Insights into maize genome editing via CRISPR/Cas9

Belhaj K, Chaparro-Garcia A, Kamoun S, Nekrasov V (2013) Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system. Plant Methods 9:39 Beumer KJ, Trautman JK, Christian M, Dahlem TJ, Lake CM, Hawley RS, Grunwald DJ, Voytas DF, Carroll D (2013) Comparing zinc finger nucleases and transcription activator-like effector nucleases for gene targeting in Drosophila. G3 Genes Genomes Genet 3(10):1717–1725 Bortesi L, Fischer R (2015) The CRISPR/Cas9 system for plant genome editing and beyond. Biotechnol Adv 33:41–52 Brooks C, Nekrasov V, Lippman ZB, 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 Brutnell TP (2002) Transposon tagging in maize. Funct Integr Genomics 2:4–12 Char SN, Neelakandan AK, Nahampun H, Frame B, Main M, Spalding MH, Becraft PW, Meyers BC, Walbot V, Wang K, Yang B (2017) An Agrobacterium-delivered CRISPR/Cas9 system for high-frequency targeted mutagenesis in maize. Plant Biotechnol J 15:257–268 Chen JS, Dagdas YS, Kleinstiver BP, Welch MM, Sousa AA, Harrington LB, Sternberg SH, Joung JK, Yildiz A, Doudna JA (2017) Enhanced proofreading governs CRISPR–Cas9 targeting accuracy. Nature 550(7676):407–410 Doudna JA, Charpentier E (2014) The new frontier of genome engineering with CRISPR–Cas9. Science 346(6213):1258096 Feng C, Yuan J, Wang R, Liu Y, Birchler JA, Han F (2016) Efficient targeted genome modification in maize using CRISPR/Cas9 system. J Genet Genomics 43:37–43 Gao J, Wang G, Ma S, Xie X, Wu X, Zhang X, Wu Y, Zhao P, Xia Q (2015) CRISPR/Cas9-mediated targeted mutagenesis in Nicotiana tabacum. Plant Mol Biol 87:99–110 Gasser CS, Fraley RT (1992) Transgenic crops. Sci Am 266:62–69 Gilbert LA, Larson MH, Morsut L, Liu Z, Brar GA, Torres SE, Stern-Ginossar N, Brandman O, Whitehead EH, Doudna JA, Lim WA (2013) CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154(2):442–451 Haeussler M, Schönig K, Eckert H, Eschstruth A, Mianné J, Renaud JB, Maunoury SS, Shkumatava A, Teboul L, Joly JS (2016) Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biol 17:148 Jia H, Wang N (2014) Targeted genome editing of sweet orange using Cas9/sgRNA. PLoS ONE 9:e93806 Jiang W, Zhou H, Bi H, Fromm M, Yang B, Weeks DP (2013) Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice. Nucleic Acids Res 41:e188 Jiang W, Yang B, Weeks DP (2014) Efficient CRISPR/Cas9-mediated gene editing in Arabidopsis thaliana and inheritance of modified genes in the T2 and T3 generations. PLoS ONE 9:e99225 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 Joung JK, Sander JD (2013) TALENs: a widely applicable technology for targeted genome editing. Nat Rev Mol Cell Biol 14(1):49–55. https://doi.org/10.1038/nrm3486 Kim H, Kim JS (2014) A guide to genome engineering with programmable nucleases. Nat Rev Genet 15:321–334 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 31:688–691 Liang Z, Zhang K, Chen K, Gao C (2014) Targeted mutagenesis in Zea mays using TALENs and the CRISPR/Cas system. J Genet Genomics 41:63–68 Mali P, Esvelt KM, Church GM (2013) Cas9 as a versatile tool for engineering biology. Nat Methods 10:957–963 Mazumdar S, Quick WP, Bandyopadhyay A (2016) CRISPR–Cas9 mediated genome editing in rice, advancements and future possibilities. Indian J Plant Physiol 21:437–445 Mikami M, Toki S, Endo M (2016) Precision targeted mutagenesis via Cas9 paired nickases in rice. Plant Cell Physiol 57:1058–1068 Murugan K, Babu K, Sundaresan R, Rajan R, Sashital DG (2017) The Revolution continues: newly discovered systems expand the CRISPR-Cas toolkit. Mol Cell 68(1):15–25 Newman M, Ausubel FM (2016) Introduction to gene editing and manipulation using CRISPR/Cas9 technology. Curr Protoc Mol Biol 115:1–6 O’Connell MR, Oakes BL, Sternberg SH, East-Seletsky A, Kaplan M, Doudna JA (2014) Programmable RNA recognition and cleavage by CRISPR/Cas9. Nature 516(7530):263–266 Pegoraro C, Mertz LM, da Maia LC, Rombaldi CV, de Oliveira AC (2011) Importance of heat shock proteins in maize. J Crop Sci Biotechnol 14:85–95 Peng R, Lin G, Li J (2016) Potential pitfalls of CRISPR/Cas9-mediated genome editing. FEBS J 283:1218–1231 Pennisi E (2015) US researchers call for greater oversight of powerful genetic technology. Science Insider. http://news.sciencemag.org/biology/2014/07/us-researchers-call-greater-oversight-powerful-genetic-technology. Accessed 3 May 2015 Puchta H, Dujon B, Hohn B (1993) Homologous recombination in plant cells is enhanced by in vivo induction of double strand breaks into DNA by a site-specific endonuclease. Nucl Acids Res 21:5034–5040 Qi W, Zhu T, Tian Z, Li C, Zhang W, Song R (2016) High-efficiency CRISPR/Cas9 multiplex gene editing using the glycine tRNA-processing system-based strategy in maize. BMC Biotechnol 16:58 Radzisheuskaya A, Shlyueva D, Müller I, Helin K (2016) Optimizing sgRNA position markedly improves the efficiency of CRISPR/dCas9-mediated transcriptional repression. Nucl Acids Res 44:e141 Reis A, Hornblower B, Robb B, Tzertzinis G (2014) CRISPR/Cas9 and targeted genome editing: a new era in molecular biology. NEB Expr 1:3–6 Sander JD, Joung JK (2014) CRISPR-Cas systems for editing, regulating and targeting genomes. Nat Biotechnol 32:347–355 Shalem O, Sanjana NE, Zhang F (2015) High-throughput functional genomics using CRISPR–Cas9. Nat Rev Genet 16:299–311 Shan Q, Wang Y, Li J, Gao C (2014) Genome editing in rice and wheat using the CRISPR/Cas system. Nat Protoc 9:2395–2410 Shen B, Zhang W, Zhang J, Zhou J, Wang J, Chen L, Wang L, Hodgking A, Iyer V, Huang X, Skarnes WC (2014) Efficient genome modification by CRISPR–Cas9 nickase with minimal off-target effects. Nat Methods 11:399–402 Shi J, Gao H, Wang H, Lafitte HR, Archibald RL, Yang M, Hakimi SM, Mo H, Habben JE (2017) ARGOS8 variants generated by CRISPR–Cas9 improve maize grain yield under field drought stress conditions. Plant Biotechnol J 15:207–216 Singh R, Kuscu C, Quinlan A, Qi Y, Adli M (2015) Cas9-chromatin binding information enables more accurate CRISPR off-target prediction. Nucleic Acids Res 43:e118 Stemmer M, Thumberger T, del Sol Keyer M, Wittbrodt J, Mateo JL (2015) CCTop: an intuitive, flexible and reliable CRISPR/Cas9 target prediction tool. PLoS ONE 10:e0124633 Sun X, Hu Z, Chen R, Jiang Q, Song G, Zhang H, Xi Y (2015) Targeted mutagenesis in soybean using the CRISPR–Cas9 system. Sci Rep 5:10342 Svitashev S, Young JK, Schwartz C, Gao H, Falco SC, Cigan AM (2015) Targeted mutagenesis, precise gene editing, and site-specific gene insertion in maize using Cas9 and guide RNA. Plant Physiol 169:931–945 Svitashev S, Schwartz C, Lenderts B, Young JK, Cigan AM (2016) Genome editing in maize directed by CRISPR–Cas9 ribonucleoprotein complexes. Nat Commun 7:13274 Walbot V (2000) Saturation mutagenesis using maize transposons. Curr Opin Plant Biol 3:103–107 Waltz E (2016) CRISPR-edited crops free to enter market, skip regulation. Nat Biotechnol 34:582–583 Wang T, Wei JJ, Sabatini DM, Lander ES (2014) Genetic screens in human cells using the CRISPR–Cas9 system. Science 343:80–84 Wang S, Zhang S, Wang W, Xiong X, Meng F, Cui X (2015) Efficient targeted mutagenesis in potato by the CRISPR/Cas9 system. Plant Cell Rep 34:1473–1476 Wu X, Scott DA, Kriz AJ, Chiu AC, Hsu PD, Dadon DB, Cheng AW, Trevino AE, Konermann S, Chen S, Jaenisch R (2014) Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat Biotechnol 32:670–676 Xie K, Zhang J, Yang Y (2014) Genome-wide prediction of highly specific guide RNA spacers for CRISPR–Cas9-mediated genome editing in model plants and major crops. Mol Plant 7:923–926 Xing HL, Dong L, Wang ZP, Zhang HY, Han CY, Liu B, Wang XC, Chen QJ (2014) A CRISPR/Cas9 toolkit for multiplex genome editing in plants. BMC Plant Biol 14:327 Yadava P, Abhishek A, Singh R, Singh I, Kaul T, Pattanayak A, Agrawal PK (2017) Advances in maize transformation technologies and development of transgenic maize. Front Plant Sci 7:1949 Zhang XH, Tee LY, Wang XG, Huang QS, Yang SH (2015) Off-target effects in CRISPR/Cas9-mediated genome engineering. Mol Ther Nucleic Acids 4:e264 Zhang Y, Liang Z, Zong Y, Wang Y, Liu J, Chen K, Qiu JL, Gao C (2016) Efficient and transgene-free genome editing in wheat through transient expression of CRISPR/Cas9 DNA or RNA. Nat Commun 7:12617 Zhao Y, Zhang C, Liu W, Gao W, Liu C, Song G, Li WX, Mao L, Chen B, Xu Y, Li X, Xie C (2016) An alternative strategy for targeted gene replacement in plants using a dual-sgRNA/Cas9 design. Sci Rep 6:23890 Zhu J, Song N, Sun S, Yang W, Zhao H, Song W, Lai J (2016) Efficiency and inheritance of targeted mutagenesis in maize using CRISPR–Cas9. J Genet Genomics 43:25–36 Zong Y, Wang Y, Li C, Zhang R, Chen K, Ran Y, Qiu JL, Wang D, Gao C (2017) Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion. Nat Biotechnol 35:438–440