Current status of potential applications of repurposed Cas9 for structural and functional genomics of plants

Biochemical and Biophysical Research Communications

Volumn 480, Issue 4, 2016, Pages 499-507

  Seth, Kunal ^a   Harish, ^a  

^a M L SUKHADIA UNIVERSITY   (India)

Author keywords

CRISPR; Crop improvement; dCas9; Epigenetics; Gene editing; Gene regulation

Indexed keywords

ACYLTRANSFERASE; FLUORESCENT DYE; GUIDE RNA; LONG UNTRANSLATED RNA; METHYLTRANSFERASE;

CAS9 SYSTEM; CHROMOSOME; CRISPR CAS SYSTEM; EPIGENETICS; FLUORESCENCE IMAGING; FUNCTIONAL GENOMICS; GENE ACTIVATION; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE REPRESSION; GENE SILENCING; GENETIC ENGINEERING; GENETIC REGULATION; MOLECULAR INTERACTION; NONHUMAN; PLANT; PRIORITY JOURNAL; REPRESSOR GENE; SHORT SURVEY; STRUCTURAL GENOMICS; FORECASTING; GENE EDITING; GENETIC ENHANCEMENT; GENETICS; GENOMICS; PLANT GENOME; TRANSGENIC PLANT; TRENDS;

CRISPR-CAS SYSTEMS; FORECASTING; GENE EDITING; GENETIC ENHANCEMENT; GENOME, PLANT; GENOMICS; PLANTS; PLANTS, GENETICALLY MODIFIED;

EID: 84994633260     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2016.10.130     Document Type: Short Survey

References (79)

1. [1] Ishino, Y., Shinagawa, H., Makino, K., et al. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J. Bacteriol. 169 (1987), 5429–5433.
2. [2] Makarova, K.S., Wolf, Y.I., Alkhnbashi, O.S., et al. An updated evolutionary classification of CRISPR-Cas systems. Nat. Rev. Microbiol. 13 (2015), 722–736.
3. [3] Doudna, J.A., Charpentier, E., The new frontier of genome engineering with CRISPR-Cas9. Science, 346, 2014, 1258096, 10.1126/science.1258096.
4. [4] Sonoda, E., Hochegger, H., Saberi, A., et al. Differential usage of non-homologous end-joining and homologous recombination in double strand break repair. DNA Repair 5 (2006), 1021–1029.
5. [5] Sander, J.D., Joung, J.K., CRISPR-Cas systems for editing, regulating and targeting genomes. Nat. Biotechnol. 32 (2014), 347–355.
6. [6] DiCarlo, J.E., Norville, J.E., Mali, P., et al. Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucl. Acids Res. 41 (2013), 4336–4343.
7. [7] Jacobs, J.Z., Ciccaglione, K.M., Tournier, V., et al. Implementation of the CRISPR-Cas9 system in fission yeast. Nat. Commun., 5, 2014, 5344, 10.1038/ncomms6344.
8. [8] Horwitz, A.A., Walter, J.M., Schubert, M.G., et al. Efficient multiplexed integration of synergistic alleles and metabolic pathways in yeasts via CRISPR-Cas. Cell Syst. 1 (2015), 88–96.
9. [9] Weninger, A., Hatzl, A.M., Schmid, C., et al. Combinatorial optimization of CRISPR/Cas9 expression enables precision genome engineering in the methylotrophic yeast Pichia pastoris. J. Biotechnol. 235 (2016), 139–149.
10. [10] Nymark, M., Sharma, A.K., Sparstad, T., et al. A CRISPR/Cas9 system adapted for gene editing in marine algae. Sci. Rep., 6, 2016, 24951, 10.1038/srep24951.
11. [11] Shin, S.E., Lim, J.M., Koh, H.G., et al. CRISPR/Cas9-induced knockout and knock-in mutations in Chlamydomonas reinhardtii. Sci. Rep., 6, 2016, 27810, 10.1038/srep27810.
12. [12] Khlestkina, E.K., Shumny, V.K., Prospects for application of breakthrough technologies in breeding: the CRISPR/Cas9 system for plant genome editing. Russ. J. Genet. 52 (2016), 676–687.
13. [13] Li, M., Li, X., Zhou, Z., et al. Reassessment of the four yield-related genes Gn1a, DEP1, GS3, and IPA1 in rice using a CRISPR/Cas9 System. Front. Plant Sci., 7, 2016, 377, 10.3389/fpls.2016.00377.
14. [14] Ito, Y., Nishizawa-Yokoi, A., Endo, M., et al. CRISPR/Cas9-mediated mutagenesis of the RIN locus that regulates tomato fruit ripening. Biochem. Biophys. Res. Commun. 467 (2015), 76–82.
15. [15] Waltz, E., Gene-edited CRISPR mushroom escapes US regulation. Nature, 532, 2016, 293, 10.1038/nature.2016.19754.
16. [16] Samanta, M.K., Dey, A., Gayen, S., CRISPR/Cas9: an advanced tool for editing plant genomes. Transgenic Res. 25 (2016), 561–573.
17. [17] Bortesi, L., Zhu, C., Zischewski, J., et al. Patterns of CRISPR/Cas9 activity in plants, animals and microbes. Plant Biotechnol. J., 2016, 10.1111/pbi.12634.
18. [18] Puchta, H., The repair of double-strand breaks in plants: mechanisms and consequences for genome evolution. J. Exp. Bot. 56 (2005), 1–14.
19. [19] Li, J.F., Norville, J.E., Aach, J., et al. Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nat. Biotechnol. 31 (2013), 688–691.
20. [20] Svitashev, S., Young, J.K., Schwartz, C., et al. Targeted mutagenesis, precise gene editing, and site-specific gene insertion in maize using Cas9 and guide RNA. Plant Physiol. 169 (2015), 931–945.
21. [21] Sauer, N.J., Narváez-Vásquez, J., Mozoruk, J., et al. Oligonucleotide-mediated genome editing provides precision and function to engineered nucleases and antibiotics in plants. Plant Physiol. 170 (2016), 1917–1928.
22. [22] Zhao, Y., Zhang, C., Liu, W., et al. An alternative strategy for targeted gene replacement in plants using a dual-sgRNA/Cas9 design. Sci. Rep., 6, 2016, 23890, 10.1038/srep23890.
23. [23] Sun, Y., Zhang, X., Wu, C., et al. Engineering herbicide-resistant rice plants through CRISPR/Cas9-mediated homologous recombination of acetolactate synthase. Mol. Plant 9 (2016), 628–631.
24. [24] Woo, J.W., Kim, J., Kwon, S.I., et al. DNA-free genome editing in plants with preassembled CRISPR-Cas9 ribonucleoproteins. Nat. Biotechnol. 33 (2015), 1162–1164.
25. [25] Lowder, L., Zhang, Y., Baltes, N., et al. A CRISPR/Cas9 toolbox for multiplexed plant genome editing and transcriptional regulation. Plant Physiol. 169 (2015), 971–985.
26. [26] Xie, K., Minkenberg, B., Yang, Y., Boosting CRISPR/Cas9 multiplex editing capability with the endogenous tRNA-processing system. Proc. Natl. Acad. Sci. U. S. A. 112 (2015), 3570–3575.
27. [27] Ma, X., Zhang, Q., Zhu, Q., et al. A robust CRISPR/Cas9 system for convenient, high-efficiency multiplex genome editing in monocot and dicot plants. Mol. Plant 8 (2015), 1274–1284.
28. [28] Feng, Z., Mao, Y., Xu, N., et al. Multigeneration analysis reveals the inheritance, specificity, and patterns of CRISPR/Cas-induced gene modifications in Arabidopsis. Proc. Natl. Acad. Sci. U. S. A. 111 (2014), 4632–4637.
29. [29] Pan, C., Ye, L., Qin, L., et al. CRISPR/Cas9-mediated efficient and heritable targeted mutagenesis in tomato plants in the first and later generations. Sci. Rep., 6, 2016, 24765, 10.1038/srep24765.
30. [30] Zhang, H., Zhang, J., Wei, P., et al. The CRISPR/Cas9 system produces specific and homozygous targeted gene editing in rice in one generation. Plant Biotechnol. J. 12 (2014), 797–807.
31. [31] Endo, M., Mikami, M., Toki, S., Multi-gene knockout utilizing off-target mutations of the CRISPR/Cas9 system in rice. Plant Cell Physiol. 56 (2015), 41–47.
32. [32] Xie, K., Yang, Y., RNA-guided genome editing in plants using a CRISPR–Cas system. Mol. Plant 6 (2013), 1975–1983.
33. [33] Xie, K., Zhang, J., Yang, Y., Genome-wide prediction of highly specific guide RNA spacers for CRISPR-Cas9-mediated genome editing in model plants and major crops. Mol. Plant 7 (2014), 923–926.
34. [34] Jain, M., Function genomics of abiotic stress tolerance in plants: a CRISPR approach. Front. Plant Sci., 6, 2015, 375, 10.3389/fpls.2015.00375.
35. [35] Shi, J., Gao, H., Wang, H., et al. ARGOS8 variants generated by CRISPR-Cas9 improve maize grain yield under field drought stress conditions. Plant Biotechnol. J., 2016, 10.1111/pbi.12603.
36. [36] Osakabe, Y., Watanabe, T., Sugano, S.S., et al. Optimization of CRISPR/Cas9 genome editing to modify abiotic stress responses in plants. Sci. Rep., 6, 2016, 26685, 10.1038/srep26685.
37. [37] Alagoz, Y., Gurkok, T., Zhang, B., et al. Manipulating the biosynthesis of bioactive compound alkaloids for next-generation metabolic engineering in opium poppy using CRISPR-Cas 9 genome editing technology. Sci. Rep., 2016, 10.1038/srep30910.
38. [38] Bikard, D., Jiang, W., Samai, P., et al. Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucl. Acids Res. 41 (2013), 7429–7437.
39. [39] Tanenbaum, M.E., Gilbert, L.A., Qi, L.S., et al. A protein-tagging system for signal amplification in gene expression and fluorescence imaging. Cell 159 (2014), 635–646.
40. [40] Konermann, S., Brigham, M.D., Trevino, A.E., et al. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature 517 (2015), 583–588.
41. [41] Chavez, A., Scheiman, J., Vora, S., et al. Highly efficient Cas9-mediated transcriptional programming. Nat. Methods 12 (2015), 326–328.
42. [42] Farzadfard, F., Perli, S.D., Lu, T.K., Tunable and multifunctional eukaryotic transcription factors based on CRISPR/Cas. ACS Synth. Biol. 2 (2013), 604–613.
43. [43] Piatek, A., Ali, Z., Baazim, H., et al. RNA-guided transcriptional regulation in planta via synthetic dCas9-based transcription factors. Plant Biotechnol. J. 13 (2015), 578–589.
44. [44] Chavez, A., Tuttle, M., Pruitt, B.W., et al. Comparison of Cas9 activators in multiple species. Nat. Methods 13 (2016), 563–567.
45. [45] Qi, L.S., Larson, M.H., Gilbert, L.A., et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152 (2013), 1173–1183.
46. [46] Gilbert, L.A., Larson, M.H., Morsut, L., et al. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154 (2013), 442–451.
47. [47] La Russa, M.F., Qi, L.S., The new state of the art: cas9 for gene activation and repression. Mol. Cell. Biol. 35 (2015), 3800–3809.
48. [48] Mercx, S., Tollet, J., Magy, B., et al. Gene inactivation by CRISPR-Cas9 in Nicotiana tabacum BY-2 suspension cells. Front. Plant Sci., 7, 2016, 40, 10.3389/fpls.2016.00040.
49. [49] Vojta, A., Dobrinić, P., Tadić, V., et al. Repurposing the CRISPR-Cas9 system for targeted DNA methylation. Nucl. Acids Res. 44 (2016), 5615–5628.
50. [50] Hilton, I.B., D'Ippolito, A.M., Vockley, C.M., et al. Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat. Biotechnol. 33 (2015), 510–517.
51. [51] Kearns, N.A., Pham, H., Tabak, B., et al. Functional annotation of native enhancers with a Cas9-histone demethylase fusion. Nat. Methods 12 (2015), 401–403.
52. [52] Paszkowshi, J., Controlled activation of retrotransposition for plant breeding. Curr. Opin. Biotechnol. 32 (2015), 200–206.
53. [53] Chen, B., Gilbert, L.A., Cimini, B.A., et al. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 155 (2013), 1479–1491.
54. [54] Ma, H., Naseri, A., Reyes-Gutierrez, P., et al. Multicolor CRISPR labeling of chromosomal loci in human cells. Proc. Natl. Acad. Sci. U. S. A. 112 (2015), 3002–3007.
55. [55] Schaeffer, S.C., Nakata, P.A., The expanding footprint of CRISPR/Cas9 in the plant sciences. Plant Cell Rep. 35 (2016), 1451–1468.
56. [56] Liang, P., Xu, Y., Zhang, X., et al. CRISPR/Cas9-mediated gene editing in human tripronuclear zygotes. Protein Cell 6 (2015), 363–372.
57. [57] Nejat, N., Rookes, J., Mantri, N.L., et al. Plant–pathogen interactions: toward development of next-generation disease-resistant plants. Crit. Rev. Biotechnol. 22 (2016), 1–9.
58. [58] Belhaj, K., Chaparro-Garcia, A., Kamoun, S., et al. Editing plant genomes with CRISPR/Cas9. Curr. Opin. Biotechnol. 32 (2015), 76–84.
59. [59] Gross, M., Harvest time for CRISPR-Cas?. Curr. Biol. 26 (2016), R903–R905.
60. [60] Jiang, W., Zhou, H., Bi, H., et al. Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice. Nucl. Acids Res., 41, 2013, 10.1093/nar/gkt780.
61. [61] Upadhyay, S.K., Kumar, J., Alok, A., et al. RNA-guided Genome Editing for Target Gene Mutations in Wheat. 2013, 2233–2238 G3 (Bethesda) 3.
62. [62] Shan, Q., Wang, Y., Li, J., et al. Targeted genome modification of crop plants using a CRISPR-Cas system. Nat. Biotechnol. 31 (2013), 686–688.
63. [63] Wang, Y., Cheng, X., Shan, Q., et al. Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. Nat. Biotechnol. 32 (2014), 947–951.
64. [64] Martinelli, F., Grillone, G., Sgroi, F., Proposal of a genome editing system for genetic resistance to tomato spotted wilt virus. Am. J. Appl. Sci. 11 (2014), 1904–1913.
65. [65] Brooks, C., Nekrasov, V., Lippman, Z.B., et al. Efficient gene editing in tomato in the first generation using the clustered regularly interspaced short palindromic repeats/CRISPR-associated9 system. Plant Physiol. 166 (2014), 1292–1297.
66. [66] Jia, H., Wang, N., Targeted genome editing of sweet orange using Cas9/sgRNA. PloS One, 9, 2014, e93806, 10.1371/journal.pone.0093806.
67. [67] Liang, Z., Zhang, K., Chen, K., et al. Targeted mutagenesis in Zea mays using TALENs and the CRISPR/Cas system. J. Genet. Genomics 41 (2014), 63–68.
68. [68] Xu, R., Li, H., Qin, R., et al. Gene targeting using the Agrobacterium tumefaciens-mediated CRISPR-Cas system in rice. Rice, 7, 2014, 5, 10.1186/s12284-014-0005-6.
69. [69] Fauser, F., Schiml, S., Puchta, H., Both CRISPR/Cas-based nucleases and nickases can be used efficiently for genome engineering in Arabidopsis thaliana. Plant J 79 (2014), 348–359.
70. [70] Sugano, S.S., Shirakawa, M., Takagi, J., et al. CRISPR/Cas9 mediated targeted mutagenesis in the liverwort Marchantia polymorpha L. Plant Cell Physiol. 55 (2014), 475–481.
71. [71] Ali, Z., Abulfaraj, A., Idris, A., et al. CRISPR/Cas9-mediated viral interference in plants. Genome Biol., 16, 2015, 238, 10.1186/s13059-015-0799-6.
72. [72] Ji, X., Zhang, H., Zhang, Y., et al. Establishing a CRISPR–Cas-like immune system conferring DNA virus resistance in plants. Nat. Plants, 1, 2015, 15144, 10.1038/nplants.2015.144.
73. [73] Baltes, N.J., Hummel, A.W., Konecna, E., et al. Conferring resistance to geminiviruses with the CRISPR–Cas prokaryotic immune system. Nat. Plants, 1, 2015, 15145, 10.1038/nplants.2015.145.
74. [74] Gao, J., Wang, G., Ma, S., et al. CRISPR/Cas9-mediated targeted mutagenesis in Nicotiana tabacum. Plant Mol. Biol. 87 (2015), 99–110.
75. [75] Fan, D., Liu, T., Li, C., et al. Efficient CRISPR/Cas9-mediated targeted mutagenesis in Populus in the first generation. Sci. Rep., 5, 2015, 12217, 10.1038/srep12217.
76. [76] Chandrasekaran, J., Brumin, M., Wolf, D., et al. Development of broad virus resistance in non-transgenic cucumber using CRISPR/Cas9 technology. Mol. Plant Pathol. 17 (2016), 1140–1153.
77. [77] Wang, F., Wang, C., Liu, P., et al. Enhanced rice blast resistance by CRISPR/Cas9-targeted mutagenesis of the ERF transcription factor gene OsERF922. PloS One, 11, 2016, e0154027, 10.1371/journal.pone.0154027.
78. [78] Nishitani, C., Hirai, N., Komori, S., et al. Efficient genome editing in apple using a CRISPR/Cas9 system. Sci. Rep., 6, 2016, 31481, 10.1038/srep31481.
79. [79] Ren, C., Liu, X., Zhang, Z., et al. CRISPR/Cas9-mediated efficient targeted mutagenesis in Chardonnay (Vitis vinifera L.). Sci. Rep., 6, 2016, 32289, 10.1038/srep32289.