Genome-wide assessment of efficiency and specificity in crispr/cas9 mediated multiple site targeting in arabidopsis

PLoS ONE

Volumn 11, Issue 9, 2016, Pages

  Peterson, Brenda A ^a,c   Haak, David C ^c   Nishimura, Marc T ^a   Teixeira, Paulo J P L ^a   James, Sean R ^a,c   Dangl, Jeffery L ^a,b   Nimchuk, Zachary L ^a,c  

^a UNIVERSITY OF NORTH CAROLINA   (United States)

^b UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^c VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CASPASE 9; CRISPR ASSOCIATED PROTEIN; RNA;

ARABIDOPSIS THALIANA; ARTICLE; CHROMOSOME ABERRATION; CHROMOSOME TRANSLOCATION; EMBRYO DEVELOPMENT; GENE EXPRESSION; GENE LOCUS; GENE MAPPING; GENE SEQUENCE; GENE TRANSLOCATION; GENOME-WIDE ASSOCIATION STUDY; INDEL MUTATION; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; PHENOTYPE; PLANT GENETICS; PROMOTER REGION; PROTEIN SYNTHESIS; ARABIDOPSIS; CRISPR CAS SYSTEM; GENE TARGETING; GENETICS; PLANT GENOME; PROCEDURES;

ARABIDOPSIS; CRISPR-CAS SYSTEMS; GENE TARGETING; GENETIC LOCI; GENOME, PLANT; GENOME-WIDE ASSOCIATION STUDY; TRANSLOCATION, GENETIC;

EID: 84991721657     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0162169     Document Type: Article

References (32)

1. Lozano-Juste J, Cutler SR. Plant genome engineering in full bloom. Trends Plant Sci. 2014; 19(5):7-284. doi:10.1016/j.tplants.2014.02.014 PMID: 24674878.
2. O'Geen H, Yu AS, Segal DJ. How specific is CRISPR/Cas9 really? Curr Opin Chem Biol. 2015; 29:8-72. doi:10.1016/j.cbpa.2015.10.001PMID: 26517564; PubMed Central PMCID:PMCPMC4684463.
3. Feng Z, Mao Y, Xu N, Zhang B, Wei P, Yang DL, et al. Multigeneration analysis reveals the inheritance, specificity, and patterns of CRISPR/Cas-induced gene modifications in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. 2014; 111(12):7-4632. doi:10.1073/pnas.1400822111PMID: 24550464; PubMed Central PMCID:PMCPMC3970504.
4. Nekrasov V, Staskawicz B, Weigel D, Jones JD, Kamoun S. Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease. Nature biotechnology. 2013; 31 (8):3-691. doi:10.1038/nbt.2655 PMID: 23929340.
5. Ran FA, Hsu PD, Lin CY, Gootenberg JS, Konermann S, Trevino AE, et al. Double nicking by RNAguided CRISPR Cas9 for enhanced genome editing specificity. Cell. 2013; 154(6):9-1380. doi:10.1016/j.cell.2013.08.021 PMID: 23992846; PubMed Central PMCID: PMCPMC3856256.
6. Kleinstiver BP, Pattanayak V, Prew MS, Tsai SQ, Nguyen NT, Zheng Z, et al. High-fidelity CRISPRCas9 nucleases with no detectable genome-wide off-Target effects. Nature. 2016; 529(7587):5-490. doi:10.1038/nature16526 PMID: 26735016.
7. Fu Y, Sander JD, Reyon D, Cascio VM, Joung JK. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nature biotechnology. 2014; 32(3):84-279. doi:10.1038/nbt.2808 PMID: 24463574; PubMed Central PMCID:PMCPMC3988262.
8. Fernandez A, Hilson P, Beeckman T. GOLVEN peptides as important regulatory signalling molecules of plant development. Journal of experimental botany. 2013; 64(17):8-5863. doi:10.1093/jxb/ert248 PMID: 23975768.
9. Meng L, Buchanan BB, Feldman LJ, Luan S. CLE-like (CLEL) peptides control the pattern of root growth and lateral root development in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. 2012; 109(5):5-1760. doi:10.1073/pnas.1119864109 PMID: 22307643; PubMed Central PMCID: PMC3277184.
10. Matsuzaki Y, Ogawa-Ohnishi M, Mori A, Matsubayashi Y. Secreted peptide signals required for maintenance of root stem cell niche in Arabidopsis. Science. 2010; 329(5995):7-1065. doi:10.1126/science. 1191132 PMID: 20798316.
11. Jun J, Fiume E, Roeder AH, Meng L, SharmaVK, Osmont KS, et al. Comprehensive analysis of CLE polypeptide signaling gene expression and overexpression activity in Arabidopsis. Plant physiology. 2010; 154(4):36-1721. doi:10.1104/pp.110.163683PMID: 20884811; PubMed Central PMCID: PMC2996011.
12. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):60-1754. doi:10.1093/bioinformatics/btp324 PMID: 19451168; PubMed Central PMCID:PMCPMC2705234.
13. Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv. 2012;preprint arXiv:1207.3907 [q-bio.GN].
14. Thorvaldsdottir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013; 14(2):92-178. doi:10.1093/bib/bbs017PMID: 22517427; PubMed Central PMCID:PMCPMC3603213.
15. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNAguided DNA endonuclease in adaptive bacterialimmunity. Science. 2012; 337(6096):21-816. doi:10.1126/science.1225829PMID: 22745249.
16. Lei Y, Lu L, Liu HY, Li S, Xing F, Chen LL. CRISPR-P: A web tool for synthetic single-guide RNA design of CRISPR-system in plants. Molecular plant. 2014; 7(9):6-1494. doi:10.1093/mp/ssu044 PMID: 24719468.
17. Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nature biotechnology. 2013; 31(9):32-827. doi:10.1038/nbt.2647 PMID: 23873081; PubMed Central PMCID:PMCPMC3969858.
18. Choi PS, Meyerson M. Targeted genomic rearrangements using CRISPR/Cas technology. Nature communications. 2014; 5:3728. doi:10.1038/ncomms4728 PMID: 24759083; PubMed Central PMCID: PMCPMC4170920.
19. Torres R, MartinMC, Garcia A, Cigudosa JC, Ramirez JC, Rodriguez-Perales S. Engineering human tumour-Associated chromosomal translocations with the RNA-guided CRISPR-Cas9 system. Nature communications. 2014; 5:3964. doi:10.1038/ncomms4964 PMID: 24888982.
20. Ossowski S, Schneeberger K, Lucas-Lledo JI, Warthmann N, Clark RM, Shaw RG, et al. The rate and molecular spectrumof spontaneousmutations in Arabidopsis thaliana. Science. 2010; 327(5961):4-92. doi:10.1126/science.1180677 PMID: 20044577; PubMed Central PMCID:PMCPMC3878865.
21. Du H, Zeng X, Zhao M, Cui X, Wang Q, Yang H, et al. Efficient targetedmutagenesis in soybean by TALENs and CRISPR/Cas9. J Biotechnol. 2016; 217:7-90. doi:10.1016/j.jbiotec.2015.11.005 PMID: 26603121.
22. Mahfouz MM, Piatek A, StewartCN Jr., Genome engineering via TALENs and CRISPR/Cas9 systems: challenges and perspectives. Plant Biotechnol J. 2014; 12(8):14-1006. doi:10.1111/pbi.12256 PMID: 25250853.
23. Morbitzer R, Romer P, Boch J, Lahaye T. Regulation of selected genome loci using de novo-engineered transcription activator-like effector (TALE)-Type transcription factors. Proceedings of the National Academy of Sciences of the United States of America. 2010; 107(50):22-21617. doi:10.1073/pnas.1013133107PMID: 21106758; PubMed Central PMCID:PMCPMC3003021.
24. Zhang F, Maeder ML, Unger-Wallace E, Hoshaw JP, Reyon D, Christian M, et al. High frequency targetedmutagenesis in Arabidopsis thaliana using zinc finger nucleases. Proceedings of the National Academy of Sciences of the United States of America. 2010; 107(26):33-12028. doi:10.1073/pnas.0914991107PMID:20508152; PubMed Central PMCID:PMCPMC2900673.
25. Clark KA, Krysan PJ. Chromosomal translocations are a common phenomenon in Arabidopsis thaliana T-DNA insertion lines. The Plant journal: for cell and molecular biology. 2010; 64(6):990-1001. doi:10.1111/j.1365-313X.2010.04386.xPMID:21143679; PubMed Central PMCID:PMCPMC3079379.
26. CurtisMJ, Belcram K, Bollmann SR, Tominey CM, HoffmanPD, Mercier R, et al. Reciprocal chromosome translocation associated with TDNA-insertion mutation in Arabidopsis: genetic and cytological analyses of consequences for gametophyte development and for construction of doublymutant lines. Planta. 2009; 229(4):45-371. doi:10.1007/s00425-008-0868-0 PMID: 19082841; PubMed Central PMCID:PMCPMC4186712.
27. Zhang XH, Tee LY, Wang XG, Huang QS, Yang SH. Off-Target Effects in CRISPR/Cas9-mediated Genome Engineering. Mol Ther Nucleic Acids. 2015; 4:e264. doi:10.1038/mtna.2015.37 PMID: 26575098; PubMed Central PMCID:PMCPMC4877446.
28. Cutler SR, EhrhardtDW, Griffitts JS, Somerville CR. Random GFP::cDNA fusions enable visualization of subcellular structures in cells of Arabidopsis at a high frequency. Proceedings of the National Academy of Sciences of the United States of America. 2000; 97(7):23-3718. PMID: 10737809; PubMed Central PMCID: PMC16306.
29. Nimchuk ZL, Tarr PT, Ohno C, Qu X, Meyerowitz EM. Plant stem cell signaling involves ligand-dependent trafficking of the CLAVATA 1 receptor kinase. Curr Biol. 2011; 21(5):52-245. doi:10.1016/j.cub.2011.01.039PMID: 21333538; PubMed Central PMCID: PMC3072602.
30. Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, et al. RNA-guided human genome engineering via Cas9. Science. 2013; 339(6121):6-823. doi:10.1126/science.1232033 PMID: 23287722; PubMed Central PMCID: PMC3712628.
31. Clough SJ, Bent AF. Floral dip: A simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. The Plant journal: for cell and molecular biology. 1998; 16(6):43-735. PMID: 10069079.
32. Zerbino DR, Birney E. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome research. 2008; 18(5):9-821. doi:10.1101/gr.074492.107PMID: 18349386; PubMed Central PMCID: PMC2336801.