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Developing CRISPR Technology in Major Crop Plants

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Advances in New Technology for Targeted Modification of Plant Genomes

Abstract

Targeted genome modification (TGM) by sequence-specific nucleases (SSNs) is a powerful tool for elucidating gene function and improving crops. Very recently, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system-based RNA-guided endonucleases have been added to the SSN toolbox. TGMs generated by this system rely on a synthetic single guide RNA (sgRNA) to direct the Cas9 protein to cleave a predetermined DNA sequence. Unlike previous SSNs, CRISPR provides a simple, cost-effective and versatile approach to multiplex genome engineering. In this review, we describe the molecular mechanisms involved in the CRISPR system, and summarize and discuss the applications of this technology in plant genome engineering.

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References

  • (2013) Genetic microsurgery for the masses. Science 342:1434–1435.

    Google Scholar 

  • Auer TO, Duroure K, De Cian A, Concordet JP, Del Bene F (2014) Highly efficient CRISPR/Cas9-mediated knock-in in zebrafish by homology-independent DNA repair. Genome Res 24:142–153

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Baena-Lopez LA, Alexandre C, Mitchell A, Pasakarnis L, Vincent JP (2013) Accelerated homologous recombination and subsequent genome modification in Drosophila. Development 140:4818–4825

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Barrangou R (2012) RNA-mediated programmable DNA cleavage. Nat Biotechnol 30:836–838

    Article  CAS  PubMed  Google Scholar 

  • Barrangou R (2013) CRISPR-Cas systems and RNA-guided interference. Wiley Interdiscip Rev RNA 4:267–278

    Article  CAS  PubMed  Google Scholar 

  • Bassett AR, Tibbit C, Ponting CP, Liu JL (2013) Highly efficient targeted mutagenesis of Drosophila with the CRISPR/Cas9 system. Cell Rep 11:220–228

    Article  Google Scholar 

  • Belhaj K, Chaparro-Garcia A, Kamoun S, Nekrasov V (2013) Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system. Plant Methods 9:39

    Article  PubMed Central  PubMed  Google Scholar 

  • Bikard D, Jiang W, Samai P, Hochschild A, Zhang F, Marraffini LA (2013) Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Res 41:7429–7437

    Google Scholar 

  • Blackburn PR, Campbell JM, Clark KJ, Ekker SC (2013) The CRISPR system–keeping zebrafish gene targeting fresh. Zebrafish 10:116–118

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Carroll D (2011) Genome engineering with zinc-finger nucleases. Genetics 188:773–782

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Chang N, Sun C, Gao L et al (2013) Genome editing with RNA-guided Cas9 nuclease in zebrafish embryos. Cell Res 23:465–472

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Chen K, Gao C (2013) TALENs: customizable molecular DNA scissors for genome engineering of plants. J Genet Genomics 40:271–279

    Article  PubMed  Google Scholar 

  • Chen K, Gao C (2014) Targeted genome modification technologies and their applications in crop improvements. Plant Cell Rep 33(4):575–583. doi:10.1007/s00299-013-1539-6, Epub 2013 Nov 24

    Article  CAS  PubMed  Google Scholar 

  • Chen B, Gilbert LA, Cimini BA et al (2013) Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas System. Cell 155(7):1479–1491

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Cheng AW, Wang H, Yang H et al (2013) Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system. Cell Res 23:1163–1171

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Cho SW, Kim S, Kim JM, Kim JS (2013) Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat Biotechnol 31:230–232

    Article  CAS  PubMed  Google Scholar 

  • Cho SW, Kim S, Kim Y et al (2014) Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Res 24:132–141

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Cong L, Ran FA, Cox D et al (2013) Multiplex genome engineering using CRISPR/Cas systems. Science 339:819–823

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Cradick TJ, Fine EJ, Antico CJ, Bao G (2013) CRISPR/Cas9 systems targeting beta-globin and CCR5 genes have substantial off-target activity. Nucleic Acids Res 41:9584–9592

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Curtin SJ, Voytas DF, Stupar RM (2012) Genome engineering of crops with designer nucleases. Plant Genome 5:42–50

    Article  CAS  Google Scholar 

  • Deltcheva E, Chylinski K, Sharma CM et al (2011) CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471:602–607

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Dicarlo JE, Norville JE, Mali P, Rios X, Aach J, Church GM (2013) Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res 41:4336–4343

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Feng Z, Zhang B, Ding W et al (2013) Efficient genome editing in plants using a CRISPR/Cas system. Cell Res 23:1229–1232

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Friedland AE, Tzur YB, Esvelt KM, Colaiacovo MP, Church GM, Calarco JA (2013) Heritable genome editing in C. elegans via a CRISPR-Cas9 system. Nat Methods 10:741–743

    Article  CAS  PubMed  Google Scholar 

  • Fu Y, Foden JA, Khayter C et al (2013) High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat Biotechnol 31:822–826

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Gaj T, Gersbach CA, Barbas Iii CF (2013) ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol 31:397–405

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Gilbert Luke A, Larson Matthew H, Morsut L et al (2013) CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154:442–451

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Gratz SJ, Cummings AM, Nguyen JN et al (2013) Genome engineering of Drosophila with the CRISPR RNA-guided Cas9 nuclease. Genetics 194:1029–1035

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Hou Z, Zhang Y, Propson NE et al (2013) Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis. Proc Natl Acad Sci U S A 110:15644–15649

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Hsu PD, Scott DA, Weinstein JA et al (2013) DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol 31:827–832

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Hu X, Chang N, Wang X et al (2013) Heritable gene-targeting with gRNA/Cas9 in rats. Cell Res 23:1322–1325

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Hwang WY, Fu Y, Reyon D et al (2013) Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol 31:227–229

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Jao LE, Wente SR, Chen W (2013) Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system. Proc Natl Acad Sci U S A 110:13904–13909

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Jiang W, Bikard D, Cox D, Zhang F, Marraffini LA (2013a) RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol 31:233–239

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Jiang W, Zhou H, Bi H, Fromm M, Yang B, Weeks DP (2013b) Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice. Nucleic Acids Res 41:e188

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • 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 337:816–821

    Article  CAS  PubMed  Google Scholar 

  • Jinek M, East A, Cheng A, Lin S, Ma E, Doudna J (2013) RNA-programmed genome editing in human cells. eLife 2:e00471

    Article  PubMed Central  PubMed  Google Scholar 

  • Joung JK, Sander JD (2012) TALENs: a widely applicable technology for targeted genome editing. Nat Rev Mol Cell Biol 14(1):49–55

    Article  PubMed Central  PubMed  Google Scholar 

  • Konermann S, Brigham MD, Trevino A et al (2013) Optical control of mammalian endogenous transcription and epigenetic states. Nature 500:472–476

    CAS  PubMed  Google Scholar 

  • Kuzma J, Kokotovich A (2011) Renegotiating GM crop regulation. EMBO Rep 12:883–888

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Li D, Qiu Z, Shao Y et al (2013a) Heritable gene targeting in the mouse and rat using a CRISPR-Cas system. Nat Biotechnol 31:681–683

    Article  CAS  PubMed  Google Scholar 

  • Li JF, Norville JE, Aach J et al (2013b) Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nat Biotechnol 31:688–691

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Liang Z, Zhang K, Chen K, Gao C (2014) Targeted mutagenesis in Zea mays using TALENs and the CRISPR/Cas system. J Genet Genomics 41:63–68. doi:10.1016/j.jgg.2013.12.001

    Article  CAS  PubMed  Google Scholar 

  • Lusser M, Parisi C, Plan D, Rodríguez-Cerezo E (2012) Deployment of new biotechnologies in plant breeding. Nat Biotechnol 30:231–239

    Article  CAS  PubMed  Google Scholar 

  • Maeder ML, Linder SJ, Cascio VM, Fu Y, Ho QH, Joung JK (2013a) CRISPR RNA-guided activation of endogenous human genes. Nat Methods 10:977–979

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Maeder ML, Angstman JF, Richardson ME et al (2013b) Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins. Nat Biotechnol 31:1137–1142

    Article  CAS  PubMed  Google Scholar 

  • Makarova KS, Haft DH, Barrangou R et al (2011) Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol 9:467–477

    Article  CAS  PubMed  Google Scholar 

  • Mali P, Yang L, Esvelt KM et al (2013a) RNA-guided human genome engineering via Cas9. Science 339:823–826

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Mali P, Aach J, Stranges PB et al (2013b) CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol 31:833–838

    Article  CAS  PubMed  Google Scholar 

  • 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 6:2008–2011

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Mendenhall EM, Williamson KE, Reyon D et al (2013) Locus-specific editing of histone modifications at endogenous enhancers. Nat Biotechnol 31:1133–1136

    Article  CAS  PubMed  Google Scholar 

  • Miao J, Guo D, Zhang J et al (2013) Targeted mutagenesis in rice using CRISPR-Cas system. Cell Res 23:1233–1236

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • 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 31:691–693

    Article  CAS  PubMed  Google Scholar 

  • 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 31:839–843

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Pauwels K, Podevin N, Breyer D, Carroll D, Herman P (2014) Engineering nucleases for gene targeting: safety and regulatory considerations. N Biotechnol 31:18–27

    Article  CAS  PubMed  Google Scholar 

  • Pennisi E (2013) The CRISPR craze. Science 341:833–836

    Article  CAS  PubMed  Google Scholar 

  • Perez-Pinera P, Ousterout DG, Gersbach CA (2012) Advances in targeted genome editing. Curr Opin Chem Biol 16:268–277

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Perez-Pinera P, Kocak DD, Vockley CM et al (2013) RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nat Methods 10:973–976

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Podevin N, Devos Y, Davies HV, Nielsen KM (2012) Transgenic or not? No simple answer! EMBO Rep 13:1057–1061

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Podevin N, Davies HV, Hartung F, Nogué F, Casacuberta JM (2013) Site-directed nucleases: a paradigm shift in predictable, knowledge-based plant breeding. Trends Biotechnol 31:375–383

    Article  CAS  PubMed  Google Scholar 

  • Porteus MH, Carroll D (2005) Gene targeting using zinc finger nucleases. Nat Biotechnol 23:967–973

    Article  CAS  PubMed  Google Scholar 

  • Qi LS, Larson MH, Gilbert LA et al (2013) Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152:1173–1183

    Article  PubMed Central  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Sun N, Zhao H (2013) Transcription activator-like effector nucleases (TALENs): a highly efficient and versatile tool for genome editing. Biotechnol Bioeng 110:1811–1821

    Article  CAS  PubMed  Google Scholar 

  • Upadhyay SK, Kumar J, Alok A, Tuli R (2013) RNA guided genome editing for target gene mutations in wheat. G3 3:2233–2238

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Urnov FD, Rebar EJ, Holmes MC, Zhang HS, Gregory PD (2010) Genome editing with engineered zinc finger nucleases. Nat Rev Genet 11:636–646

    Article  CAS  PubMed  Google Scholar 

  • Voytas DF (2013) Plant genome engineering with sequence-specific nucleases. Annu Rev Plant Biol 64:327–350

    Article  CAS  PubMed  Google Scholar 

  • Waltz E (2012) Tiptoeing around transgenics. Nat Biotechnol 30:215–217

    Article  CAS  PubMed  Google Scholar 

  • Wiedenheft B, Sternberg SH, Doudna JA (2012) RNA-guided genetic silencing systems in bacteria and archaea. Nature 482:331–338

    Article  CAS  PubMed  Google Scholar 

  • Wyman C, Kanaar R (2006) DNA double-strand break repair: all’s well that ends well. Annu Rev Genet 40:363–383

    Article  CAS  PubMed  Google Scholar 

  • Xie K, Yang Y (2013) RNA-guided genome editing in plants using a CRISPR-Cas system. Mol Plant 6:1975–1983

    Article  CAS  PubMed  Google Scholar 

  • Yang H, Wang H, Shivalila CS, Cheng AW, Shi L, Jaenisch R (2013) One-step generation of mice carrying reporter and conditional alleles by CRISPR/Cas-mediated genome engineering. Cell 154:1370–1379

    Article  PubMed Central  CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang, Beijing, 100101, P. R. China

    Kunling Chen Ph.D. & Caixia Gao Ph.D.

Authors
  1. Kunling Chen Ph.D.
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  2. Caixia Gao Ph.D.
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Corresponding author

Correspondence to Caixia Gao Ph.D. .

Editor information

Editors and Affiliations

  1. Cellectis Plant Sciences, New Brighton, Minnesota, USA

    Feng Zhang

  2. Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany

    Holger Puchta

  3. Crop Improvement and Genetics Unit, USDA Agricultural Research Service, Western Regional Research Center, Albany, California, USA

    James G. Thomson

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Chen, K., Gao, C. (2015). Developing CRISPR Technology in Major Crop Plants. In: Zhang, F., Puchta, H., Thomson, J. (eds) Advances in New Technology for Targeted Modification of Plant Genomes. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-2556-8_8

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