Knocking Out MicroRNA Genes in Rice with CRISPR-Cas9.

CRISPR-Cas Systems / genetics Genome, Plant / genetics MicroRNAs / genetics Oryza / genetics
CRISPR-Cas9 Genome editing MicroRNAs Rice SSCP

Journal

Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969

Informations de publication

Date de publication:
2019
Historique:
entrez: 6 1 2019
pubmed: 6 1 2019
medline: 18 6 2019
Statut: ppublish

Résumé

MicroRNAs (miRNAs) are small noncoding RNAs that play important roles in plant development and stress responses. Loss-of-function analysis of miRNA genes has been traditionally challenging due to lack of appropriate knockout tools. In this chapter, we describe a method of using CRISPR-Cas9 for knocking out microRNA genes in rice by Agrobacterium-mediated transformation. We also demonstrate single-strand conformation polymorphism (SSCP) as an effective genotyping method for screening CRISPR-Cas9-induced mutations.

Sections du résumé

BACKGROUND
MicroRNAs (miRNAs) are small noncoding RNAs that play important roles in plant development and stress responses. Loss-of-function analysis of miRNA genes has been traditionally challenging due to lack of appropriate knockout tools. In this chapter, we describe a method of using CRISPR-Cas9 for knocking out microRNA genes in rice by Agrobacterium-mediated transformation. We also demonstrate single-strand conformation polymorphism (SSCP) as an effective genotyping method for screening CRISPR-Cas9-induced mutations.

Identifiants

DOI: 10.1007/978-1-4939-8991-1_9 PMID: 30610632
pubmed: 30610632
doi: 10.1007/978-1-4939-8991-1_9
doi:

Substances chimiques

MicroRNAs 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

109-119

Références

Voinnet O (2009) Origin, biogenesis, and activity of plant microRNAs. Cell 136(4):669–687
doi: 10.1016/j.cell.2009.01.046 pubmed: 19239888
Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116(2):281–297
doi: 10.1016/S0092-8674(04)00045-5 pubmed: 14744438
Meister G (2013) Argonaute proteins: functional insights and emerging roles. Nat Rev Genet 14(7):447–459
doi: 10.1038/nrg3462 pubmed: 23732335
Chen X (2012) Small RNAs in development – insights from plants. Curr Opin Genet Dev 22(4):361–367
doi: 10.1016/j.gde.2012.04.004 pubmed: 22578318 pmcid: 3419802
Franco-Zorrilla JM, Valli A, Todesco M, Mateos I, Puga MI, Rubio-Somoza I, Leyva A, Weigel D, Garcia JA, Paz-Ares J (2007) Target mimicry provides a new mechanism for regulation of microRNA activity. Nat Genet 39(8):1033–1037
doi: 10.1038/ng2079 pubmed: 17643101
Todesco M, Rubio-Somoza I, Paz-Ares J, Weigel D (2010) A collection of target mimics for comprehensive analysis of microRNA function in Arabidopsis thaliana. PLoS Genet 6(7):e1001031
doi: 10.1371/journal.pgen.1001031 pubmed: 20661442 pmcid: 2908682
Yan J, Gu Y, Jia X, Kang W, Pan S, Tang X, Chen X, Tang G (2012) Effective small RNA destruction by the expression of a short tandem target mimic in Arabidopsis. Plant Cell 24(2):415–427
doi: 10.1105/tpc.111.094144 pubmed: 22345490 pmcid: 3315224
Reichel M, Li Y, Li J, Millar AA (2015) Inhibiting plant microRNA activity: molecular SPONGEs, target MIMICs and STTMs all display variable efficacies against target microRNAs. Plant Biotechnol J 13(7):915–926
doi: 10.1111/pbi.12327 pubmed: 25600074
Lowder LG, Zhang D, Baltes NJ, Paul JW 3rd, Tang X, Zheng X, Voytas DF, Hsieh TF, Zhang Y, Qi Y (2015) A CRISPR/Cas9 toolbox for multiplexed plant genome editing and transcriptional regulation. Plant Physiol 169(2):971–985
doi: 10.1104/pp.15.00636 pubmed: 26297141 pmcid: 4587453
Zhang Y, Zhang F, Li XH, Christian M, Bogdanove AJ, Qi YP, Starker CG, Bogdanove AJ, Voytas DF (2013) Transcription activator-like effector nucleases enable efficient plant genome engineering. Plant Physiol 161(1):20–27
doi: 10.1104/pp.112.205179 pubmed: 23124327
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):e82
doi: 10.1093/nar/gkr218 pubmed: 21493687 pmcid: 3130291
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):819–823
doi: 10.1126/science.1231143 pubmed: 23287718 pmcid: 3795411
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(6096):816–821
doi: 10.1126/science.1225829 pubmed: 22745249 pmcid: 6286148
Shan Q, Wang Y, Li J, Zhang Y, Chen K, Liang Z, Zhang K, Liu J, Xi JJ, Qiu J-L, Gao C (2013b) Targeted genome modification of crop plants using a CRISPR-Cas system. Nat Biotechnol 31(8):686–688
doi: 10.1038/nbt.2650 pubmed: 23929338
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):1229–1232
doi: 10.1038/cr.2013.114 pubmed: 23958582 pmcid: 3790235
Tang X, Lowder LG, Zhang T, Malzahn AA, Zheng X, Voytas DF, Zhong Z, Chen Y, Ren Q, Li Q, Kirkland ER, Zhang Y, Qi Y (2017) A CRISPR–Cpf1 system for efficient genome editing and transcriptional repression in plants. Nat Plants 3:17018
doi: 10.1038/nplants.2017.18 pubmed: 28211909
Tang X, Zheng X, Qi Y, Zhang D, Cheng Y, Tang A, Voytas DF, Zhang Y (2016) A single transcript CRISPR-Cas9 system for efficient genome editing in plants. Mol Plant 9(7):1088–1091
doi: 10.1016/j.molp.2016.05.001 pubmed: 27212389
Zhou J, Deng K, Cheng Y, Zhong Z, Tian L, Tang X, Tang A, Zheng X, Zhang T, Qi Y, Zhang Y (2017) CRISPR-Cas9 based genome editing reveals new insights into MicroRNA function and regulation in rice. Front Plant Sci 8:1598. https://doi.org/10.3389/fpls.2017.01598
doi: 10.3389/fpls.2017.01598 pubmed: 28955376 pmcid: 5602353
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):688–691
doi: 10.1038/nbt.2654 pubmed: 23929339 pmcid: 4078740
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(8):691–693
doi: 10.1038/nbt.2655 pubmed: 23929340
Paul JW 3rd, Qi Y (2016) CRISPR/Cas9 for plant genome editing: accomplishments, problems and prospects. Plant Cell Rep 35(7):1417–1427
doi: 10.1007/s00299-016-1985-z pubmed: 27114166
Cui W, Liu W, Wu G (1995) A simple method for the transformation of agrobacterium tumefaciens by foreign DNA. Chin J Biotechnol 11(4):267–274
pubmed: 8739105
Toki S, Hara N, Ono K, Onodera H, Tagiri A, Oka S, Tanaka H (2006) Early infection of scutellum tissue with agrobacterium allows high-speed transformation of rice. Plant J 47:969–976
doi: 10.1111/j.1365-313X.2006.02836.x pubmed: 16961734
Zheng XL, Yang SX, Zhang DW, Zhong ZH, Tang X, Deng KJ, Zhou JP, Qi YP, Zhang Y (2016) Effective screen of CRISPR/Cas9-induced mutants in rice by single-strand conformation polymorphism. Plant Cell Rep 35(7):1545–1554
doi: 10.1007/s00299-016-1967-1 pubmed: 27007717

Auteurs

Jianping Zhou (J)

Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.

Zhaohui Zhong (Z)

Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.

Hongqiao Chen (H)

Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.

Qian Li (Q)

Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.

Xuelian Zheng (X)

Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.

Yiping Qi (Y)

Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA.
Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA.

Yong Zhang (Y)

Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China. zhangyong916@uestc.edu.cn.

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Classifications MeSH

questionsmedicales.fr › Phénomènes génétiques › Régulation de l'expression des gènes › Épigenèse génétique › Extinction de l'expression des gènes › Systèmes CRISPR-Cas › Knocking Out MicroRNA Genes in Rice with CRISPR-Cas9.
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome végétal › Knocking Out MicroRNA Genes in Rice with CRISPR-Cas9.
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN non traduit › Petit ARN non traduit › microARN › Knocking Out MicroRNA Genes in Rice with CRISPR-Cas9.
questionsmedicales.fr › Eucaryotes › Viridiplantae › Streptophyta › Embryophyta › Tracheobionta › Magnoliopsida › Poaceae › Oryza › Knocking Out MicroRNA Genes in Rice with CRISPR-Cas9.