (2015) Editing plant genomes with CRISPR/Cas9. Curr Opin Biotechnol 32:76–84CrossRefPubMedGoogle Scholar
  3. Boch J, Scholze H, Schornack S, Landgraf A, Hahn S, Kay S, Lahaye T, Nickstadt A, Bonas U (2009) Breaking the code of DNA binding specificity of TAL-type III effectors. Science 326:1509–1512CrossRefPubMedGoogle Scholar
  4. Bogdanove AJ, Voytas DF (2011) TAL effectors: customizable proteins for DNA targeting. Science 333:1843–1846CrossRefPubMedGoogle Scholar
  5. Brooks C, Nekrasov V, Lippman ZB, Van Eck J (2014) Efficient gene editing in tomato in the first generation using the clustered regularly interspaced short palindromic repeats/CRISPR-associated9 system. Plant Physiol 166:1292–1297CrossRefPubMedPubMedCentralGoogle Scholar
  6. Brouns SJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJ, Snijders AP, Dickman MJ, Makarova KS, Koonin EV, van der Oost J (2008) Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321:960–964CrossRefPubMedGoogle Scholar
  7. Cai Y, Chen L, Liu X, Sun S, Wu C, Jiang B, Han T, Hou W (2015) CRISPR/Cas9-mediated genome editing in soybean hairy roots. PLoS ONE 10(8):e0136064CrossRefPubMedPubMedCentralGoogle Scholar
  8. Cermak T, Doyle EL, Christian M, Wang L, Zhang Y, Schmidt C, Baller JA, Somia NV, Bogdanove AJ, Voytas DF (2011) Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res 39(12):e82CrossRefPubMedPubMedCentralGoogle Scholar
  9. Cho SW, Kim S, Kim JM, Kim JS (2013) Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat Biotechnol 31:230–232CrossRefPubMedGoogle Scholar
  10. Christian M, Cermak T, Doyle EL, Schmidt C, Zhang F, Hummel A, Bogdanove AJ, Voytas DF (2010) Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186(2):757–761CrossRefPubMedPubMedCentralGoogle Scholar
  11. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F (2013) Multiplex genome engineering using CRISPR/Cas systems. Science 339(6121):819–823CrossRefPubMedPubMedCentralGoogle Scholar
  12. Dianov GL, Hubscher U (2013) Mammalian base excision repair: the forgotten archangel. Nucleic Acids Res 41:3483–3490CrossRefPubMedPubMedCentralGoogle Scholar
  13. Doench JG, Hartenian E, Graham DB, Tothova Z, Hegde M, Smith I, Sullender M, Ebert BL, Xavier RJ, Root DE (2014) Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation. Nat Biotechnol 32(12):1262–1267CrossRefPubMedPubMedCentralGoogle Scholar
  14. Fan D, Liu T, Li C, Jiao B, Li S, Hou Y, Luo K (2015) Efficient CRISPR/Cas9-mediated targeted mutagenesis in populous in the first generation. Sci Rep 5:12217CrossRefPubMedPubMedCentralGoogle Scholar
  15. Fauser F, Schiml S, Puchta H (2014) Both CRISPR/Cas-based nucleases and nickases can be used efficiently for genome engineering in Arabidopsis thaliana. Plant J 79:348–359CrossRefPubMedGoogle Scholar
  16. Feng Z, Zhang B, Ding W, Liu X, Yang DL, Wei P, Cao F, Zhu S, Zhang F, Mao Y, Zhu JK (2013) Efficient genome editing in plants using a CRISPR/Cas system. Cell Res 23(10):1229–1232CrossRefPubMedPubMedCentralGoogle Scholar
  17. Feng Z, Mao Y, Xu N, Zhang B, Wei P, Yang D, Wang Z, Zhang Z, Zheng R, Yang L, Zeng L, Liu X, Zhu JK (2014) Multigeneration analysis reveals the inheritance, specificity, and patterns of CRISPR/Cas-induced gene modifications in Arabidopsis. Proc Natl Acad Sci USA 111(12):4632–4637CrossRefPubMedPubMedCentralGoogle Scholar
  18. Fu Y, Sander JD, Reyon D, Cascio VM, Joung JK (2014) Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat Biotechnol 32:279–284CrossRefPubMedPubMedCentralGoogle Scholar
  19. Fusi N, Smith I, Doench J, Listgarten J (2015) In silico predictive modeling of CRISPR/Cas9 guide efficiency. bioRxiv, http://dx.doi.org/10.1101/021568
  20. Gao J, Wang G, Ma S, Xie X, Wu X, Zhang X, Wu Y, Zhao P, Xia Q (2015) CRISPR/Cas9-mediated targeted mutagenesis in Nicotiana tabacum. Plant Mol Biol 87:99–110CrossRefPubMedGoogle Scholar
  21. Garneau JE, Dupuis ME, Villion M, Romero DA, Barrangou R, Boyaval P, Fremaux C, Horvath P, Magadan AH, Moineau S (2010) The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468(7320):67–71CrossRefPubMedGoogle Scholar
  22. Gasiunas G, Barrangou R, Horvath P, Siksnys V (2012) Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc Natl Acad Sci USA 109:E2579–E2586CrossRefPubMedPubMedCentralGoogle Scholar
  23. Griggs D, Stafford-Smith M, Gaffney O, Rockstrom J, Ohman MC, Shyamsundar P, Steffen W, Glaser G, Kanie N, Noble I (2013) Sustainable development goals for people and planet. Nature 495:305–307CrossRefPubMedGoogle Scholar
  24. Heigwer F, Kerr G, Boutros M (2014) E-CRISP: fast CRISPR target site identification. Nat Methods 11:122–123CrossRefPubMedGoogle Scholar
  25. Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O, Cradicj TJ, Marraffini LA, Bao G, Zhang F (2013) DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol 31(9):827–832CrossRefPubMedPubMedCentralGoogle Scholar
  26. 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(12):5429–5433PubMedPubMedCentralGoogle Scholar
  27. Jacobs TB, LaFayette PR, Schmitz RJ, Parrott WA (2015) Targeted genome modifications in soybean with CRISPR/Cas9. BMC Biotechnol 15:16CrossRefPubMedPubMedCentralGoogle Scholar
  28. Jansen R, Embden JD, Gaastra W, Schouls LM (2002) Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol 43(6):1565–1575CrossRefPubMedGoogle Scholar
  29. Jiang W, Zhou H, Bi H, Fromm M, Yang B, Weeks DP (2013) Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice. Nucleic Acids Res 41(20):e188CrossRefPubMedPubMedCentralGoogle Scholar
  30. Jiang W, Yang B, Weeks DP (2014) Efficient CRISPR/Cas9-mediated gene editing in Arabidopsis thaliana and inheritance of modified genes in the T2 and T3 generations. PLoS ONE 9(6):e99225CrossRefPubMedPubMedCentralGoogle Scholar
  31. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337:816–821CrossRefPubMedGoogle Scholar
  32. Jinek M, East A, Cheng A, Lin S, Ma E, Doudna J (2013) RNA programmed genome editing in human cells. eLife 2:e00471Google Scholar
  33. Kim YG, Cha J, Chandrasegaran S (1996) Hybrid restriction enzymes: zinc finger fusions to FokI cleavage domain. Proc Natl Acad Sci USA 93(3):1156–1160CrossRefPubMedPubMedCentralGoogle Scholar
  34. Kuscu C, Arslan S, Singh R, Thorpe J, Adli M (2014) Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease. Nat Biotechnol 32:677–683CrossRefPubMedGoogle Scholar
  35. Lei Y, Lu L, Liu HY, Li S, Xing F, Chen LL (2014) CRISPR-P: a web tool for synthetic single-guide RNA design of CRISPR-system in plants. Mol Plant 7:1494–1496CrossRefPubMedGoogle Scholar
  36. Li T, Liu B, Spalding MH, Weeks DP, Yang B (2012) High-efficiency TALEN based gene editing produces disease-resistant rice. Nat Biotechnol 30:390–392CrossRefPubMedGoogle Scholar
  37. Li JF, Norville JE, Aach J, McCormack M, Zhang D, Bush J, Church GM, Sheen J (2013) Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nat Biotechnol 31(8):688–691CrossRefPubMedPubMedCentralGoogle Scholar
  38. Ma M, Ye AY, Zheng W, Kong L (2013) A guide RNA sequence design platform for the CRISPR/Cas9 system for model organism genomes. Biomed Res Int 2013:270805PubMedPubMedCentralGoogle Scholar
  39. Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M, Kosuri S, Yang L, Church GM (2013a) CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol 31:833–838CrossRefPubMedPubMedCentralGoogle Scholar
  40. Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM (2013b) RNA-guided human genome engineering via Cas9. Science 339:823–826CrossRefPubMedPubMedCentralGoogle Scholar
  41. Mani M, Kandavelou K, Fei JD, Durai S, Chandrasegaran S (2005) Design, engineering and characterization of zinc finger nucleases. Biochem Biophys Res Commun 335:447–457CrossRefPubMedGoogle Scholar
  42. Mao Y, Zhang H, Xu N, Zhang B, Gao F, Zhu JK (2013) Application of the CRISPR-Cas system for efficient genome engineering in plants. Mol Plant 6:2008–2011CrossRefPubMedPubMedCentralGoogle Scholar
  43. Marraffini LA, Sontheimer EJ (2008) CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 322:1843–1845CrossRefPubMedPubMedCentralGoogle Scholar
  44. Miao J, Guo D, Zhang J, Huang Q, Qin G, Zhang X, Wan J, Gu H, Qu LJ (2013) Targeted mutagenesis in rice using CRISPR-Cas system. Cell Res 23(10):1233–1236CrossRefPubMedPubMedCentralGoogle Scholar
  45. Miller JC, Tan S, Qiao G, Barlow KA, Wang J, Xia DF, Meng X, Paschon DE, Leung E, Hinkley SJ, Dulay GP, Hua KL, Ankoudinova I, Cost GJ, Urnov FD, Zhang HS, Holmes MC, Gregory PD, Zhang L, Rebar EJ (2011) A TALE nuclease architecture for efficient genome editing. Nat Biotechnol 29(2):143–148CrossRefPubMedGoogle Scholar
  46. Mojica FJ, Diez-Villasen C, Garcia-Martinez J, Soria E (2005) Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J Mol Evol 60(2):174–182CrossRefPubMedGoogle Scholar
  47. Montague TG, Cruz JM, Gagnon JA, Church GM, Valen E (2014) CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic Acids Res 42:W401–W407CrossRefPubMedPubMedCentralGoogle Scholar
  48. Moscou MJ, Bogdanove AJ (2009) A simple cipher governs DNA recognition by TAL effectors. Science 326:1501CrossRefPubMedGoogle Scholar
  49. Nekrasov V, Staskawicz B, Weigel D, Jones JDG, Kamoun S (2013) Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease. Nat Biotechnol 31:691–693CrossRefPubMedGoogle Scholar
  50. O’Brien A, Bailey TL (2014) GT-Scan: identifying unique genomic targets. Bioinformatics 30:2673–2675CrossRefPubMedPubMedCentralGoogle Scholar
  51. Podevin N, Davies HV, Hartung F, Nogue F, Casacuberta JM (2013) Sitedirected nucleases: a paradigm shift in predictable, knowledge-based plant breeding. Trends Biotechnol 31(6):375–383CrossRefPubMedGoogle Scholar
  52. 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 151:653–663CrossRefPubMedGoogle Scholar
  53. Ran FA, Hsu PD, Lin CY, Gootenberg JS, Konermann S, Trevino AE, Scott DA, Inoue A, Matoba S, Zhang Y, Zhang F (2013) Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 154(6):1380–1389CrossRefPubMedPubMedCentralGoogle Scholar
  54. Ron M, Kajala K, Pauluzzi G, Wang D, Reynoso MA, Zumstein K, Garcha J, Winte S, Masson H, Inaqaki S, Fedirici F, Sinha N, Deal RB, Bailey-Serres J, Brady SM (2014) Hairy root transformation using Agrobacterium rhizogenes as a tool for exploring cell type-specific gene expression and function using tomato as a model. Plant Physiol 166(2):455–469CrossRefPubMedPubMedCentralGoogle Scholar
  55. Sapranauskas R, Gasiunas G, Fremaux C, Barrangou R, Horvath P, Siksnys V (2011) The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli. Nucleic Acids Res 39(21):9275–9282CrossRefPubMedPubMedCentralGoogle Scholar
  56. Schiml S, Fauser F, Puchta H (2014) The CRISPR/Cas system can be used as nuclease for in planta gene targeting and as paired nickases for directed mutagenesis in Arabidopsis resulting in heritable progeny. The Plant J 80:1139–1150CrossRefPubMedGoogle Scholar
  57. Shan Q, Wang Y, Li J, Zhang Y, Chen K, Liang Z, Zhang K, Liu J, Xi JJ, Qiu JL, Gao C (2013) Targeted genome modification of crop plants using a CRISPR-Cas system. Nat Biotechnol 31(8):686–688CrossRefPubMedGoogle Scholar
  58. Shan Q, Wang Y, Li J, Gao C (2014) Genome editing in rice and wheat using the CRISPR/Cas system. Nat Protoc 9:2395–2410CrossRefPubMedGoogle Scholar
  59. Stemmer M, Thumberger T, Del Sol Keyer M, Wittbrodt J, Mateo JL (2015) CCTop: an intuitive, flexible and reliable CRISPR/Cas9 target prediction tool. PLoS ONE 10:e0124633CrossRefPubMedPubMedCentralGoogle Scholar
  60. Streubel J, Blucher C, Landgraf A, Boch J (2012) TAL effector RVD specificities and efficiencies. Nat Biotechnol 30:593–595CrossRefPubMedGoogle Scholar
  61. Sugano SS, Shirakawa M, Takagi J, Matsuda Y, Shimada T, Hara-Nishimura I, Kohchi T (2014) CRISPR/Cas9-mediated targeted mutagenesis in the liverwort Marchantia polymorpha L. Plant Cell Physiol 55:475–481CrossRefPubMedGoogle Scholar
  62. Svitashev S, Young JK, Schwartz C, Gao H, Falco SC, Cigan AM (2015) Targeted mutagenesis, precise gene editing and site-specific gene insertion in maize using Cas9 and guide RNA. Plant Physiol 169(2):931–945CrossRefPubMedPubMedCentralGoogle Scholar
  63. Urnov FD, Miller JC, Lee YL, Beausejour CM, Rock JM, Augustus S, Jamieson AC, Porteus MH, Gregory PD, Holmes MC (2005) Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature 435(7042):646–651CrossRefPubMedGoogle Scholar
  64. Voytas DF, Gao C (2014) Precision genome engineering and agriculture: opportunities and regulatory challenges. PLoS Biol 12(6):e1001877CrossRefPubMedPubMedCentralGoogle Scholar
  65. Wang H, Yang H, Shivalila CS, Dawlaty MM, Cheng AW, Zhang F, Jaenisch R (2013) One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell 153(4):910–918CrossRefPubMedPubMedCentralGoogle Scholar
  66. Wang T, Wei JJ, Sabatini DM, Lander ES (2014) Genetic screens in human cells using the CRISPR-Cas9 system. Science 343:80–84CrossRefPubMedGoogle Scholar
  67. Wang S, Zhang S, Wang W, Xiong X, Meng F, Cui X (2015) Efficient targeted mutagenesis in potato by the CRISPR/Cas9 system. Plant Cell Rep 34:1473–1476CrossRefPubMedGoogle Scholar
  68. Weeks DP, Spalding MH, Yang B (2015) Use of designer nucleases for targeted gene and genome editing in plants. Plant Biotechnol J 1–13Google Scholar
  69. Wu X, Scott DA, Kriz AJ, Chiu AC, Hsu PD, Dadon DB, Cheng AW, Trevino AE, Konermann S, Chen S, Jaenisch R, Zhang F, Sharp PA (2014) Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat Biotechnol 32(7):670–676CrossRefPubMedPubMedCentralGoogle Scholar
  70. Xiao A, Cheng Z, Kong L, Zhu Z, Lin S, Gao G, Zhang B (2014) CasOT: a genome-wide Cas9/gRNA off-target searching tool. Bioinformatics 30:1180–1182CrossRefGoogle Scholar
  71. Xie K, Yang Y (2013) RNA-guided genome editing in plants using a CRISPR-Cas system. Mol Plant 6(6):1975–1983CrossRefPubMedGoogle Scholar
  72. Xie K, Zhang J, Yang Y (2014a) Genome-wide prediction of highly specific guide RNA spacers for CRISPR-Cas9-mediated genome editing in model plants and major crops. Mol Plant 7:923–926CrossRefPubMedGoogle Scholar
  73. Xie S, Shen B, Zhang C, Huang X, Zhang Y (2014b) sgRNAcas9: a software package for designing CRISPR sgRNA and evaluating potential off-target cleavage sites. PLoS ONE 9:e100448CrossRefPubMedPubMedCentralGoogle Scholar
  74. Xing HL, Dong L, Wang ZP, Zhang HY, Han CY, Liu B, Wang XC, Chen QJ (2014) A CRISPR/Cas9 toolkit for multiplex genome editing in plants. BMC Plant Biol 14:327CrossRefPubMedPubMedCentralGoogle Scholar
  75. Xu R, Li H, Qin R, Wang L, Li L, Wei P, Yang J (2014) Gene targeting using the Agrobacterium tumefaciens-mediated CRISPR-Cas system in rice. Rice (New York). 7(1):5PubMedCentralGoogle Scholar
  76. Xu RF, Li H, Qin RY, Li J, Qiu CH, Yang YC, Ma H, Li L, Wei PC, Yang JB (2015) Generation of inheritable and “transgene clean” targeted genome-modified rice in later generations using the CRISPR/Cas9 system. Sci Rep 5:11491CrossRefPubMedGoogle Scholar
  77. Zhang Y, Zhang F, Li X, Baller JA, Qi Y, Starker CG, Bogdanove AJ, Voytas DF (2013) Transcription activator-like effector nucleases enable efficient plant genome engineering. Plant Physiol 161(1):20–27CrossRefPubMedGoogle Scholar
  78. Zhang H, Zhang J, Wei P, Zhang B, Gou F, Feng Z, Mao Y, Yang L, Zhang H, Xu N, Zhu JK (2014) The CRISPR/Cas9 system produces specific and homozygous targeted gene editing in rice in one generation. Plant Biotechnol J 12(6):797–807CrossRefPubMedGoogle Scholar
  79. Zhou H, Liu B, Weeks DP, Spalding MH, Yang B (2014) Large chromosomal deletions and heritable small genetic changes induced by CRISPR/Cas9 in rice. Nucleic Acids Res 42(17):10903–10914CrossRefPubMedPubMedCentralGoogle Scholar
  80. Zhu LJ, Holmes BR, Aronin N, Brodsky MH (2014) CRISPRseek: a bioconductor package to identify target-specific guide RNAs for CRISPR-Cas9 genome-editing systems. PLoS ONE 9(9):e108424CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Milan Kumar Samanta
    • 1
  • Avishek Dey
    • 1
  • Srimonta Gayen
    • 2
  1. 1.Advanced Laboratory for Plant Genetic EngineeringIndian Institute of TechnologyKharagpurIndia
  2. 2.Department of Human GeneticsUniversity of MichiganAnn ArborUSA

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