Function genomics of abiotic stress tolerance in plants: A CRISPR approach

Frontiers in Plant Science

Volumn 6, Issue MAY, 2015, Pages 1-4

  Jain, Mukesh ^a  

^a NATIONAL INSTITUTE OF PLANT GENOME RESEARCH   (India)

Author keywords

Abiotic stress; CRISPR Cas9; Gene function; Genome editing; Transcription

Indexed keywords

EID: 84934878723     PISSN: None     EISSN: 1664462X     Source Type: Journal    
DOI: 10.3389/fpls.2015.00375     Document Type: Article

References (38)

1. Belhaj, K., Chaparro-Garcia, A., Kamoun, S., and Nekrasov, V. (2013). Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system. Plant Methods9: 39. doi: 10. 1186/1746-4811-9-39.
2. Bhaya, D., Davison, M., and Rodolphe, B. (2011). CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation. Ann. Rev. Genet. 45, 273-297. doi: 10. 1146/annurev-genet-110410-132430.
3. Brooks, C., Nekrasov, V., Lippman, Z. B., and 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, 1292-1297. doi: 10. 1104/pp. 114. 247577.
4. Cho, S. W., Kim, S., Kim, Y., Kweon, J., Kim, H. S., Bae, S., et al. (2014). Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Res. 24, 132-141. doi: 10. 1101/gr. 162339. 113.
5. Feng, Z., Zhang, B., Ding, W., Liu, X., Yang, D. L., Wei, P., et al. (2013). Efficient genome editing in plants using a CRISPR/Cas system. Cell Res. 23, 1229-1232. doi: 10. 1038/cr. 2013. 114.
6. Garg, R., Verma, M., Agrawal, S., Shankar, R., Majee, M., and Jain, M. (2014). Deep transcriptome sequencing of wild halophyte rice, Porteresia coarctata, provides novel insights into the salinity and submergence tolerance factors. DNA Res. 21, 69-84. doi: 10. 1093/dnares/dst042.
7. Gilbert, L. A., Larson, M. H., Morsut, L., Liu, Z., Brar, G. A., Torres, S. E., et al. (2013). CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154, 442-451. doi: 10. 1016/j. cell. 2013. 06. 044.
8. Harrison, M. M., Jenkins, B. V., O'Connor-Giles, K. M., and Wildonger, J. (2014). A CRISPR view of development. Genes Dev. 28, 1859-1872. doi: 10. 1101/gad. 248252. 114.
9. Hirayama, T., and Shinozaki, K. (2010). Research on plant abiotic stress responses in the post-genome era: past, present and future. Plant J. 61, 1041-1052. doi: 10. 1111/j. 1365-313X. 2010. 04124. x.
10. Hsu, P. D., Lander, E. S., and Zhang, F. (2014). Development and applications of CRISPR-Cas9 for genome engineering. Cell 157, 1262-1278. doi: 10. 1016/j. cell. 2014. 05. 010.
11. Hsu, P. D., Scott, D. A., Weinstein, J. A., Ran, F. A., Konermann, S., Agarwala, V., et al. (2013). DNA targeting specificity of RNA-guided Cas9 nucleases. Nat. Biotechnol. 31, 827-832. doi: 10. 1038/nbt. 2647.
12. Jiang, W., Zhou, H., Bi, H., Fromm, M., Yang, B., and Weeks, D. P. (2013). Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice. Nucl. Acids Res. 41, e188. doi: 10. 1093/nar/gkt780.
13. Kim, J. M., Kim, D., Kim, S., and Kim, J. S. (2014). Genotyping with CRISPR-Cas-derived RNA-guided endonucleases. Nat. Commun. 5, 3157. doi: 10. 1038/ncomms4157.
14. Konermann, S., Brigham, M. D., Trevino, A. E., Hsu, P. D., Heidenreich, M., Cong, L., et al. (2013). Optical control of mammalian endogenous transcription and epigenetic states. Nature 500, 472-476. doi: 10. 1038/nature12466.
15. Kumar, V., and Jain, M. (2015). The CRISPR-Cas system for plant genome editing: advances and opportunities. J. Exp. Bot. 66, 47-57. doi: 10. 1093/jxb/eru429.
16. Lei, Y., Lu, L., Liu, H. Y., Li, S., Xing, F., and Chen, L. L. (2014). CRISPR-P: a web tool for synthetic single-guide RNA design of CRISPR-system in plants. Mol. Plant 7, 1494-1496. doi: 10. 1093/mp/ssu044.
17. Li, J., Norville, J. E., Aach, J., McCormack, M., Zhang, D., Bush, J., et al. (2013). Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamianausing guide RNA and Cas9. Nat. Biotechnol. 31, 688-691. doi: 10. 1038/nbt. 2654.
18. Mahfouz, M. M., Piatek, A., and Stewart, C. N. Jr. (2014). Genome engineering via TALENs and CRISPR/Cas9 systems: challenges and perspectives. Plant Biotechnol. J. 12, 1006-1014. doi: 10. 1111/pbi. 12256.
19. Mali, P., Yang, L., Esvelt, K. M., Aach, J., Guell, M., Dicarlo, J. E., et al. (2013). RNA-guided human genome engineering via Cas9. Science 339, 823-826. doi: 10. 1126/science. 1232033.
20. Mao, Y., Zhang, H., Xu, N., Zhang, B., Gou, F., and Zhu, J. K. (2013). Application of the CRISPR-Cas system for efficient genome engineering in plants. Mol. Plant 6, 2008-2011. doi: 10. 1093/mp/sst121.
21. Marton, I., Zuker, A., Shklarman, E., Zeevi, V., Tovkach, A., Roffe, S., et al. (2010). Nontransgenic genome modification in plant cells. Plant Physiol. 154, 1079-1087. doi: 10. 1104/pp. 110. 164806.
22. Mickelbart, M. V., Hasegawa, P. M., and Bailey-Serres, J. (2015). Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability. Nat. Rev. Genet. 16, 237-251. doi: 10. 1038/nrg3901.
23. Montague, T. G., Cruz, J. M., Gagnon, J. A., Church, G. M., and Valen, E. (2014). CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing. Nucl. Acids Res. 42, W401-W407. doi: 10. 1093/nar/gku410.
24. Nakashima, K., Ito, Y., and Yamaguchi-Shinozaki, K. (2009). Transcriptional regulatory networks in response to abiotic stresses in Arabidopsis and grasses. Plant Physiol. 149, 88-95. doi: 10. 1104/pp. 108. 129791.
25. Nekrasov, V., Staskawicz, B., Weigel, D., Jones, J. D., and Kamoun, S. (2013). Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9-guided endonuclease. Nat. Biotechnol. 31, 691-693. doi: 10. 1038/nbt. 2655.
26. Osakabe, K., Osakabe, Y., and Toki, S. (2010). Site-directed mutagenesis in Arabidopsis using custom-designed zinc finger nucleases. Proc. Natl. Acad. Sci. U. S. A. 107, 12034-12039. doi: 10. 1073/pnas. 1000234107.
27. Perez-Pinera, P., Kocak, D. D., Vockley, C. M., Adler, A. F., Kabadi, A. M., Polstein, L. R., et al. (2013). RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nat. Methods10, 973-976. doi: 10. 1038/nmeth. 2600.
28. Piatek, A., Ali, Z., Baazim, H., Li, L., Abulfaraj, A., Al-Shareef, S., et al. (2015). RNA-guided transcriptional regulation in planta via synthetic dCas9-based transcription factors. Plant Biotechnol. J. 13, 578-589. doi: 10. 1111/pbi. 12284.
29. Qi, L. S., Larson, M. H., Gilbert, L. A., Doudna, J. A., Weissman, J. S., Arkin, A. P., et al. (2013). Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152, 1173-1183. doi: 10. 1016/j. cell. 2013. 02. 022.
30. Sander, J. D., and Joung, J. K. (2014). CRISPR-Cas systems for editing, regulating and targeting genomes. Nat. Biotechnol. 32, 347-155. doi: 10. 1038/nbt. 2842.
31. Shalem, O., Sanjana, N. E., Hartenian, E., Shi, X., Scott, D. A., Mikkelsen, T. S., et al. (2014). Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 343, 84-87. doi: 10. 1126/science. 1247005.
32. Shan, Q., Wang, Y., Li, J., and Gao, C. (2014). Genome editing in rice and wheat using the CRISPR/Cas system. Nat. Protoc. 9, 2395-2410. doi: 10. 1038/nprot. 2014. 157.
33. Shan, Q., Wang, Y., Li, J., Zhang, Y., Chen, K., Liang, Z., et al. (2013). Targeted genome modification of crop plants using a CRISPR-Cas system. Nat. Biotechnol. 31, 686-688. doi: 10. 1038/nbt. 2650.
34. Voytas, D. F. (2013). Plant genome engineering with sequence-specific nucleases. Ann. Rev. Plant Biol. 64, 327-350. doi: 10. 1146/annurev-arplant-042811-105552.
35. Wang, T., Wei, J. J., Sabatini, D. M., and Lander, E. S. (2014). Genetic screens in human cells using the CRISPR-Cas9 system. Science 343, 80-84. doi: 10. 1126/science. 1246981.
36. Xing, H. L., Dong, L., Wang, Z. P., Zhang, H. Y., Han, C. Y., Liu, B., et al. (2014). A CRISPR/Cas9 toolkit for multiplex genome editing in plants. BMC Plant Biol. 14: 327. doi: 10. 1186/s12870-014-0327-y.
37. Zhang, H., Zhang, J., Wei, P., Zhang, B., Gou, F., Feng, Z., et al. (2014). The CRISPR/Cas9 system produces specific and homozygous targeted gene editing in rice in one generation. Plant Biotechnol. J. 12, 797-807. doi: 10. 1111/pbi. 12200.
38. Zhou, H., Liu, B., Weeks, D. P., Spalding, M. H., and Yang, B. (2014). Large chromosomal deletions and heritable small genetic changes induced by CRISPR/Cas9 in rice. Nucl. Acids Res. 42, 10903-10914. doi: 10. 1093/nar/gku806.