THE JOURNEY OF CRISPR-CAS9 FROM BACTERIAL DEFENSE MECHANISM TO A GENE EDITING TOOL IN BOTH ANIMALS AND PLANTS

T Tahir; Q Ali; MS Rashid; A Malik

doi:10.54112/bcsrj.v2020i1.17

Authors

T Tahir Institute of Molecular Biology & Biotechnology, University of Lahore, Lahore, Pakistan
Q Ali Institute of Biotechnology and Molecular Biology, The University of Lahore, Lahore
MS Rashid Institute of Molecular Biology & Biotechnology, University of Lahore, Lahore, Pakistan
A Malik Institute of Molecular Biology & Biotechnology, University of Lahore, Lahore, Pakistan

DOI:

https://doi.org/10.54112/bcsrj.v2020i1.17

Keywords:

CRISPR-Cas9, endonucleases, geen editing, immune system, zinc finger, TALENS

Abstract

Today we can use multiple of endonucleases for genome editing which has become very important and used in number of applications. We use sequence specific molecular scissors out of which, most important are mega nucleases, zinc finger nucleases, TALENS (Transcription Activator Like-Effector Nucleases) and CRISPR-Cas9 which is currently the most famous due to a number of reasons, they are cheap, easy to build, very specific in nature and their success rate in plants and animals is also high. Who knew that one day these CRISPR discovered as a part of immune system of bacteria will be this much worthwhile in the field of genetic engineering? This review interprets the science behind their mechanism and how several advancements were made with the passage of time to make them more efficient for the assigned job.

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References

Abudayyeh O.O., Gootenberg J.S., Essletzbichler P., Han S., Joung J., Belanto J.J., Verdine V., Cox D.B.T., Kellner M.J., Regev A., et al. (2017). RNA targeting with CRISPR-Cas13. Nature. 550:280–284. DOI: https://doi.org/10.1038/nature24049

Abudayyeh O.O., Gootenberg J.S., Konermann S., Joung J., Slaymaker I.M., Cox D.B.T., Shmakov S., Makarova K.S., Semenova E., Minakhin L., et al. (2016). C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science 353:aaf5573. DOI: https://doi.org/10.1126/science.aaf5573

Ahi YS, Bangari DS, Mittal SK. (2011). Adenoviral vector immunity: its implications and circumvention strategies. CGT 11:307–20. DOI: https://doi.org/10.2174/156652311796150372

Ali, Z., Abul Faraj A., Li L., Ghosh N., Piatek M., Mahjoub A., Aouida M., et al. (2015). Efficient virus mediated genome editing in plants using the CRISPR/Cas9 system. Molecular Plant 8: 1288–1291. DOI: https://doi.org/10.1016/j.molp.2015.02.011

Altpeter, F. , Springer N. M., Bartley L. E., Blechl A. E., Brutnell T. P., Citovsky V., Conrad L. J., et al. (2016). Advancing crop transformation in the era of genome editing. The Plant Cell 28: 1510–1520. DOI: https://doi.org/10.1105/tpc.16.00196

Antonio Regalado, China's CRISPR twins might have had their brains inadvertently enhanced, mit tech. rev (Feb. 21, 2019), https://www.technologyreview.com/s/612997/the-crispr-twins-had-their-brains-altered/ (accessed Mar. 12, 2019)

Arnould, Sylvain; Perez, Christophe; Cabaniols, Jean-Pierre; Smith, Julianne; Gouble, Agnès; Grizot, Sylvestre; Epinat, Jean-Charles; Duclert, Aymeric; Duchateau, Philippe (2007-08-03). "Engineered I-CreI derivatives cleaving sequences from the human XPC gene can induce highly efficient gene correction in mammalian cells". Journal of Molecular Biology. 371 (1): 49–65. DOI: https://doi.org/10.1016/j.jmb.2007.04.079

Badis, G., Berger, M.F., Philippakis, A.A., et al. (2009). Diversity and complexity in DNA recognition by transcription factors. Science. 324(5935):1720–1723. DOI: https://doi.org/10.1126/science.1162327

Bao A., Burritt D. J., Chen H., Zhou X., Cao D., Tran L. P. (2019). The CRISPR/Cas9 system and its applications in crop genome editing. Crit. Rev. Biotechnol. 39, 1–16. DOI: https://doi.org/10.1080/07388551.2018.1554621

Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., Moineau, S., Romero, D.A., Horvath, P. (2007). CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:1709–1712. DOI: https://doi.org/10.1126/science.1138140

Barrangou, R., Marraffini, L.A. (2014). CRISPR-cas systems: Prokaryotes upgrade to adaptive immunity. Mol. Cell. 54:234–244. DOI: https://doi.org/10.1016/j.molcel.2014.03.011

Bassuk, A.G., Zheng, A., Li, Y., Tsang, S.H. and Mahajan, V.B., (2016). Precision medicine: genetic repair of retinitis pigmentosa in patient-derived stem cells. Scientific reports, 6, p.19969. DOI: https://doi.org/10.1038/srep19969

Bayat, H., Modarressi, M.H., Rahimpour, A. (2018). The conspicuity of CRISPR-Cpf1 system as a significant breakthrough in genome editing. Curr Microbiol. 75(1):107–115. DOI: https://doi.org/10.1007/s00284-017-1406-8

Bestor TH. (2000). Gene silencing as a threat to the success of gene therapy. J Clin Invest 105:409–11. DOI: https://doi.org/10.1172/JCI9459

Beumer, K.J., Trautman, J.K., Bozas, A., Liu, J.L., Rutter, J., et al. (2008) Efficient gene targeting in Drosophila by direct embryo injection with zinc-finger nucleases. Proc Natl Acad Sci U S A 105: 19821–19826 DOI: https://doi.org/10.1073/pnas.0810475105

Bhat J.A., Ali S., Salgotra R.K., Mir Z.A., Dutta S., Jadon V., Tyagi A., Mushtaq M., Jain N., Singh P. (2017). Genomic selection in the era of next generation sequencing for complex traits in plant breeding. Front. Genet. 7:221. DOI: https://doi.org/10.3389/fgene.2016.00221

Bikard D., Jiang W., Samai P., Hochschild A., Zhang F., Marraffini L.A. (2013). Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Res. 41:7429–7437. DOI: https://doi.org/10.1093/nar/gkt520

Bo W., Zhaohui Z., Huanhuan Z., Xia W., Binglin L., Lijia Y., Xiangyan H., Deshui Y., Xuelian Z., Chunguo W. (2019). Targeted Mutagenesis of NAC Transcription Factor Gene, OsNAC041, Leading to Salt Sensitivity in Rice. Rice Sci. 26:98–108. DOI: https://doi.org/10.1016/j.rsci.2018.12.005

Boch J., Scholze H., Schornack S., Landgraf A., Hahn S., Kay S., Lahaye T., Nickstadt A., Bonas U. (2009). Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors. Science. 326:1509–1512. DOI: https://doi.org/10.1126/science.1178811

Bolukbasi, M.F., Gupta, A., Oikemus, S., et al. (2015). DNA-binding-domain fusions enhance the targeting range and precision of Cas9. Nat Methods 12:1150–6. DOI: https://doi.org/10.1038/nmeth.3624

Bonamassa B, Hai L, Liu D. (2011). Hydrodynamic gene delivery and its applications in pharmaceutical research. Pharm Res 28:694–701. DOI: https://doi.org/10.1007/s11095-010-0338-9

Brown, M.T., Cooperm J.A. (1996). Regulation, substrates and functions of src. Biochim Biophys Acta. 1287:121–149. DOI: https://doi.org/10.1016/0304-419X(96)00003-0

Bruder M. R., Pyne M. E., Moo-Young M., Chung D. A., Chou C. P. (2016). Extending CRISPR-Cas9 technology from genome editing to transcriptional engineering in Clostridium. Appl. Environ. Microbiol. 82, 6109–6119. DOI: https://doi.org/10.1128/AEM.02128-16

Campa, C.C., Weisbach N.R., Santinha A.J., Incarnato D., and Platt R.J. (2019). Multiplexed genome engineering by Cas12a and CRISPR arrays encoded on single transcripts. Nature Methods 16: 887–893. DOI: https://doi.org/10.1038/s41592-019-0508-6

Cannon, P., June, C (2011) Chemokine receptor 5 knockout strategies. Current Opinion in HIV and AIDS 6: 74–79. DOI: https://doi.org/10.1097/COH.0b013e32834122d7

Chen, S., Sanjana N.E., Zheng K., Shalem O., Shi X., Scott D.A., Song J., Pan J.Q., Weissleder R., Zhang F., et al. (2015). Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis. Cell. 160:1246–1260. DOI: https://doi.org/10.1016/j.cell.2015.02.038

Chiou SH, Winters IP, Wang J, et al. (2015). Pancreatic cancer modeling using retrograde viral vector delivery and in vivo CRISPR/Cas9-mediated somatic genome editing. Genes Dev. 29:1576–1585. DOI: https://doi.org/10.1101/gad.264861.115

Cho, S.W., Kim, S., Kim, Y., et al. (2014). Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Res 24:132–41. DOI: https://doi.org/10.1101/gr.162339.113

Choi, P.S., Meyerson, M. (2014). Targeted genomic rearrangements using CRISPR/Cas technology. Nat Commun. 5:3728. DOI: https://doi.org/10.1038/ncomms4728

Chu VT, Weber T, Wefers B, et al. (2015). Increasing the efficiency of homology-directed repair for CRISPR-Cas9-induced precise gene editing in mammalian cells. Nat Biotechnol 33:543–8. DOI: https://doi.org/10.1038/nbt.3198

Cohen S.N., Chang A.C.Y., Boyer H.W., Helling R.B. (1973). Construction of Biologically Functional Bacterial Plasmids In Vitro. Proc. Natl. Acad. Sci. USA.;70:3240–3244. DOI: https://doi.org/10.1073/pnas.70.11.3240

Cong, L., Ran, F.A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P.D., Wu, X., Jiang, W., Marraffini, L.A., Zhang, F. (2013). Multiplex genome engineering using CRISPR/Cas systems. Science 339:819–823. DOI: https://doi.org/10.1126/science.1231143

Cradick, T.J., Fine, E.J., Antico, C.J., Bao, G. (2013). CRISPR/Cas9 systems targeting beta-globin and CCR5 genes have substantial off-target activity. Nucleic Acids Res 41:9584–92. DOI: https://doi.org/10.1093/nar/gkt714

Daya S, Berns KI. (2008). Gene therapy using adeno-associated virus vectors. Clin Microbiol Rev 21:583–93. DOI: https://doi.org/10.1128/CMR.00008-08

de Miguel Beriain I, del Cano AMM. (2018). Chapter 12 Gene editing in human embryos. A comment on the ethical issues involved. In: Soniewicka M , editor. The Ethics of Reproductive Genetics: Between Utility, Principles, and Virtues. Springer, Cham; 2018. pp. 173–183. DOI: https://doi.org/10.1007/978-3-319-60684-2_12

Dellomonaco C., Fava F., Gonzalez R. (2010). The path to next generation biofuels: Successes and challenges in the era of synthetic biology. Microb. Cell Fact. 9:3 DOI: https://doi.org/10.1186/1475-2859-9-3

Deyle DR, Russell DW. (2009). Adeno-associated virus vector integration. Curr Opin Mol Ther 11:442–7.

Dufossé L., Fouillaud M., Caro Y., Mapari S. A., Sutthiwong N. (2014). Filamentous fungi are large-scale producers of pigments and colorants for the food industry. Curr. Opin. Biotech. 26, 56–61. DOI: https://doi.org/10.1016/j.copbio.2013.09.007

Elbashir S.M., Harborth J., Lendeckel W., Yalcin A., Weber K., Tuschl T. (2001). Duplexes of 21 ± nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature. 411:494–498. DOI: https://doi.org/10.1038/35078107

Elferjani R., Soolanayakanahally R. (2018). Canola responses to drought, heat, and combined stress: shared and specific effects on carbon assimilation, seed yield, and oil composition. Front. Plant Sci. 9, 1224. DOI: https://doi.org/10.3389/fpls.2018.01224

Endo A., Masafumi M., Kaya H., Toki S. (2016). Efficient targeted mutagenesis of rice and tobacco genomes using Cpf1 from Francisella novicida. Sci. Rep. 6:38169. DOI: https://doi.org/10.1038/srep38169

Epinat, Jean-Charles; Arnould, Sylvain; Chames, Patrick; Rochaix, Pascal; Desfontaines, Dominique; Puzin, Clémence; Patin, Amélie; Zanghellini, Alexandre; Pâques, Frédéric (2003-06-01). "A novel engineered meganuclease induces homologous recombination in yeast and mammalian cells". Nucleic Acids Research. 31 (11): 2952–2962. DOI: https://doi.org/10.1093/nar/gkg375

Follenzi A, Santambrogio L, Annoni A. (2007). Immune responses to lentiviral vectors. Curr Gene Ther 7:306–15. DOI: https://doi.org/10.2174/156652307782151515

Fonfara I., Richter H., BratoviÄ M., Le Rhun A., Charpentier E. (2016). The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA. Nature. 532:517–521. DOI: https://doi.org/10.1038/nature17945

Fu, Y., Foden, J.A., Khayter, C., et al. (2013). High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat Biotechnol 31:822–6. DOI: https://doi.org/10.1038/nbt.2623

Gabriel, R., Lombardo, A., Arens, A., Miller, J.C., Genovese, P., Kaeppel, C., Nowrouzi, A., Bartholomae, C.C., Wang, J., Friedman, G., et al. (2011). An unbiased genome-wide analysis of zinc-finger nuclease specificity. Nat Biotechnol 29: 816–823. DOI: https://doi.org/10.1038/nbt.1948

Gao L., Cox D.B.T., Yan W.X., Manteiga J.C., Schneider M.W., Yamano T., Nishimasu H., Nureki O., Crosetto N., Zhang F. (2016). Engineered Cpf1 variants with altered PAM specificities. Nat. Biotechnol. 35:789–792.

Gao, L., Cox D. B. T., Yan W. X., Manteiga J. C., Schneider M. W., Yamano T., et al. (2017). Engineered Cpf1 variants with altered PAM specificities. Nat. Biotechnol. 35, 789–792. DOI: https://doi.org/10.1038/nbt.3900

Gasiunas, G., Barrangou, R., Horvath, P., Siksnys, V. (2012). Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc Natl Acad Sci U S A 109:E2579–E2586. DOI: https://doi.org/10.1073/pnas.1208507109

Geurts, A.M., Cost, G.J., Freyvert, Y., Zeitler, B., Miller, J.C., et al. (2009) Knockout Rats via Embryo Microinjection of Zinc-Finger Nucleases. Science 325: 433. DOI: https://doi.org/10.1126/science.1172447

Glass, Z. , Lee M., Li Y., and Xu Q.. 2018. Engineering the delivery system for CRISPR‐based genome editing. Trends in Biotechnology 36: 173–185. DOI: https://doi.org/10.1016/j.tibtech.2017.11.006

Grissa, I., Vergnaud, G., Pourcel, C. (2007). The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinform. 8:1–10. DOI: https://doi.org/10.1186/1471-2105-8-172

Guan Y, Ma Y, Li Q, et al. (2016). CRISPR/Cas9-mediated somatic correction of a novel coagulator factor IX gene mutation ameliorates hemophilia in mouse. EMBO Mol Med 8:477–88. DOI: https://doi.org/10.15252/emmm.201506039

Guilinger, J.P., Pattanayak, V., Reyon, D., Tsai, S.Q., Sander, J.D., Joung, J.K., Liu, D.R. (2014a). Broad specificity profiling of TALENs results in engineered nucleases with improved DNA-cleavage specificity. Nat Methods 11: 429–435. DOI: https://doi.org/10.1038/nmeth.2845

Halterman D., Guenthner J., Collinge S., Butler N., Douches D. (2015). Biotech Potatoes in the 21st Century: 20 years since the first biotech potato. Am. J. Potato 93: 1–20. DOI: https://doi.org/10.1007/s12230-015-9485-1

Hao Z., Su X. (2019). Fast gene disruption in Trichoderma reesei using in vitro assembled Cas9/gRNA complex. BMC Biotechnol. 19:2. DOI: https://doi.org/10.1186/s12896-018-0498-y

Horii T, Arai Y, Yamazaki M, et al. (2014). Validation of microinjection methods for generating knockout mice by CRISPR/Cas-mediated genome engineering. Sci Rep 4:4513. DOI: https://doi.org/10.1038/srep04513

Hunter M. C., Smith R. G., Schipanski M. E., Atwood L. W., Mortensen D. A. (2017). Agriculture in 2050: recalibrating targets for sustainable intensification. Bioscience 67, 385–390. DOI: https://doi.org/10.1093/biosci/bix010

Hsu PD, Lander ES, Zhang F. Development and applications of CRISPR-Cas9 for genome engineering. Cell. 2014;157:1262–1278 DOI: https://doi.org/10.1016/j.cell.2014.05.010

Ishino, Y., Shinagawam H., Makinom K., Amemura, M., Nakata, A. (1987). Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J Bacteriol 169:5429–5433. DOI: https://doi.org/10.1128/jb.169.12.5429-5433.1987

Jacobs J. Z., Ciccaglione K. M., Tournier V., Zaratiegui M. (2014). Implementation of the CRISPR-Cas9 system in fission yeast. Nat. Commun. 5:5344. 10.1038/ncomms6344 DOI: https://doi.org/10.1038/ncomms6344

Jansen, R., van Emben, J.D.A., Gaastra, W. and Schouls L.M. (2002). Identification of genes that are associated with DNA repeats in prokaryotes. Mol. Microbiol. 43 1565– DOI: https://doi.org/10.1046/j.1365-2958.2002.02839.x

Ji X. J., Ren L. J., Nie Z. K., Huang H., Ouyang P. K. (2014). Fungal arachidonic acid-rich oil: research, development and industrialization. Crit. Rew. Biotechnol. 34, 197–214. DOI: https://doi.org/10.3109/07388551.2013.778229

Jiang W, Bikard D, Cox D, Zhang F, Marraffini LA. (2013). RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat. Biotechnol. 31:233–239.

Jiang, F., Doudna J. A. (2017). CRISPR-Cas9 structures and mechanisms. Annu. Rev. Biophys. 46, 505–529.

Jiang, F., Doudna J. A. (2017). CRISPR-Cas9 structures and mechanisms. Annu. Rev. Biophys. 46, 505–529. DOI: https://doi.org/10.1146/annurev-biophys-062215-010822

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. Nucleic Acids Research 41: e188.

Jiang, W., Bikard, D., Cox, D., et al. (2013). RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol 31:233–9. DOI: https://doi.org/10.1038/nbt.2508

Jinek M, Chylinski K, Fonfara I, et al. (2012). A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337:816–21. DOI: https://doi.org/10.1126/science.1225829

Kabadi AM, Ousterout DG, Hilton IB, Gersbach CA. (2014). Multiplex CRISPR/Cas9-based genome engineering from a single lentiviral vector. Nucleic Acids Res 42:e147. DOI: https://doi.org/10.1093/nar/gku749

Kaminski R., Chen Y., Fischer T., Tedaldi E., Napoli A., Zhang Y., Karn J., Hu W., Khalili K. (2016). Elimination of HIV-1 Genomes from Human T-lymphoid Cells by CRISPR/Cas9 Gene Editing. Sci. Rep. 6:1–14. DOI: https://doi.org/10.1038/srep22555

Kaneko T., Sakuma T., Yamamoto T., Mashimo T. (2014). Simple knockout by electroporation of engineered endonucleases into intact rat embryos. Sci. Rep. 4:1–5. DOI: https://doi.org/10.1038/srep06382

Kaur N., Alok A., Shivani, Kaur N., Pandey P., Awasthi P., et al. . (2018). CRISPR/Cas9-mediated efficient editing in phytoene desaturase (PDS) demonstrates precise manipulation in banana cv. rasthali genome. Funct. Integr. Genomics 18, 89–99. DOI: https://doi.org/10.1007/s10142-017-0577-5

Kawamura, N., Nimura K., Nagano H., Yamaguchi S., Nonomura N., Kaneda Y. (2015) CRISPR/Cas9-mediated gene knockout of NANOG and NANOGP8 decreases the malignant potential of prostate cancer cells. Oncotarget. 6:22361–22374. DOI: https://doi.org/10.18632/oncotarget.4293

Kennedy, E.M., Bassit L.C., Mueller H., Kornepati A.V.R., Bogerd H.P., Nie T., Chatterjee P., Javanbakht H., Schinazi R.F., Cullen B.R. (2015). Suppression of hepatitis B virus DNA accumulation in chronically infected cells using a bacterial CRISPR/Cas RNA-guided DNA endonuclease. Virology. 476:196–205. DOI: https://doi.org/10.1016/j.virol.2014.12.001

Kerem B., Rommens J.M., Buchanan J.A., Markiewicz D., Cox T.K., Chakravarti A., Buchwald M., Tsui L.C. (1989). Identification of the cystic fibrosis gene: Genetic analysis. Science. 245:1073–1080. DOI: https://doi.org/10.1126/science.2570460

Khatodia, S., Bhatotia K., Passricha N., Khurana S. M., Tuteja N. (2016). The CRISPR/Cas genome-editing tool: application in improvement of crops. Front. Plant Sci. 7:506. DOI: https://doi.org/10.3389/fpls.2016.00506

Kim D, et al. (2016). Genome-wide analysis reveals specificities of Cpf1 endonucleases in human cells. Nat Biotechnol. 34:863–868. DOI: https://doi.org/10.1038/nbt.3609

Kim D., Kim D., Alptekin B., Budak H. (2017). CRISPR/Cas9 genome editing in wheat. Funct. Integr. Genomics. 18:31–41. DOI: https://doi.org/10.1007/s10142-017-0572-x

Kim H., Kim J.S. (2014). A guide to genome engineering with programmable nucleases. Nat. Rev. Genet. 15:321–334. DOI: https://doi.org/10.1038/nrg3686

Kim H., Kim S.T., Ryu J., Kang B.C., Kim J.S., Kim S.G. (2017). CRISPR/Cpf1-mediated DNA-free plant genome editing. Nat. Commun. 8:14406. DOI: https://doi.org/10.1038/ncomms14406

Kim S.K., Seong W., Han G.H., Lee D.H., Lee S.G. (2017). CRISPR interference-guided multiplex repression of endogenous competing pathway genes for redirecting metabolic flux in Escherichia coli. Microb. Cell Fact. 16:188. DOI: https://doi.org/10.1186/s12934-017-0802-x

Kim, D., Bae, S., Park, J., et al. (2015). Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells. Nat Methods. 12(3):237–243. DOI: https://doi.org/10.1038/nmeth.3284

Kim, S., Kim, D., Cho, S.W., et al. (2014). Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins. Genome Res 24:1012–9. DOI: https://doi.org/10.1101/gr.171322.113

Kim, Y.G., Cha, J., Chandrasegaran, S. (1996). Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proc Natl Acad Sci U S A 93: 1156–1160. DOI: https://doi.org/10.1073/pnas.93.3.1156

Kleinstiver, B.P., Pattanayak, V., Prew, M.S., et al. (2016). High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects. Nature 529:490–5. DOI: https://doi.org/10.1038/nature16526

Kleinstiver, B.P., Prew, M.S., Tsai, S.Q., et al. (2015). Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition. Nat Biotechnol 33:1293–8. DOI: https://doi.org/10.1038/nbt.3404

Klimek-Chodacka M., Oleszkiewicz T., Lowder L.G., Qi Y., Baranski R. (2018). Efficient CRISPR/Cas9-based genome editing in carrot cells. Plant Cell Rep. 37:575–586. DOI: https://doi.org/10.1007/s00299-018-2252-2

Langner T., Kamoun S., Belhaj K. (2018). CRISPR Crops: Plant Genome Editing Toward Disease Resistance. Annu. Rev. Phytopathol. 56:479–512. DOI: https://doi.org/10.1146/annurev-phyto-080417-050158

Lanzkron S., Carroll C.P., Haywood C., Jr. (2013). Mortality rates and age at death from sickle cell disease: U.S., 1979–2005. Public Health Rep.128:110–116. DOI: https://doi.org/10.1177/003335491312800206

Lee K, Conboy M, Park HM, et al. (2017). Nanoparticle delivery of Cas9 ribonucleoprotein and donor DNA in vivo induces homology-directed DNA repair. Nat Biomed Eng 1:889–901. DOI: https://doi.org/10.1038/s41551-017-0137-2

Lee, H.J., Kim, E., Kim, J.S. (2010). Targeted chromosomal deletions in human cells using zinc finger nucleases. Genome Res 20: 81–89. DOI: https://doi.org/10.1101/gr.099747.109

Li A., Jia S., Yobi A., Ge Z., Sato S. J., Zhang C., et al. (2018a). Editing of an Alpha-Kafirin gene family increases, digestibility and protein quality in Sorghum. Plant Physiol. 177, 1425–1438. DOI: https://doi.org/10.1104/pp.18.00200

Li B., Niu Y., Ji W., Dong Y. Strategies for the CRISPR-Based Therapeutics. Trends Pharmacol. Sci. 2020;41:55–65. DOI: https://doi.org/10.1016/j.tips.2019.11.006

Li C., Ding L., Sun C.W., Wu L.C., Zhou D., Pawlik K.M., Khodadadi-Jamayran A., Westin E., Goldman F.D., Townes T.M. (2016). Novel HDAd/EBV Reprogramming Vector and Highly Efficient Ad/CRISPR-Cas Sickle Cell Disease Gene Correction. Sci. Rep. 6:1–10 DOI: https://doi.org/10.1038/srep30422

Li H., Shen C. R., Huang C. H., Sung L. Y., Wu M. Y., Hu Y. C. (2016). CRISPR-Cas9 for the genome engineering of Cyanobacteria and succinate production. Metab. Eng. 38, 293–302. DOI: https://doi.org/10.1016/j.ymben.2016.09.006

Liang, P.P., Xu, Y.W., Zhang, X.Y., et al. (2015). CRISPR/Cas9-mediated gene editing in human tripronuclear zygotes. Protein Cell. 6(5):363–372. DOI: https://doi.org/10.1007/s13238-015-0153-5

Lin, S., Staahl, B.T., Alla, R.K., Doudna, J.A. (2014). Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery. Elife 3:e04766. DOI: https://doi.org/10.7554/eLife.04766

Liu, G. , Li J., and Godwin I. D.. 2019. Genome editing by CRISPR/Cas9 in sorghum through biolistic bombardment In Zhao Z. Y. and Dahlberg J. [eds.], Sorghum, 169–183. Humana Press, New York, New York, USA DOI: https://doi.org/10.1007/978-1-4939-9039-9_12

Liu, T., Shen J.K., Li Z., Choy E., Hornicek F.J., Duan Z. (2016). Development and potential applications of CRISPR-Cas9 genome editing technology in sarcoma. Cancer Lett. 373:109–118. DOI: https://doi.org/10.1016/j.canlet.2016.01.030

Ma H, Dang Y, Wu Y, et al. (2015). A CRISPR-based screen identifies genes essential for West-Nile-Virus-induced cell death. Cell Rep 12:673–83. DOI: https://doi.org/10.1016/j.celrep.2015.06.049

Ma, Y., Shen, B., Zhang, X., et al. (2014). Heritable multiplex genetic engineering in rats using CRISPR/Cas9. PLoS One 9:e89413 DOI: https://doi.org/10.1371/journal.pone.0089413

Macovei A., Sevilla N. R., Cantos C., Jonson G. B., Slamet-Loedin I., Èermák T., et al. (2018). Novel alleles of rice eIF4G generated by CRISPR/Cas9-targeted mutagenesis confer resistance to Rice tungro spherical virus. Plant Biotechnol. J. 16 1918–1927. DOI: https://doi.org/10.1111/pbi.12927

Mahas A., Neal Stewart C., Mahfouz M.M. (2018). Harnessing CRISPR/Cas systems for programmable transcriptional and post-transcriptional regulation. Biotechnol. Adv. 36:295–310. DOI: https://doi.org/10.1016/j.biotechadv.2017.11.008

Makarova, K.S., Grishin, N.V., Shabalina, S.A., Wolf, Y.I., and Koonin, E.V. (2006). A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol. Direct. 17 DOI: https://doi.org/10.1186/1745-6150-1-7

Mali P, Aach J, Stranges PB, et al. (2013). CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol 31:833–8. DOI: https://doi.org/10.1038/nbt.2675

Mali, P., Yang, L., Esvelt, K.M., Aach, J., Guell, M., DiCarlo, J.E., Norville, J.E., Church, G.M. (2013). RNA-guided human genome engineering via Cas9. Science 339:823–826. DOI: https://doi.org/10.1126/science.1232033

Malnoy M., Viola R., Jung M.-H., Koo O.-J., Kim S., Kim J.-S., Velasco R., Nagamangala Kanchiswamy C. (2016). DNA-free genetically edited grapevine and apple protoplast using CRISPR/Cas9 ribonucleoproteins. Front. Plant Sci.7:1904. DOI: https://doi.org/10.3389/fpls.2016.01904

Maruyama, T., Dougan, S.K., Truttmann, M.C., et al. (2015). Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining. Nat Biotechnol 33:538–42. DOI: https://doi.org/10.1038/nbt.3190

Miao J., Guo D., Zhang J., Huang Q., Qin G., Zhang X., et al. (2013). Targeted mutagenesis in rice using CRISPR-Cas system. Cell Res. 23 1233–1236. DOI: https://doi.org/10.1038/cr.2013.123

Modrzejewski, D., Hartung F., Sprink T., Krause D., Kohl C., and Wilhelm R. (2019). What is the available evidence for the range of applications of genome editing as a new tool for plant trait modification and the potential occurrence of associated off target effects: A systematic map. Environmental Evidence 8: 27. DOI: https://doi.org/10.1186/s13750-019-0171-5

Moehle, E.A., Rock, J.M., Lee, Y.L., Jouvenot, Y., DeKelver, R.C., Gregory, P.D., Urnov, F.D., Holmes, MC. (2007). Targeted gene addition into a specified location in the human genome using designed zinc finger nucleases. Proc Natl Acad Sci 104: 3055–3060. DOI: https://doi.org/10.1073/pnas.0611478104

Mojica MJ, Juez G, Rodríguez-Valera F. 1993. Transcription at different salinities of Haloferax mediterranei sequences adjacent to partially modified PstI sites. Mol Microbiol 9:613–621. DOI: https://doi.org/10.1111/j.1365-2958.1993.tb01721.x

Moore, J.K., Haber J.E. (1996). Cell cycle and genetic requirements of two pathways of nonhomologous end-joining repair of double-strand breaks in Saccharomyces cerevisiae. Mol. Cell. Biol. 16:2164–2173. DOI: https://doi.org/10.1128/MCB.16.5.2164

Moscou, M.J., Bogdanove, A.J. (2009). A simple cipher governs DNA recognition by TAL effectors. Science 326: 1501. DOI: https://doi.org/10.1126/science.1178817

Mout R, Ray M, Yesilbag Tonga G, et al. (2017). Direct cytosolic delivery of CRISPR/Cas9-ribonucleoprotein for efficient gene editing. ACS Nano 11:2452–8. DOI: https://doi.org/10.1021/acsnano.6b07600

Mussolino, C., Alzubi, J., Fine, E.J., Morbitzer, R., Cradick, T.J., Lahaye, T., Bao, G., Cathomen, T. (2014). TALENs facilitate targeted genome editing in human cells with high specificity and low cytotoxicity. Nucleic Acids Res 42: 6762–6773. DOI: https://doi.org/10.1093/nar/gku305

Nekrasov V, Staskawicz B, Weigel D, Jones JD, Kamoun S. (2013). Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease. Nat Biotechnol 31: 691-693. DOI: https://doi.org/10.1038/nbt.2655

Nishitani C., Hirai N., Komori S., Wada M., Okada K., Osakabe K., et al. (2016). Efficient genome editing in apple using a CRISPR/Cas9 system. Sci. Rep. 6:31481. DOI: https://doi.org/10.1038/srep31481

Osakabe Y., Osakabe K. Progress in Molecular Biology and Translational Science. Volume 149. Elsevier; Amsterdam, The Netherlands: 2017. Genome Editing to Improve Abiotic Stress Responses in Plants; pp. 99–109. DOI: https://doi.org/10.1016/bs.pmbts.2017.03.007

Papapetrou EP, Schambach A. (2016). Gene insertion into genomic safe harbors for human gene therapy. Mol Ther 24:678–84. DOI: https://doi.org/10.1038/mt.2016.38

Paques, F., Duchateau, P. (2007). Meganucleases and DNA double-strand break-induced recombination: perspectives for gene therapy. Curr Gene Ther 7: 49-66. DOI: https://doi.org/10.2174/156652307779940216

Pardo B., Gómez-González B., Aguilera A. (2009). DNA double-strand break repair: How to fix a broken relationship. Cell. Mol. Life Sci. 66:1039–1056. DOI: https://doi.org/10.1007/s00018-009-8740-3

Pattanayak, V., Ramirez, C.L., Joung, J.K., Liu, D.R. (2011). Revealing off-target cleavage specificities of zinc-finger nucleases by in vitro selection. Nat Methods 8: 765–770. DOI: https://doi.org/10.1038/nmeth.1670

Pessina S., Lenzi L., Perazzolli M., Campa M., Dalla Costa L., Urso S., Valè G., Salamini F., Velasco R., Malnoy M. (2016). Knockdown of MLO genes reduces susceptibility to powdery mildew in grapevine. Hortic. Res. 3:16016. DOI: https://doi.org/10.1038/hortres.2016.16

Platt R.J., Chen S., Zhou Y., Yim M.J., Swiech L., Kempton H.R., Dahlman J.E., Parnas O., Eisenhaure T.M., Jovanovic M., et al. (2014).CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling. Cell. 159:440–455. DOI: https://doi.org/10.1016/j.cell.2014.09.014

Porteus MH, Carroll D. (2005). Gene targeting using zinc finger nucleases. Nat Biotechnol 23: 967–973. DOI: https://doi.org/10.1038/nbt1125

Pyne M. E., Bruder M., Moo-Young M., Chung D. A., Chou C. P. (2014). Technical guide for genetic advancement of underdeveloped and intractable Clostridium. Biotechnol. Adv. 32, 623–641. DOI: https://doi.org/10.1016/j.biotechadv.2014.04.003

Pyott D. E., Sheehan E., Molnar A. (2016). Engineering of CRISPR/Cas9-mediated potyvirus resistance in transgene-free Arabidopsis plants. Mol. Plant Pathol. 17 1276–1288. DOI: https://doi.org/10.1111/mpp.12417

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. DOI: https://doi.org/10.1186/s12896-016-0289-2

Ramakrishna, S., Kwaku, Dad, A.B., Beloor, J., et al. (2014). Gene disruption by cell-penetrating peptide-mediated delivery of Cas9 protein and guide RNA. Genome Res 24:1020–7. DOI: https://doi.org/10.1101/gr.171264.113

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). Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 154: 1380–1389. DOI: https://doi.org/10.1016/j.cell.2013.08.021

Raschmanova H., Weninger A., Glieder A., Kovar K., Vogl T. (2018). Implementing CRISPR-Cas technologies in conventional and non-conventional yeasts: current state and future prospects. Biotechnol. Adv. 36, 641–665. DOI: https://doi.org/10.1016/j.biotechadv.2018.01.006

Ricroch A., Clairand P., Harwood W. (2017). Use of CRISPR systems in plant genome editing: toward new opportunities in agriculture. Emerg. Top. Life Sci. 1: 169–182. DOI: https://doi.org/10.1042/ETLS20170085

Rodríguez-Leal D., Lemmon Z. H., Man J., Bartlett M. E., Lippman Z. B. (2017). Engineering quantitative trait variation for crop improvement by genome editing. Cell 171, 470–480.e8. DOI: https://doi.org/10.1016/j.cell.2017.08.030

Rosinski-Chupin, I., Sauvage E., Fouet A., Poyart C., Glaser P. (2019). Conserved and specific features of Streptococcus pyogenes and Streptococcus agalactiae transcriptional landscapes. BMC Genomics 20, 236. DOI: https://doi.org/10.1186/s12864-019-5613-5

Samulski RJ, Muzyczka N. (2014). AAV-mediated gene therapy for research and therapeutic purposes. Annu Rev Virol 1:427–51. DOI: https://doi.org/10.1146/annurev-virology-031413-085355

Sánchez-León S., Gil-Humanes J., Ozuna C.V., Giménez M.J., Sousa C., Voytas D.F., Barro F. (2018). Low-gluten, nontransgenic wheat engineered with CRISPR/Cas9. Plant Biotechnol. J. 16:902–910. DOI: https://doi.org/10.1111/pbi.12837

Sander, J. D., and Joung J. K.. 2014. CRISPR‐Cas systems for editing, regulating and targeting genomes. Nature Biotechnology 32: 347–355. DOI: https://doi.org/10.1038/nbt.2842

Savary S., Ficke A., Aubertot J. N., Hollier C. (2012). Crop losses due to diseases and their implications for global food production losses and food security. Food Secur. 4 519–537. DOI: https://doi.org/10.1007/s12571-012-0200-5

Savary S., Willocquet L., Pethybridge S.J., Esker P., McRoberts N., Nelson A. (2019). The global burden of pathogens and pests on major food crops. Nat. Ecol. Evol. 3:430–439. DOI: https://doi.org/10.1038/s41559-018-0793-y

Schwank G., Koo B.K., Sasselli V., Dekkers J.F., Heo I., Demircan T., Sasaki N., Boymans S., Cuppen E., Van Der Ent C.K., et al. (2013). Functional repair of CFTR by CRISPR/Cas9 in intestinal stem cell organoids of cystic fibrosis patients. Cell Stem Cell. 13:653–658. DOI: https://doi.org/10.1016/j.stem.2013.11.002

Shah T., Andleeb T., Lateef S., Noor M. A. (2018). Genome editing in plants: advancing crop transformation and overview of tools. Plant Physiol. Biochem. 131, 12–21. DOI: https://doi.org/10.1016/j.plaphy.2018.05.009

Shan, Q. , Wang Y., Li J., Zhang Y., Chen K., Liang Z., Zhang K., et al. 2013. Targeted genome modification of crop plants using a CRISPR-Cas9 system. Nature Biotechnology 31: 686–688. DOI: https://doi.org/10.1038/nbt.2650

Shan, S. , Mavrodiev E. V., Li R., Zhang Z., Hauser B. A., Soltis P. S., Soltis D. E., and Yang B.. (2018). Application of CRISPR/Cas9 to Tragopogon (Asteraceae), an evolutionary model for the study of polyploidy. Molecular Ecology Resources 18: 1427–1443. DOI: https://doi.org/10.1111/1755-0998.12935

Shen B., Zhang W., Zhang J., Zhou J., Wang J., Chen L., Wang L., Hodgkins A., Iyer V., Huang X., and Skarnes W. C. (2014) Efficient genome modification by CRISPR-Cas9 nickase with minimal off-target effects. Nat. Meth. 11, 399–402 DOI: https://doi.org/10.1038/nmeth.2857

Shen, B., Zhang, J., Wu, H., et al. (2013). Generation of gene-modified mice via Cas9/RNA-mediated gene targeting. Cell Res 23:720–3. DOI: https://doi.org/10.1038/cr.2013.46

Shi J., Gao H., Wang H., Lafitte H. R., Archibald R. L., Yang M., et al. (2017). ARGOS 8 variants generated by CRISPR-Cas9 improve maize grain yield under field drought stress conditions. Plant Biotechnol. J. 15, 207–216. DOI: https://doi.org/10.1111/pbi.12603

Shukla, V.K., Doyon, Y., Miller, J.C., DeKelver, R.C., Moehle, E.A., et al. (2009) Precise genome modification in the crop species Zea mays using zinc-finger nucleases. Nature 459: 437–441. DOI: https://doi.org/10.1038/nature07992

Slaymaker, I.M., Gao, L., Zetsche, B., et al. (2016). Rationally engineered Cas9 nucleases with improved specificity. Science 351:84–8. DOI: https://doi.org/10.1126/science.aad5227

Smith. J., Grizot, S., Arnould, S., Duclert, A., Epinat, J.C., Chames, P., Prieto, J., Redondo, P., Blanco, F.J., Bravo, J., Montoya, G., Pâques, F., Duchateau, P. (2006). A combinatorial approach to create artificial homing endonucleases cleaving chosen sequences. Nucleic Acids Res. 34(22):e149. DOI: https://doi.org/10.1093/nar/gkl720

Sternberg S. H., Redding S., Jinek M., Greene E. C., Doudna J. A. (2014). DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 507: 62–67. 10.1038/nature13011. DOI: https://doi.org/10.1038/nature13011

Stoddard, B.L. (2005). Homing endonuclease structure and function. Q Rev Biophys 38: 49-95.

Stoddard, Barry L. (2006). "Homing endonuclease structure and function". Quarterly Reviews of Biophysics. 38 (1): 49-95. DOI: https://doi.org/10.1017/S0033583505004063

Suda T, Gao X, Stolz DB, Liu D. (2007). Structural impact of hydrodynamic injection on mouse liver. Gene Ther 14:129–37. DOI: https://doi.org/10.1038/sj.gt.3302865

Sun W, Ji W, Hall JM, et al. (2015). Self-assembled DNA nanoclews for the efficient delivery of CRISPR-Cas9 for genome editing. Angew Chem Int Ed Engl 54:12029–33. DOI: https://doi.org/10.1002/anie.201506030

Sun W, Jiang T, Lu Y, et al. (2014). Cocoon-like self-degradable DNA nanoclew for anticancer drug delivery. J Am Chem Soc 136:14722–5. DOI: https://doi.org/10.1021/ja5088024

Sun Y., Jiao G., Liu Z., Zhang X., Li J., Guo X., Du W., Du J., Francis F., Zhao Y., et al. (2018). Generation of High-Amylose Rice through CRISPR/Cas9-Mediated Targeted Mutagenesis of Starch Branching Enzymes. Front. Plant Sci. 8:298. DOI: https://doi.org/10.3389/fpls.2017.00298

Swiech L., Heidenreich M., Banerjee A., Habib N., Li Y., Trombetta J., Sur M., Zhang F. (2015). In vivo interrogation of gene function in the mammalian brain using CRISPR-Cas9. Nat. Biotechnol. 33:102–106. DOI: https://doi.org/10.1038/nbt.3055

Szostak J.W., Orr-Weaver T.L., Rothstein R.J., Stahl F.W. (1983). The double-strand-break repair model for recombination. Cell, 33:25–35. DOI: https://doi.org/10.1016/0092-8674(83)90331-8

Takeuchi, R., Choi, M., Stoddard, B.L. (2014). Redesign of extensive protein-DNA interfaces of meganucleases using iterative cycles of in vitro compartmentalization. Proc Natl Acad Sci U S A. 111(11):4061-6. DOI: https://doi.org/10.1073/pnas.1321030111

Thomas V., Hartner F. S., Anton G. (2013). New opportunities by synthetic biology for biopharmaceutical production in Pichia pastoris. Curr. Opin. Biotech. 24, 1094–1101. 10.1016/j.copbio.2013.02.024 DOI: https://doi.org/10.1016/j.copbio.2013.02.024

Thomazella D.P.D.T., Brail Q., Dahlbeck D., Staskawicz B.J. (2016). CRISPR-Cas9 mediated mutagenesis of a DMR6 ortholog in tomato confers broad-spectrum disease resistance. bioRxiv. 2016.

Thyme, S.B., Boissel, S.J., Arshiya, Quadri, S., Nolan, T., Baker, D.A., Park, R.U., Kusak, L., Ashworth, J., Baker, D. (2014). Reprogramming homing endonuclease specificity through computational design and directed evolution. Nucleic Acids Res. 42(4):2564-76 DOI: https://doi.org/10.1093/nar/gkt1212

Torres, R., Martin, M.C., Garcia, A., Cigudosa, J.C., Ramirez, J.C., Rodriguez-Perales, S. (2014). Engineering human tumour-associated chromosomal translocations with the RNA-guided CRISPR-Cas9 system. Nat Commun 5: 3964 DOI: https://doi.org/10.1038/ncomms4964

Trenberth K. E., Dai A., Van Der Schrier G., Jones P. D., Barichivich J., Briffa K. R., et al. (2014). Global warming and changes in drought. Nat. Clim. Change 4, 17. DOI: https://doi.org/10.1038/nclimate2067

Urnov, F.D., Rebar, E.J., Holmes, M.C., Zhang, H.S., Gregory, P.D. (2010). Genome editing with engineered zinc finger nucleases. Nat Rev Genet 11: 636–646. DOI: https://doi.org/10.1038/nrg2842

Valsalakumari J., Baby J., Bijin E., Constantine I., Manjila S., Pramod K. (2013). Novel gene delivery systems. Int. J. Pharm. Investig. 3:1. DOI: https://doi.org/10.4103/2230-973X.108958

van Regenmortel M.H., Mahy B.W. Desk Encyclopedia of Plant and Fungal Virology. Elsevier; San Diego, CA, USA: 2009.

Vartak, S.V., Raghavan, S.C. (2015). Inhibition of nonhomologous end joining to increase the specificity of CRISPR/Cas9 genome editing. FEBS J 282:4289–94. DOI: https://doi.org/10.1111/febs.13416

Voets O, Tielen F, Elstak E, et al. (2017). Highly efficient gene inactivation by adenoviral CRISPR/Cas9 in human primary cells. PLoS One 12:e0182974. DOI: https://doi.org/10.1371/journal.pone.0182974

Waltz E. (2016). Gene-edited CRISPR mushroom escapes US regulation. Nature 532: 293. DOI: https://doi.org/10.1038/nature.2016.19754

Wang D., Samsulrizal N.H., Yan C., Allcock N.S., Craigon J., Blanco-Ulate B., Ortega-Salazar I., Marcus S.E., Bagheri H.M., Fons L.P. (2019). Characterization of CRISPR Mutants Targeting Genes Modulating Pectin Degradation in Ripening Tomato. Plant Physiol. 179:544–557. DOI: https://doi.org/10.1104/pp.18.01187

Wang F., Wang C., Liu P., Lei C., Hao W., Gao Y., Liu Y.-G., Zhao K. (2016). Enhanced rice blast resistance by CRISPR/Cas9-targeted mutagenesis of the ERF transcription factor gene OsERF922. PLoS ONE. 11:e0154027. DOI: https://doi.org/10.1371/journal.pone.0154027

Wang L., Chen L., Li R., Zhao R., Yang M., Sheng J., et al. (2017). Reduced drought tolerance by CRISPR/Cas9-mediated SlMAPK3 mutagenesis in tomato plants. J. Agric. Food Chem. 65, 8674–8682. DOI: https://doi.org/10.1021/acs.jafc.7b02745

Wang M, Zuris JA, Meng F, et al. (2016). Efficient delivery of genome-editing proteins using bioreducible lipid nanoparticles. Proc Natl Acad Sci USA 113:2868–73. DOI: https://doi.org/10.1073/pnas.1520244113

Wang S., Dong S., Wang P., Tao Y., Wang Y. (2017). Genome Editing in Clostridium saccharoperbutylacetonicum N1-4 with the CRISPR-Cas9 system. Appl. Environ. Microbiol. 83:e00233-17. DOI: https://doi.org/10.1128/AEM.00233-17

Wang W., Pan Q., He F., Akhunova A., Chao S., Trick H., et al. (2018). Transgenerational CRISPR-Cas9 activity facilitates multiplex gene editing in allopolyploid wheat. CRISPR J. 1, 65–74. DOI: https://doi.org/10.1089/crispr.2017.0010

Wang X., Wang Y., Wu X., Wang J., Wang Y., Qiu Z., Chang T., Huang H., Lin R.J., Yee J.K. (2015). Unbiased detection of off-target cleavage by CRISPR-Cas9 and TALENs using integrase-defective lentiviral vectors. Nat. Biotechnol. 33:175–178. DOI: https://doi.org/10.1038/nbt.3127

Wang Y., Cheng X., Shan Q., Zhang Y., Liu J., Gao C., Qiu J. (2014). Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. Nat. Biotechnol. 32:947. DOI: https://doi.org/10.1038/nbt.2969

Waters, C.A., Strande N.T., Pryor J.M., Strom C.N., Mieczkowski P., Burkhalter M.D., Oh S., Qaqish B.F., Moore D.T., Hendrickson E.A., et al. (2014). The fidelity of the ligation step determines how ends are resolved during nonhomologous end joining. Nat. Commun. 5:4286. DOI: https://doi.org/10.1038/ncomms5286

Weeks, D.P., Spalding M. H., Yang B. (2016). Use of designer nucleases for targeted gene and genome editing in plants. Plant Biotechnol. J. 14: 483–495. DOI: https://doi.org/10.1111/pbi.12448

Weirauch MT, Hughes TR. (2010). Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same. Trends in Genetics. 26(2):66–74. DOI: https://doi.org/10.1016/j.tig.2009.12.002

Wenzhi, J., Huanbin, Z., Honghao, B., Michael, F. and Bing, Y., Weeks Donald P. (2013): Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice. Nucleic Acids Research, 41, pp.e188-e188. DOI: https://doi.org/10.1093/nar/gkt780

White MK, Khalili K. (2016). CRISPR/Cas9 and cancer targets: future possibilities and present challenges. Oncotarget. 7:12305–12317. DOI: https://doi.org/10.18632/oncotarget.7104

Wolt J. D., Wang K., Yang B. (2016). The regulatory status of genome-edited crops. Plant Biotechnol. J. 14 510–518. DOI: https://doi.org/10.1111/pbi.12444

Woo, J. W. , Kim J., Kwon S. I., Corvalán C., Cho S. W., Kim H., Kim S. G., et al. (2015). DNA‐free genome editing in plants with preassembled CRISPR-Cas9 ribonucleoproteins. Nature Biotechnology 33: 1162–1164. DOI: https://doi.org/10.1038/nbt.3389

Wu J.J., Du G.C., Chen J., Zhou J.W. (2015). Enhancing flavonoid production by systematically tuning the central metabolic pathways based on a CRISPR interference system in Escherichia coli. Sci. Rep. 5:13477. DOI: https://doi.org/10.1038/srep13477

Wu Z, Yang H, Colosi P. (2010). Effect of genome size on AAV vector packaging. Mol Ther 18:80–6 DOI: https://doi.org/10.1038/mt.2009.255

Xie, K. , and Yang Y.. 2013. RNAguided genome editing in plants using a CRISPR-Cas9 system. Molecular Plant 6: 1975 DOI: https://doi.org/10.1093/mp/sst119

Xu R., Yang Y., Qin R., Li H., Qiu C., Li L., et al. . (2016). Rapid improvement of grain weight via highly efficient CRISPR/Cas9-mediated multiplex genome editing in rice. J. Genet. Genomics 43, 529–532. DOI: https://doi.org/10.1016/j.jgg.2016.07.003

Xu, T., Li, Y., Shi, Z., Hemme, C.L., Li, Y., Zhu, Y., Van, Nostrand, J.D., He, Z., Zhou, J. (2015). Efficient genome editing in Clostridium cellulolyticum via CRISPR-Cas9 nickase. Appl Environ Microbiol 81:4423–4431. DOI: https://doi.org/10.1128/AEM.00873-15

Xue W., Chen S., Yin H., Tammela T., Papagiannakopoulos T., Joshi N.S., Cai W., Yang G., Bronson R., Crowley D.G., et al. (2014). CRISPR-mediated direct mutation of cancer genes in the mouse liver. Nature. 514:380–384. DOI: https://doi.org/10.1038/nature13589

Yin H, Song CQ, Dorkin JR, et al. (2016). Therapeutic genome editing by combined viral and non-viral delivery of CRISPR system components in vivo. Nat Biotechnol 34:328–33. DOI: https://doi.org/10.1038/nbt.3471

Yin H., Xue W., Chen S., Bogorad R.L., Benedetti E., Grompe M., Koteliansky V., Sharp P.A., Jacks T., Anderson D.G. (2013). Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype. Nat. Biotechnol. 32:551–553. DOI: https://doi.org/10.1038/nbt.2884

Yu, C., Liu, Y., Ma, T., et al. (2015). Small molecules enhance CRISPR genome editing in pluripotent stem cells. Cell Stem Cell 16:142–7. DOI: https://doi.org/10.1016/j.stem.2015.01.003

Zeisel, M.B., Lucifora J., Mason W.S., Sureau C., Beck J., Levrero M., Kann M., Knolle P.A., Benkirane M., Durantel D., et al. (2015). Towards an HBV cure: State-of-the-art and unresolved questions-report of the ANRS workshop on HBV cure. Gut. 64:1314–1326. DOI: https://doi.org/10.1136/gutjnl-2014-308943

Zetsche B., Gootenberg J.S., Abudayyeh O.O., Slaymaker I.M., Makarova K.S., Essletzbichler P., Volz S.E., Joung J., van der Oost J., Regev A., et al. (2015). Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell.163:759–771. DOI: https://doi.org/10.1016/j.cell.2015.09.038

Zhang A., Liu Y., Wang F., Li T., Chen Z., Kong D., Bi J., Zhang F., Luo X., Wang J. (2019). Enhanced rice salinity tolerance via CRISPR/Cas9-targeted mutagenesis of the OsRR22 gene. Mol. Breed. 39:47. DOI: https://doi.org/10.1007/s11032-019-0954-y

Zhang C., Meng X., Wei X., Lu L. (2016). Highly efficient CRISPR mutagenesis by microhomology-mediated end joining in Aspergillus fumigatus. Fungal Genet. Biol. 86, 47–57. DOI: https://doi.org/10.1016/j.fgb.2015.12.007

Zhang F., Wen Y., Guo X. (2014). CRISPR for genome editing: progress, implications and challenges. Hum. Mol. Genet. 23 40–46. DOI: https://doi.org/10.1093/hmg/ddu125

Zhang J., Zhang H., Botella J.R., Zhu J. (2018). Generation of new glutinous rice by CRISPR/Cas9-targeted mutagenesis of the Waxy gene in elite rice varieties. J. Integr. Plant Biol. 60:369–375. DOI: https://doi.org/10.1111/jipb.12620

Zhang X., Lu G., Long W., Zou X., Li F., Nishio T. (2014). Recent progress in drought and salt tolerance studies in Brassica crops. Breed Sci. 64, 60–73. DOI: https://doi.org/10.1270/jsbbs.64.60

Zhang Y, Ma X, Xie X, Liu Y-G. (2017). CRISPR/Cas9-based genome editing in plants. Prog Mol Biol Transl Sci 149:133–50. DOI: https://doi.org/10.1016/bs.pmbts.2017.03.008

Zhang Y., Massel K., Godwin I. D., Gao C. (2018b). Applications and potential of genome editing in crop improvement. Genome Biol. 19, 210. DOI: https://doi.org/10.1186/s13059-018-1586-y

Zhang Y., Yu L.C. (2008). Single-cell microinjection technology in cell biology. BioEssays. 30:606–610. DOI: https://doi.org/10.1002/bies.20759

Zhen S, Hua L, Liu YH, et al. (2015). Harnessing the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated Cas9 system to disrupt the hepatitis B virus. Gene Ther 22:404–12. DOI: https://doi.org/10.1038/gt.2015.2

Zhou Y, Zhu S, Cai C, et al. (2014). High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells. Nature 509:487–91. DOI: https://doi.org/10.1038/nature13166

Zhu M., Monroe J. G., Suhail Y., Villiers F., Mullen J., Pater D., et al. (2016). Molecular and systems approaches towards drought-tolerant canola crops. New Phytol. 210, 1169–1189. DOI: https://doi.org/10.1111/nph.13866