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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
Abstract
Summary: The CRISPR/C as nuclease is becoming a major tool for targeted mutagenesis in eukaryotes by inducing double‐strand breaks (DSB s) at pre‐selected genomic sites that are repaired by non‐homologous end joining (NHEJ) in an error‐prone way. In plants, it could be demonstrated that the C as9 nuclease is able to induce heritable mutations in A rabidopsis thaliana and rice. Gene targeting (GT) by homologous recombination (HR) can also be induced by DSB s. Using a natural nuclease and marker genes, we previously developed an in planta GT strategy in which both a targeting vector and targeting locus are activated simultaneously via DSB induction during plant development. Here, we demonstrate that this strategy can be used for natural genes by CRISPR/C as‐mediated DSB induction. We were able to integrate a resistance cassette into the ADH 1 locus of A. thaliana via HR. Heritable events were identified using a PCR‐based genotyping approach, characterised by S outhern blotting and confirmed on the sequence level. A major concern is the specificity of the CRISPR/C as nucleases. Off‐target effects might be avoided using two adjacent sg RNA target sequences to guide the C as9 nickase to each of the two DNA strands, resulting in the formation of a DSB. By amplicon deep sequencing, we demonstrate that this C as9 paired nickase strategy has a mutagenic potential comparable with that of the nuclease, while the resulting mutations are mostly deletions. We also demonstrate the stable inheritance of such mutations in A. thaliana.
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Cites
A Revised Medium for Rapid Growth and Bio Assays with Tobacco Tissue Cultures
Murashige, T., & Skoog, F. (1962) · Physiologia Plantarum · doi:10.1111/j.1399-3054.1962.tb08052.x · Cited by 67,392
Floral dip: a simplified method forAgrobacterium‐mediated transformation ofArabidopsis thaliana
Clough, S. J., & Bent, A. F. (1998) · The Plant Journal · doi:10.1046/j.1365-313x.1998.00343.x · Cited by 21,934
A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity
Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012) · Science · doi:10.1126/science.1225829 · Cited by 17,116
Robinson, J. T., Thorvaldsdóttir, H., Winckler, W., Guttman, M., Lander, E. S., Getz, G., & Mesirov, J. P. (2011) · Nature Biotechnology · doi:10.1038/nbt.1754 · Cited by 15,390
Goecks, J., Nekrutenko, A., Taylor, J., & The Galaxy Team (2010) · Genome Biology · doi:10.1186/gb-2010-11-8-r86 · Cited by 3,453
Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity
Ran, F. A., Hsu, P. D., Lin, C.-Y., Gootenberg, J. S., Konermann, S., Trevino, A. E., Scott, D. A., Inoue, A., Matoba, S., Zhang, Y., et al. (2013) · Cell · doi:10.1016/j.cell.2013.08.021 · Cited by 3,299
High-Frequency off-Target Mutagenesis Induced by CRISPR-Cas Nucleases in Human Cells
Fu, Y., Foden, J. A., Khayter, C., Maeder, M. L., Reyon, D., Joung, J. K., & Sander, J. D. (2013) · Nature Biotechnology · doi:10.1038/nbt.2623 · Cited by 3,292
Wang, Y., Cheng, X., Shan, Q., Zhang, Y., Liu, J., Gao, C., & Qiu, J.-L. (2014) · Nature Biotechnology · doi:10.1038/nbt.2969 · Cited by 2,072
Galaxy: A platform for interactive large-scale genome analysis
Giardine, B., Riemer, C., Hardison, R. C., Burhans, R., Elnitski, L., Shah, P., Zhang, Y., Blankenberg, D., Albert, I., Taylor, J., et al. (2005) · Genome Research · doi:10.1101/gr.4086505 · Cited by 2,026
RNA-guided genetic silencing systems in bacteria and archaea
Wiedenheft, B., Sternberg, S. H., & Doudna, J. A. (2012) · Nature · doi:10.1038/nature10886 · Cited by 1,851
Targeted genome modification of crop plants using a CRISPR-Cas system
Shan, Q., Wang, Y., Li, J., Zhang, Y., Chen, K., Liang, Z., Zhang, K., Liu, J., Xi, J. J., Qiu, J.-L., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2650 · Cited by 1,810
Cermak, T., Doyle, E. L., Christian, M., Wang, L., Zhang, Y., Schmidt, C., Baller, J. A., Somia, N. V., Bogdanove, A. J., & Voytas, D. F. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr218 · Cited by 1,787
Mali, P., Aach, J., Stranges, P. B., Esvelt, K. M., Moosburner, M., Kosuri, S., Yang, L., & Church, G. M. (2013) · Nature Biotechnology · doi:10.1038/nbt.2675 · Cited by 1,752
Li, J.-F., Norville, J. E., Aach, J., McCormack, M., Zhang, D., Bush, J., Church, G. M., & Sheen, J. (2013) · Nature Biotechnology · doi:10.1038/nbt.2654 · Cited by 1,510
Galaxy: A Web‐Based Genome Analysis Tool for Experimentalists
Blankenberg, D., Kuster, G. V., Coraor, N., Ananda, G., Lazarus, R., Mangan, M., Nekrutenko, A., & Taylor, J. (2010) · Current Protocols in Molecular Biology · doi:10.1002/0471142727.mb1910s89 · Cited by 1,427
Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases
Cho, S. W., Kim, S., Kim, Y., Kweon, J., Kim, H. S., Bae, S., & Kim, J.-S. (2014) · Genome Research · doi:10.1101/gr.162339.113 · Cited by 1,356
High-efficiency TALEN-based gene editing produces disease-resistant rice
Li, T., Liu, B., Spalding, M. H., Weeks, D. P., & Yang, B. (2012) · Nature Biotechnology · doi:10.1038/nbt.2199 · Cited by 1,148
Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease
Nekrasov, V., Staskawicz, B., Weigel, D., Jones, J. D. G., & Kamoun, S. (2013) · Nature Biotechnology · doi:10.1038/nbt.2655 · Cited by 1,127
Precise genome modification in the crop species Zea mays using zinc-finger nucleases
Shukla, V. K., Doyon, Y., Miller, J. C., DeKelver, R. C., Moehle, E. A., Worden, S. E., Mitchell, J. C., Arnold, N. L., Gopalan, S., Meng, X., et al. (2009) · Nature · doi:10.1038/nature07992 · Cited by 958
Zhang, H., Zhang, J., Wei, P., Zhang, B., Gou, F., Feng, Z., Mao, Y., Yang, L., Zhang, H., Xu, N., et al. (2014) · Plant Biotechnology Journal · doi:10.1111/pbi.12200 · Cited by 792
Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease
Kuscu, C., Arslan, S., Singh, R., Thorpe, J., & Adli, M. (2014) · Nature Biotechnology · doi:10.1038/nbt.2916 · Cited by 777
High-frequency modification of plant genes using engineered zinc-finger nucleases
Townsend, J. A., Wright, D. A., Winfrey, R. J., Fu, F., Maeder, M. L., Joung, J. K., & Voytas, D. F. (2009) · Nature · doi:10.1038/nature07845 · Cited by 737
Fauser, F., Schiml, S., & Puchta, H. (2014) · The Plant Journal · doi:10.1111/tpj.12554 · Cited by 713
Self-citationTargeted Mutagenesis in Zea mays Using TALENs and the CRISPR/Cas System
Liang, Z., Zhang, K., Chen, K., & Gao, C. (2014) · Journal of Genetics and Genomics · doi:10.1016/j.jgg.2013.12.001 · Cited by 658
Feng, Z., Mao, Y., Xu, N., Zhang, B., Wei, P., Yang, D.-L., Wang, Z., Zhang, Z., Zheng, R., Yang, L., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1400822111 · Cited by 657
The repair of double-strand breaks in plants: mechanisms and consequences for genome evolution
Puchta, H. (2004) · Journal of Experimental Botany · doi:10.1093/jxb/eri025 · Cited by 601
Self-citationTranscription Activator-Like Effector Nucleases Enable Efficient Plant Genome Engineering
Zhang, Y., Zhang, F., Li, X., Baller, J. A., Qi, Y., Starker, C. G., Bogdanove, A. J., & Voytas, D. F. (2012) · Plant Physiology · doi:10.1104/pp.112.205179 · Cited by 486
Veres, A., Gosis, B. S., Ding, Q., Collins, R., Ragavendran, A., Brand, H., Erdin, S., Cowan, C. A., Talkowski, M. E., & Musunuru, K. (2014) · Cell Stem Cell · doi:10.1016/j.stem.2014.04.020 · Cited by 474
Precision genome engineering and agriculture: opportunities and regulatory challenges
Voytas, D. F., & Gao, C. (2014) · PLoS Biology · doi:10.1371/journal.pbio.1001877 · Cited by 458
Targeted mutagenesis using zinc-finger nucleases in Arabidopsis
Lloyd, A., Plaisier, C. L., Carroll, D., & Drews, G. N. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409339102 · Cited by 417
Mahfouz, M. M., Li, L., Shamimuzzaman, M., Wibowo, A., Fang, X., & Zhu, J.-K. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1019533108 · Cited by 417
Puchta, H., Dujon, B., & Hohn, B. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.10.5055 · Cited by 400
Self-citationHigh frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases
Zhang, F., Maeder, M. L., Unger-Wallace, E., Hoshaw, J. P., Reyon, D., Christian, M., Li, X., Pierick, C. J., Dobbs, D., Peterson, T., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0914991107 · Cited by 379
High‐frequency homologous recombination in plants mediated by zinc‐finger nucleases
Wright, D. A., Townsend, J. A., Winfrey, R. J., Irwin, P. A., Rajagopal, J., Lonosky, P. M., Hall, B. D., Jondle, M. D., & Voytas, D. F. (2005) · The Plant Journal · doi:10.1111/j.1365-313x.2005.02551.x · Cited by 370
Capture of genomic and T-DNA sequences during double-strand break repair in somatic plant cells
Salomon, S. (1998) · The EMBO Journal · doi:10.1093/emboj/17.20.6086 · Cited by 355
Smith, C., Gore, A., Yan, W., Abalde-Atristain, L., Li, Z., He, C., Wang, Y., Brodsky, R. A., Zhang, K., Cheng, L., et al. (2014) · Cell stem cell · doi:10.1016/j.stem.2014.06.011 · Cited by 342
Targeted Mutagenesis of Duplicated Genes in Soybean with Zinc-Finger Nucleases
Curtin, S. J., Zhang, F., Sander, J. D., Haun, W. J., Starker, C., Baltes, N. J., Reyon, D., Dahlborg, E. J., Goodwin, M. J., Coffman, A. P., et al. (2011) · Plant Physiology · doi:10.1104/pp.111.172981 · Cited by 332
Site-directed mutagenesis in Arabidopsis using custom-designed zinc finger nucleases
Osakabe, K., Osakabe, Y., & Toki, S. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000234107 · Cited by 302
Puchta, H., Dujon, B., & Hohn, B. (1993) · Nucleic Acids Research · doi:10.1093/nar/21.22.5034 · Cited by 292
Self-citationRapid and Efficient Gene Modification in Rice and Brachypodium Using TALENs
Shan, Q., Wang, Y., Chen, K., Liang, Z., Li, J., Zhang, Y., Zhang, K., Liu, J., Voytas, D. F., Zheng, X., et al. (2013) · Molecular Plant · doi:10.1093/mp/sss162 · Cited by 288
Non-homologous DNA end joining in plant cells is associated with deletions and filler DNA insertions
Gorbunova, V (1997) · Nucleic Acids Research · doi:10.1093/nar/25.22.4650 · Cited by 283
Hartung, F., & Schiemann, J. (2014) · The Plant Journal · doi:10.1111/tpj.12413 · Cited by 277
Synthetic nucleases for genome engineering in plants: prospects for a bright future
Puchta, H., & Fauser, F. (2014) · The Plant Journal · doi:10.1111/tpj.12338 · Cited by 261
Self-citationHill, J. T., Demarest, B. L., Bisgrove, B. W., Su, Y., Smith, M., & Yost, H. J. (2014) · Developmental Dynamics · doi:10.1002/dvdy.24183 · Cited by 242
Heritable targeted mutagenesis in maize using a designed endonuclease
Gao, H., Smith, J., Yang, M., Jones, S., Djukanovic, V., Nicholson, M. G., West, A., Bidney, D., Falco, S. C., Jantz, D., et al. (2010) · The Plant Journal · doi:10.1111/j.1365-313x.2009.04041.x · Cited by 241
Fauser, F., Roth, N., Pacher, M., Ilg, G., Sánchez-Fernández, R., Biesgen, C., & Puchta, H. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1202191109 · Cited by 214
Self-citationSpecies-specific double-strand break repair and genome evolution in plants
Kirik, A. (2000) · The EMBO Journal · doi:10.1093/emboj/19.20.5562 · Cited by 193
Wendt, T., Holm, P. B., Starker, C. G., Christian, M., Voytas, D. F., Brinch-Pedersen, H., & Holme, I. B. (2013) · Plant Molecular Biology · doi:10.1007/s11103-013-0078-4 · Cited by 191
Phenotypic plasticity and the changing environment
(2005) · Journal of Experimental Botany · doi:10.1093/jxb/eri123 · Cited by 181
Gene targeting in plants: 25 years later
Puchta, H., & Fauser, F. (2013) · The International Journal of Developmental Biology · doi:10.1387/ijdb.130194hp · Cited by 175
Self-citationJiang, W., Yang, B., & Weeks, D. P. (2014) · PLoS ONE · doi:10.1371/journal.pone.0099225 · Cited by 163
Targeted molecular trait stacking in cotton through targeted double‐strand break induction
D'Halluin, K., Vanderstraeten, C., Van Hulle, J., Rosolowska, J., Van Den Brande, I., Pennewaert, A., D'Hont, K., Bossut, M., Jantz, D., Ruiter, R., et al. (2013) · Plant Biotechnology Journal · doi:10.1111/pbi.12085 · Cited by 162
Siebert, R., & Puchta, H. (2002) · The Plant Cell · doi:10.1105/tpc.001727 · Cited by 159
Self-citationAbortive Gap Repair: Underlying Mechanism for Ds element Formation
Rubin, E., & Levy, A. A. (1997) · Molecular and Cellular Biology · doi:10.1128/mcb.17.11.6294 · Cited by 123
Puchta, H. (1998) · The Plant Journal · doi:10.1046/j.1365-313x.1998.00035.x · Cited by 121
Self-citationTrue-Breeding Targeted Gene Knock-Out in Barley Using Designer TALE-Nuclease in Haploid Cells
Gurushidze, M., Hensel, G., Hiekel, S., Chamas, S., Valkov, V. T., & Kumlehn, J. (2014) · PLoS ONE · doi:10.1371/journal.pone.0092046 · Cited by 108
DNA recombination in somatic plant cells: mechanisms and evolutionary consequences
Knoll, A., Fauser, F., & Puchta, H. (2014) · Chromosome Research · doi:10.1007/s10577-014-9415-y · Cited by 98
Self-citationde Pater, S., Pinas, J. E., Hooykaas, P. J. J., & van der Zaal, B. J. (2012) · Plant Biotechnology Journal · doi:10.1111/pbi.12040 · Cited by 78
Targeted DNA excision in Arabidopsis by a re-engineered homing endonuclease
Antunes, M. S., Smith, J., Jantz, D., & Medford, J. I. (2012) · BMC Biotechnology · doi:10.1186/1472-6750-12-86 · Cited by 61
Pacher, M., Schmidt-Puchta, W., & Puchta, H. (2006) · Genetics · doi:10.1534/genetics.106.065185 · Cited by 59
Self-citationGene targeting in maize by somatic ectopic recombination
Ayar, A., Wehrkamp‐Richter, S., Laffaire, J., et al. (2012) · Plant Biotechnology Journal · doi:10.1111/pbi.12014 · Cited by 41
Vaughn, J. N., & Bennetzen, J. L. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1321854111 · Cited by 34
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Metadata
- Authors
- Schiml, S., Fauser, F., & Puchta, H.
- Venue
- The Plant Journal
- Publisher
- Wiley
- Published
- 2014-11-11
- Volume
- 80
- Issue
- 6
- Pages
- 1139-1150
- ISSN
- 0960-7412 (ISSN-L)
- 1365-313X
- OpenAlex
- W2155194596
- Cited by
- 342
- References
- 62
- FWCI
- 14.84
- Type
- journal article
- Language
- en
- Open access
- closed
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