Volume 10, Issue 2 (2019)
JMBS 2019, 10(2): 263-286 |
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Emamjomeh A, Adim H, Zahiri J. Targeted Genome Editing Techniques and its Bioinformatic Tools: A Survey. JMBS 2019; 10 (2) :263-286
URL: http://biot.modares.ac.ir/article-22-14687-en.html
URL: http://biot.modares.ac.ir/article-22-14687-en.html
1- Academic staff- Department of Plant Breeding and Biotechnology, Department of Bioinformatics, Agriculture Faculty, University of Zabol, Zabol, Iran. , aliimamjomeh@uoz.ac.ir
2- North Khorasan Agricultural & Natural Resources Research Center, North Khorasan Agricultural and Natural Resources Research Center (AREEO), Bojnurd, Iran
3- Biophysics Department, Biological Sciences Faculty, Tarbiat Modares University, Tehran, Iran
2- North Khorasan Agricultural & Natural Resources Research Center, North Khorasan Agricultural and Natural Resources Research Center (AREEO), Bojnurd, Iran
3- Biophysics Department, Biological Sciences Faculty, Tarbiat Modares University, Tehran, Iran
Abstract: (9326 Views)
Genome editing using targetable nucleases is an emerging technology for precise genome modification in many organisms with hight ability and capability. All targeted genome engineering relies on the introduction of a site-specific double-strand break (DSB) in a pre-determined genomic locus by a rare-cutting DNA endonuclease . Subsequent repair of this DSB by non-homologous end joining (NHEJ) or homology-directed repair (HDR) generates the desired genetic modifications such as gene disruption, gene insertion, gene correction, etc. Three types of endonucleases , namely ZFNs (zinc finger nucleases), TALENs (transcription activator-like effector nucleases ), and the CRISPR (clustered regularly interspersed short palindromic regions) associated (Cas9) system have been predominantly utilized for gene editing. Targeted genome engineering or editing enables researchers to modify genomic loci of interest in a precise manner, which has a turning point in medicine, biological research, and biotechnology. Treatment of human immunodeficiency virus (HIV) infection with ZFN-mediated CCR5 gene disruption is one of the indicator examples of the ability of ZFNs in genome editing. The emergence of TALENs in 2010 has enabled the genome modification of non- model organisms, while the emergence of the CRISPR/Cas9 system in 2013 as a revolutionary genome-editing tool has allowed us to anticipate the forthcoming new era of genome editing research. Soon, it is likely that tgenome editing also will provide the possibility of treating genetic diseases. Genome editing is also hoped to be available for use in the generation of crops and livestock with useful traits. An example would be the production of edible fungi resistant to browning by inactivation of the genes encoding polyphenol oxidase in 2016 under the non-GMO genetically edited crop plants and production of herbicide-resistant rice and rapeseed using CRISPR/Cas9 systems. In this article, we review essential genome editing tools, summarize their applications in crop improvement, as well as, next-generation crop breeding and their computational resources will be discussed.
Article Type: Review |
Subject:
Agricultural Biotechnology
Received: 2018/01/29 | Accepted: 2018/02/21 | Published: 2019/06/20
Received: 2018/01/29 | Accepted: 2018/02/21 | Published: 2019/06/20
References
1. Perez-Pinera P, Ousterout DG, Gersbach CA. Advances in targeted genome editing. Curr Opin Chem Biol. 2012;16(3-4):268-77. [Link] [DOI:10.1016/j.cbpa.2012.06.007]
2. Pauwels K, Podevin N, Breyer D, Carroll D, Herman P. Engineering nucleases for gene targeting: Safety and regulatory considerations. New Biotechnol. 2014;31(1):18-27. [Link] [DOI:10.1016/j.nbt.2013.07.001]
3. Urnov FD, Rebar EJ, Holmes MC, Zhang HS, Gregory PD. Genome editing with engineered zinc finger nucleases. Nat Rev Genet. 2010;11(9):636-46. [Link] [DOI:10.1038/nrg2842]
4. Joung JK, Sander JD. TALENs: A widely applicable technology for targeted genome editing. Nat Rev Mol Cell Biol. 2013;14(1):49-55. [Link] [DOI:10.1038/nrm3486]
5. Mali P, Esvelt KM, Church GM. Cas9 as a versatile tool for engineering biology. Nat Methods. 2013;10(10):957-63. [Link] [DOI:10.1038/nmeth.2649]
6. Miller J, Mc Lachlan AD, Klug A. Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO J. 1985;4(6):1609-14. [Link] [DOI:10.1002/j.1460-2075.1985.tb03825.x]
7. Kim YG, Cha J, Chandrasegaran S. Hybrid restriction enzymes: Zinc finger fusions to Fok I cleavage domain. Proc Natl Acad Sci U S A. 1996;93(3):1156-60. [Link] [DOI:10.1073/pnas.93.3.1156]
8. Wolfe SA, Nekludova L, Pabo CO. DNA recognition by Cys2His2 zinc finger proteins. Annu Rev Biophys Biomol Struct. 2000;29:183-212. [Link] [DOI:10.1146/annurev.biophys.29.1.183]
9. Vanamee ES, Santagata S, Aggarwal AK. FokI requires two specific DNA sites for cleavage. J Mol Biol. 2001;309(1):69-78. [Link] [DOI:10.1006/jmbi.2001.4635]
10. Dreier B, Beerli RR, Segal DJ, Flippin JD, Barbas CF. Development of zinc finger domains for recognition of the 5'-ANN-3' family of DNA sequences and their use in the construction of artificial transcription factors. J Biol Chem. 2001;276(31):29466-78. [Link] [DOI:10.1074/jbc.M102604200]
11. Hiroyuki S, Susumu K. New restriction endonucleases from Flavobacterium okeanokoites (FokI) and Micrococcus luteus (MluI). Gene. 1981;16(1-3):73-8. [Link] [DOI:10.1016/0378-1119(81)90062-7]
12. Bibikova M, Beumer K, Trautman JK, Carroll D. Enhancing gene targeting with designed zinc finger nucleases. Science. 2003;300(5620):764. [Link] [DOI:10.1126/science.1079512]
13. Lieberman-Lazarovich M, Levy AA. Homologous recombination in plants: An antireview. In: Birchler J, editor. Plant chromosome engineering, methods in molecular biology (methods and protocols). 701st Volume. Totowa NJ: Humana Press; 2011. pp. 51-65. [Link] [DOI:10.1007/978-1-61737-957-4_3]
14. Pardo B, Gómez-González B, Aguilera A. DNA repair in mammalian cells: DNA double-strand break repair: How to fix a broken relationship. Cell Mol Life Sci. 2009;66(6):1039-56. [Link] [DOI:10.1007/s00018-009-8740-3]
15. Rothkamm K, Krüger I, Thompson LH, Löbrich M. Pathways of DNA double-strand break repair during the mammalian cell cycle. Mol Cell Biol. 2003;23(16):5706-15. [Link] [DOI:10.1128/MCB.23.16.5706-5715.2003]
16. Lieber MR. The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Annu Rev Biochem. 2010;79:181-211. [Link] [DOI:10.1146/annurev.biochem.052308.093131]
17. Aguilera A. Double-strand break repair: Are Rad51/RecA--DNA joints barriers to DNA replication?. Trends Genet. 2001;17(6):318-21. [Link] [DOI:10.1016/S0168-9525(01)02309-5]
18. Puchta H. Using CRISPR/Cas in three dimensions: Towards synthetic plant genomes, transcriptomes and epigenomes. Plant J. 2016;87(1):5-15. [Link] [DOI:10.1111/tpj.13100]
19. Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature. 2016;533(7603):420-4. [Link] [DOI:10.1038/nature17946]
20. Klug A. The discovery of zinc fingers and their applications in gene regulation and genome manipulation. Annu Rev Biochem. 2010;79:213-31. [Link] [DOI:10.1146/annurev-biochem-010909-095056]
21. Desjarlais JR, Berg JM. Redesigning the DNA-binding specificity of a zinc finger protein: A data base-guided approach. Proteins. 1992;12(2):101-4. [Link] [DOI:10.1002/prot.340120202]
22. Miller JC, Holmes MC, Wang J, Guschin DY, Lee YL, Rupniewski I, et al. An improved zinc-finger nuclease architecture for highly specific genome editing. Nat Biotechnol. 2007;25(7):778-85. [Link] [DOI:10.1038/nbt1319]
23. Ramirez CL, Foley JE, Wright DA, Müller-Lerch F, Rahman SH, Cornu TI, et al. Unexpected failure rates for modular assembly of engineered zinc fingers. Nat Methods. 2008;5(5):374-5. [Link] [DOI:10.1038/nmeth0508-374]
24. Pattanayak V, Ramirez CL, Keith Joung J, Liu DR. Revealing off-target cleavage specificities of zinc-finger nucleases by in vitro selection. Nat Methods. 2011;8:765-70. [Link] [DOI:10.1038/nmeth.1670]
25. Smith J, Bibikova M, Whitby FG, Reddy AR, Chandrasegaran S, Carroll D. Requirements for double-strand cleavage by chimeric restriction enzymes with zinc finger DNA-recognition domains. Nucleic Acids Res. 2000;28(17):3361-9. [Link] [DOI:10.1093/nar/28.17.3361]
26. Bitinaite J, Wah DA, Aggarwal AK, Schildkraut I. FokI dimerization is required for DNA cleavage. Proc Natl Acad Sci U S A. 1998;95(18):10570-5. [Link] [DOI:10.1073/pnas.95.18.10570]
27. Moore M, Choo Y, Klug A. Design of polyzinc finger peptides with structured linkers. Proc Natl Acad Sci U S A. 2001;98(4):1432-6. [Link] [DOI:10.1073/pnas.98.4.1432]
28. Fine EJ, Cradick TJ, Zhao CL, Lin Y, Bao G. An online bioinformatics tool predicts zinc finger and TALE nuclease off-target cleavage. Nucleic Acids Res. 2014;42(6):e42. [Link] [DOI:10.1093/nar/gkt1326]
29. Abarrategui-Pontes C, Créneguy A, Thinard R, Fine EJ, Thepenier V, Fournier le RL, et al. Codon swapping of zinc finger nucleases confers expression in primary cells and in vivo from a single lentiviral vector. Curr Gene Ther. 2014;14(5):365-76. [Link] [DOI:10.2174/156652321405140926161748]
30. Händel EM, Alwin S, Cathomen T. Expanding or restricting the target site repertoire of zinc-finger nucleases: The inter-domain linker as a major determinant of target site selectivity. Mol Ther. 2009;17(1):104-11. [Link] [DOI:10.1038/mt.2008.233]
31. Durai S, Mani M, Kandavelou K, Wu J, Porteus MH, Chandrasegaran S. Zinc finger nucleases: Custom-designed molecular scissors for genome engineering of plant and mammalian cells. Nucleic Acids Res. 2005;33(18):5978-90. [Link] [DOI:10.1093/nar/gki912]
32. Sander JD, Dahlborg EJ, Goodwin MJ, Cade L, Zhang F, Cifuentes D, et al. Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA). Nat Methods. 2011;8(1):67-9. [Link] [DOI:10.1038/nmeth.1542]
33. Fu F, Voytas DF. Zinc Finger Database (ZiFDB) v2.0: A comprehensive database of C2H2 zinc fingers and engineered zinc finger arrays. Nucleic Acids Res. 2013;41(Database issue):D452-5. [Link] [DOI:10.1093/nar/gks1167]
34. Bogdanove AJ, Voytas DF. TAL effectors: Customizable proteins for DNA targeting. Science. 2011;333(6051):1843-6. [Link] [DOI:10.1126/science.1204094]
35. Boch J, Scholze H, Schornack S, Landgraf A, Hahn S, Kay S, et al. Breaking the code of DNA binding specificity of TAL-type III effectors. Science. 2009;326(5959):1509-12. [Link] [DOI:10.1126/science.1178811]
36. Moscou MJ, Bogdanove AJ. A simple cipher governs DNA recognition by TAL effectors. Science. 2009;326(5959):1501. [Link] [DOI:10.1126/science.1178817]
37. Holkers M, Maggio I, Liu J, Janssen JM, Miselli F, Mussolino C, et al. Differential integrity of TALE nuclease genes following adenoviral and lentiviral vector gene transfer into human cells. Nucleic Acids Res. 2013;41(5):e63. [Link] [DOI:10.1093/nar/gks1446]
38. Chen S, Oikonomou G, Chiu CN, Niles BJ, Liu J, Lee DA, et al. A large-scale in vivo analysis reveals that TALENs are significantly more mutagenic than ZFNs generated using context-dependent assembly. Nucleic Acids Res. 2013;41(4):2769-78. [Link] [DOI:10.1093/nar/gks1356]
39. Wu Y, Gao T, Wang X, Hu Y, Hu X, Hu Z, et al. TALE nickase mediates high efficient targeted transgene integration at the human multi-copy ribosomal DNA locus. Biochem Biophys Res Commun. 2014;446(1):261-6. [Link] [DOI:10.1016/j.bbrc.2014.02.099]
40. Cermak T, Doyle EL, Christian M, Wang L, Zhang Y, Schmidt C, et al. Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res. 2011;39(12):e82. [Link] [DOI:10.1093/nar/gkr218]
41. Sanjana NE, Cong L, Zhou Y, Cunniff MM, Feng G, Zhang F. A transcription activator-like effector toolbox for genome engineering. Nat Protoc. 2012;7(1):171-92. [Link] [DOI:10.1038/nprot.2011.431]
42. Reyon D, Khayter C, Regan MR, Keith Joung J, Sander JD. Engineering designer Transcription Activator-Like Effector Nucleases (TALENs) by REAL or REAL-Fast assembly. Curr Protoc Mol Biol. 2012;100(1):12.15.1-14. [Link] [DOI:10.1002/0471142727.mb1215s100]
43. Reyon D, Tsai SQ, Khayter C, Foden JA, Sander JD, Joung JK. FLASH assembly of TALENs for high-throughput genome editing. Nat Biotechnol. 2012;30(5):460-5. [Link] [DOI:10.1038/nbt.2170]
44. Ishino Y, Shinagawa H, Makino K, Amemura M, Nakata A. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J Bacteriol. 1987;169(12):5429-33. [Link] [DOI:10.1128/jb.169.12.5429-5433.1987]
45. Bhaya D, Davison M, Barrangou R. CRISPR-Cas systems in bacteria and archaea: Versatile small RNAs for adaptive defense and regulation. Annu Rev Genet. 2011;45:273-97. [Link] [DOI:10.1146/annurev-genet-110410-132430]
46. Wiedenheft B, Sternberg SH, Doudna JA. RNA-guided genetic silencing systems in bacteria and archaea. Nature. 2012;482(7385):331-8. [Link] [DOI:10.1038/nature10886]
47. Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, et al. Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol. 2011;9(6):467-77. [Link] [DOI:10.1038/nrmicro2577]
48. Mohanraju P, Makarova KS, Zetsche B, Zhang F, Koonin EV, Van Der Oost J. Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems. Science. 2016;353(6299):aad5147. [Link] [DOI:10.1126/science.aad5147]
49. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012;337(6096):816-21. [Link] [DOI:10.1126/science.1225829]
50. Mali P, Yang L, Esvelt KM, Aach J, Guell M, Di Carlo JE, et al. RNA-guided human genome engineering via Cas9. Science. 2013;339(6121):823-6. [Link] [DOI:10.1126/science.1232033]
51. Ousterout DG, Kabadi AM, Thakore PI, Majoros WH, Reddy TE, Gersbach CA. Multiplex CRISPR/Cas9-based genome editing for correction of dystrophin mutations that cause Duchenne muscular dystrophy. Nat Commun. 2015;6:6244. [Link] [DOI:10.1038/ncomms7244]
52. Mojica FJ, Díez-Villaseñor C, García-Martínez J, Soria E. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J Mol Evol. 2005;60(2):174-82. [Link] [DOI:10.1007/s00239-004-0046-3]
53. Pourcel C, Salvignol G, Vergnaud G. CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology. 2005;151(Pt 3):653-63. [Link] [DOI:10.1099/mic.0.27437-0]
54. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science. 2007;315(5819):1709-12. [Link] [DOI:10.1126/science.1138140]
55. Garneau JE, Dupuis MÈ, Villion M, Romero DA, Barrangou R, Boyaval P, et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature. 2010;468:67-71. [Link] [DOI:10.1038/nature09523]
56. Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y, Pirzada ZA, et al. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature. 2011;471:602-7. [Link] [DOI:10.1038/nature09886]
57. Brouns SJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJ, Snijders AP, et al. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science. 2008;321(5891):960-4 [Link] [DOI:10.1126/science.1159689]
58. Nishimasu H, Ran FA, Hsu PD, Konermann S, Shehata SI, Dohmae N, et al. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell. 2014;156(5):935-49. [Link] [DOI:10.1016/j.cell.2014.02.001]
59. Gasiunas G, Barrangou R, Horvath P, Siksnys V. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc Natl Acad Sci U S A. 2012;109(39):E2579-86. [Link] [DOI:10.1073/pnas.1208507109]
60. Jiang F, Zhou K, Ma L, Gressel S, Doudna JA. A Cas9-guide RNA complex preorganized for target DNA recognition. Science. 2015;348(6242):1477-81. [Link] [DOI:10.1126/science.aab1452]
61. Jinek M, Jiang F, Taylor DW, Sternberg SH, Kaya E, Ma E, et al. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science. 2014;343(6176):1247997. [Link] [DOI:10.1126/science.1247997]
62. Westra ER, Semenova E, Datsenko KA, Jackson RN, Wiedenheft B, Severinov K, et al. Type I-E CRISPR-cas systems discriminate target from non-target DNA through base pairing-independent PAM recognition. PLoS Genet. 2013;9(9):e1003742. [Link] [DOI:10.1371/journal.pgen.1003742]
63. Mao Y, Zhang H, Xu N, Zhang B, Gou F, Zhu JK. Application of the CRISPR-Cas system for efficient genome engineering in plants. Mol Plant. 2013;6(6):2008-11. [Link] [DOI:10.1093/mp/sst121]
64. Horvath P, Romero DA, Coûté-Monvoisin AC, Richards M, Deveau H, Moineau S, et al. Diversity, activity, and evolution of CRISPR loci in Streptococcus thermophilus. J Bacteriol. 2008;190(4):1401-12. [Link] [DOI:10.1128/JB.01415-07]
65. Sternberg SH, Redding S, Jinek M, Greene EC, Doudna JA. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature. 2014;507:62-7. [Link] [DOI:10.1038/nature13011]
66. Nakade S, Yamamoto T, Sakuma T. Cas9, Cpf1 and C2c1/2/3-what's next?. Bioengineered. 2017;8(3):265-73. [Link] [DOI:10.1080/21655979.2017.1282018]
67. Hsu PD, Scott DA, Weinstein JA, Ann Ran F, Konermann S, Agarwala V, et al. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol. 2013;31:827-32. [Link] [DOI:10.1038/nbt.2647]
68. Fu Y, Foden JA, Khayter C, Maeder ML, Reyon D, Keith Joung J, et al. High frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat Biotechnol. 2013;31(9):822-6. [Link] [DOI:10.1038/nbt.2623]
69. Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA, Zhang F. Genome engineering using the CRISPR-Cas9 system. Nat Protoc. 2013;8(11):2281-308. [Link] [DOI:10.1038/nprot.2013.143]
70. Kleinstiver BP, Pattanayak V, Prew MS, Tsai SQ, Nguyen NT, Zheng Z, et al. High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects. Nature. 2016;529(7587):490-5. [Link] [DOI:10.1038/nature16526]
71. Slaymaker IM, Gao L, Zetsche B, Scott DA, Yan WX, Zhang F. Rationally engineered Cas9 nucleases with improved specificity. Science. 2016;351(6268):84-8. [Link] [DOI:10.1126/science.aad5227]
72. Tsai SQ, Zheng Z, Nguyen NT, Liebers M, Topkar VV, Thapar V, et al. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat Biotechnol. 2015;33(2):187-97. [Link] [DOI:10.1038/nbt.3117]
73. Kim D, Bae S, Park J, Kim E, Kim S, Yu HR, et al. Digenome-seq: Genome-wide profiling of CRISPR-Cas9 off-target effects in human cells. Nat Methods. 2015;12(3):237-43. [Link] [DOI:10.1038/nmeth.3284]
74. Fu Y, Sander JD, Reyon D, Cascio VM, Joung JK. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat Biotechnol. 2014;32(3):279-84. [Link] [DOI:10.1038/nbt.2808]
75. Ran FA, Hsu PD, Lin CY, Gootenberg JS, Konermann S, Trevino AE, et al. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell. 2013;154(6):1380-9. [Link] [DOI:10.1016/j.cell.2013.08.021]
76. Shen B, Zhang W, Zhang J, Zhou J, Wang J, Chen L, et al. Efficient genome modification by CRISPR-Cas9 nickase with minimal off-target effects. Nat Methods. 2014;11(4):399-402. [Link] [DOI:10.1038/nmeth.2857]
77. Wu X, Scott DA, Kriz AJ, Chiu AC, Hsu PD, Dadon DB, et al. Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat Biotechnol. 2014;32(7):670-6. [Link] [DOI:10.1038/nbt.2889]
78. Tsai SQ, Wyvekens N, Khayter C, Foden JA, Thapar V, Reyon D, et al. Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing. Nat Biotechnol. 2014;32(6):569-76. [Link] [DOI:10.1038/nbt.2908]
79. Guilinger JP, Thompson DB, Liu DR. Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification. Nat Biotechnol. 2014;32:577-82. [Link] [DOI:10.1038/nbt.2909]
80. Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, Essletzbichler P, et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell. 2015;163(3):759-71. [Link] [DOI:10.1016/j.cell.2015.09.038]
81. Dong D, Ren K, Qiu X, Zheng J, Guo M, Guan X, et al. The crystal structure of Cpf1 in complex with CRISPR RNA. Nature. 2016;532(7600):522-6. [Link] [DOI:10.1038/nature17944]
82. Fonfara I, Richter H, Bratovič M, Le Rhun A, Charpentier E. The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA. Nature. 2016;532:517-21. [Link] [DOI:10.1038/nature17945]
83. He ZY, Men K, Qin Z, Yang Y, Xu T, Wei YQ. Non-viral and viral delivery systems for CRISPR-Cas9 technology in the biomedical field. Sci China Life Sci. 2017;60(5):458-67. [Link] [DOI:10.1007/s11427-017-9033-0]
84. Yin H, Song CQ, Dorkin JR, Zhu LJ, Li Y, Wu Q, et al. Therapeutic genome editing by combined viral and non-viral delivery of CRISPR system components in vivo. Nat Biotechnol. 2016;34(3):328-33. [Link] [DOI:10.1038/nbt.3471]
85. Ma X, Zhang Q, Zhu Q, Liu W, Chen Y, Qiu R, et al. A robust CRISPR/Cas9 system for convenient, high-efficiency multiplex genome editing in monocot and dicot plants. Mol Plant. 2015;8(8):1274-84. [Link] [DOI:10.1016/j.molp.2015.04.007]
86. Zhou H, Liu B, Weeks DP, Spalding MH, Yang B. Large chromosomal deletions and heritable small genetic changes induced by CRISPR/Cas9 in rice. Nucleic Acids Res. 2014;42(17):10903-14. [Link] [DOI:10.1093/nar/gku806]
87. Zhao C, Zhang Z, Xie S, Si T, Li Y, Zhu JK. Mutational evidence for the critical role of CBF transcription factors in cold acclimation in arabidopsis. Plant Physiol. 2016;171(4):2744-59. [DOI:10.1104/pp.16.00533]
88. Vanyushin BF, Ashapkin VV. DNA methylation in higher plants: Past, present and future. Biochimica et Biophysica Acta Gene Regulatory Mechanisms. 2011;1809(8):360-8. [Link] [DOI:10.1016/j.bbagrm.2011.04.006]
89. Miao J, Guo D, Zhang J, Huang Q, Qin G, Zhang X, et al. Targeted mutagenesis in rice using CRISPR-Cas system. Cell Res. 2013;23(10):1233-6. [Link] [DOI:10.1038/cr.2013.123]
90. Haddad L, Achadi E, Bendech MA, Ahuja A, Bhatia K, Bhutta Z, et al. The Global Nutrition Report 2014: Actions and accountability to accelerate the world's progress on nutrition. J Nutr. 2015;145(4):663-71. [Link] [DOI:10.3945/jn.114.206078]
91. Schaart JG, Van De Wiel CCM, Lotz LAP, Smulders MJM. Opportunities for products of new plant breeding techniques. Trends Plant Sci. 2016;21(5):438-49. [Link] [DOI:10.1016/j.tplants.2015.11.006]
92. Mittal V. Improving the efficiency of RNA interference in mammals. Nat Rev Genet. 2004;5(5):355-65. [Link] [DOI:10.1038/nrg1323]
93. Townson J. Recent developments in genome editing for potential use in plants. Biosci Horiz Int J Stud Res. 2017;10:1-17. [Link] [DOI:10.1093/biohorizons/hzx016]
94. Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell. 2013;152(5):1173-83. [Link] [DOI:10.1016/j.cell.2013.02.022]
95. Maeder ML, Linder SJ, Cascio VM, Fu Y, Ho QH, Joung JK. CRISPR RNA-guided activation of endogenous human genes. Nat Methods. 2013;10(10):977-9. [Link] [DOI:10.1038/nmeth.2598]
96. Perez-Pinera P, Kocak DD, Vockley CM, Adler AF, Kabadi AM, Polstein LR, et al. RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nat Methods. 2013;10(10):973-6. [Link] [DOI:10.1038/nmeth.2600]
97. Dominguez AA, Lim WA, Qi LS. Beyond editing: Repurposing CRISPR-Cas9 for precision genome regulation and interrogation. Nat Rev Mol Cell Biol. 2016;17(1):5-15. [Link] [DOI:10.1038/nrm.2015.2]
98. Jiang W, Zhou H, Bi H, Fromm M, Yang B, Weeks DP. Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice. Nucleic Acids Res. 2013;41(20):e188. [Link] [DOI:10.1093/nar/gkt780]
99. Liang Z, Zhang K, Chen K, Gao C. Targeted mutagenesis in Zea mays using TALENs and the CRISPR/Cas system. J Genet Genomics. 2014;41(2):63-8. [Link] [DOI:10.1016/j.jgg.2013.12.001]
100. Jia H, Wang N. Targeted genome editing of sweet orange using Cas9/sgRNA. PLoS One. 2014;9(4):e93806. [Link] [DOI:10.1371/journal.pone.0093806]
101. Li T, Liu B, Chen CY, Yang B. TALEN-mediated homologous recombination produces site-directed DNA base change and herbicide-resistant rice. J Genet Genomics. 2016;43(5):297-305. [Link] [DOI:10.1016/j.jgg.2016.03.005]
102. Chipman D, Barak Z, Schloss JV. Biosynthesis of 2-aceto-2-hydroxy acids: Acetolactate synthases and acetohydroxyacid synthases. Biochimica et Biophysica Acta Protein Structure and Molecular Enzymology. 1998;1385(2):401-19. [Link] [DOI:10.1016/S0167-4838(98)00083-1]
103. Wang Y, Cheng X, Shan Q, Zhang Y, Liu J, Gao C, et al. Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. Nat Biotechnol. 2014;32:947-51. [Link] [DOI:10.1038/nbt.2969]
104. Haun W, Coffman A, Clasen BM, Demorest ZL, Lowy A, Ray E, et al. Improved soybean oil quality by targeted mutagenesis of the fatty acid desaturase 2 gene family. Plant Biotechnol J. 2014;12(7):934-40. [Link] [DOI:10.1111/pbi.12201]
105. Clasen BM, Stoddard TJ, Luo S, Demorest ZL, Li J, Cedrone F, et al. Improving cold storage and processing traits in potato through targeted gene knockout. Plant Biotechnol J. 2016;14(1):169-76. [Link] [DOI:10.1111/pbi.12370]
106. Baltes NJ, Hummel AW, Konecna E, Cegan R, Bruns AN, Bisaro DM, et al. Conferring resistance to geminiviruses with the CRISPR-Cas prokaryotic immune system. Nat Plants. 2015;1:15145. [Link] [DOI:10.1038/nplants.2015.145]
107. Ali Z, Abulfaraj A, Idris A, Ali Sh, Tashkandi M, Mahfouz MM. CRISPR/Cas9-mediated viral interference in plants. Genome Biol. 2015;16:238. [Link] [DOI:10.1186/s13059-015-0799-6]
108. Karimi Ashtiyani R, Ishii T, Niessen M, Stein N, Heckmann S, Gurushidze M, et al. Point mutation impairs centromeric CENH3 loading and induces haploid plants. Proc Natl Acad Sci U S A. 2015;112(36):11211-6. [Link] [DOI:10.1073/pnas.1504333112]
109. Čermák T, Baltes NJ, Čegan R, Zhang Y, Voytas DF. High-frequency, precise modification of the tomato genome. Genome Biol. 2015;16:232. [Link] [DOI:10.1186/s13059-015-0796-9]
110. Li B, Cui G, Shen G, Zhan Z, Huang L, Chen J, et al. Targeted mutagenesis in the medicinal plant Salvia miltiorrhiza. Sci Rep. 2017;7:43320. [Link] [DOI:10.1038/srep43320]
111. Champer J, Buchman A, Akbari OS. Cheating evolution: engineering gene drives to manipulate the fate of wild populations. Nat Rev Genet. 2016;17(3):146-59. [Link] [DOI:10.1038/nrg.2015.34]
112. Champer J, Reeves R, Oh SY, Liu C, Liu J, Clark AG, et al. Novel CRISPR/Cas9 gene drive constructs in Drosophila reveal insights into mechanisms of resistance allele formation and drive efficiency in genetically diverse populations. BioRxiv. 2017 Feb. [Link] [DOI:10.1101/112011]
113. Ledford H. CRISPR, the disruptor. Nature. 2015;522(7554):20-4. [Link] [DOI:10.1038/522020a]
114. National Academies of Sciences, Engineering, and Medicine. Gene drives on the horizon: Advancing science, navigating uncertainty, and aligning research with public values. Washington DC: National Academies Press; 2016. [Link]
115. Alphey L. Genetic control of mosquitoes. Annu Rev Entomol. 2014;59:205-24. [Link] [DOI:10.1146/annurev-ento-011613-162002]
116. Mc Farlane GR, Whitelaw CBA, Lillico SG. CRISPR-based gene drives for pest control. Trends Biotechnol. 2018;36(2):130-3. [Link] [DOI:10.1016/j.tibtech.2017.10.001]
117. Duke SO. Perspectives on transgenic, herbicide-resistant crops in the United States almost 20 years after introduction. Pest Manag Sci. 2015;71(5):652-7. [Link] [DOI:10.1002/ps.3863]
118. Watanabe K, Kobayashi A, Endo M, Sage-Ono K, Toki S, Ono M. CRISPR/Cas9-mediated mutagenesis of the dihydroflavonol-4-reductase-B (DFR-B) locus in the Japanese morning glory Ipomoea (Pharbitis) nil. Sci Rep. 2017;7:10028. [Link] [DOI:10.1038/s41598-017-10715-1]
119. Kim H, Kim ST, Ryu J, Choi MK, Kweon J, Kang BC, et al. A simple, flexible and high-throughput cloning system for plant genome editing via CRISPR-Cas system. J Integr Plant Biol. 2016;58(8):705-12. [Link] [DOI:10.1111/jipb.12474]
120. Xing HL, Dong L, Wang ZP, Zhang HY, Han CY, Liu B, et al. A CRISPR/Cas9 toolkit for multiplex genome editing in plants. BMC Plant Biol. 2014;14:327. [Link] [DOI:10.1186/s12870-014-0327-y]
121. Zhu C, Bortesi L, Baysal C, Twyman RM, Fischer R, Capell T, et al. Characteristics of genome editing mutations in cereal crops. Trends Plant Sci. 2017;22(1):38-52. [Link] [DOI:10.1016/j.tplants.2016.08.009]
122. Kaur K, Gupta AK, Rajput A, Kumar M. ge-CRISPR - an integrated pipeline for the prediction and analysis of sgRNAs genome editing efficiency for CRISPR/Cas system. Sci Rep. 2016;6:30870. [Link] [DOI:10.1038/srep30870]
123. Doench JG, Hartenian E, Graham DB, Tothova Z, Hegde M, Smith I, et al. Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation. Nat Biotechnol. 2014;32(12):1262-7. [Link] [DOI:10.1038/nbt.3026]
124. Wong N, Liu W, Wang X. WU-CRISPR: Characteristics of functional guide RNAs for the CRISPR/Cas9 system. Genome Boil. 2015;16:218. [Link] [DOI:10.1186/s13059-015-0784-0]
125. Chari R, Mali P, Moosburner M, Church GM. Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach. Nat Methods. 2015;12(9):823-6. [Link] [DOI:10.1038/nmeth.3473]
126. Zhu LJ, Holmes BR, Aronin N, Brodsky MH. CRISPRseek: A bioconductor package to identify target-specific guide RNAs for CRISPR-Cas9 genome-editing systems. PLoS One. 2014;9(9):e108424. [Link] [DOI:10.1371/journal.pone.0108424]
127. Bae S, Park J, Kim JS. Cas-OFFinder: A fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics. 2014;30(10):1473-5. [Link] [DOI:10.1093/bioinformatics/btu048]
128. Cradick TJ, Qiu P, Lee CM, Fine EJ, Bao G. COSMID: A web-based tool for identifying and validating CRISPR/Cas off-target sites. Mol Ther Nucleic Acids. 2014;3:e214. [Link] [DOI:10.1038/mtna.2014.64]
129. Singh R, Kuscu C, Quinlan A, Qi Y, Adli M. Cas9-chromatin binding information enables more accurate CRISPR off-target prediction. Nucleic Acids Res. 2015;43(18):e118. [Link] [DOI:10.1093/nar/gkv575]
130. Aach J, Mali P, Church GM. CasFinder: Flexible algorithm for identifying specific Cas9 targets in genomes. BioRxiv. 2014 May. [Link] [DOI:10.1101/005074]
131. Heigwer F, Kerr G, Boutros M. E-CRISP: Fast CRISPR target site identification. Nat Methods. 2014;11(2):122-3. [Link] [DOI:10.1038/nmeth.2812]
132. Montague TG, Cruz JM, Gagnon JA, Church GM, Valen E. CHOPCHOP: A CRISPR/Cas9 and TALEN web tool for genome editing. Nucleic Acids Res. 2014;42(Web Server issue):W401-7. [Link] [DOI:10.1093/nar/gku410]
133. Sander JD, Maeder ML, Reyon D, Voytas DF, Joung JK, Dobbs D. ZiFiT (Zinc Finger Targeter): An updated zinc finger engineering tool. Nucleic Acids Res. 2010;38(Web Server issue):W462-8. [Link] [DOI:10.1093/nar/gkq319]
134. Xiao A, Cheng Z, Kong L, Zhu Z, Lin S, Gao G, et al. CasOT: A genome-wide Cas9/gRNA off-target searching tool. Bioinformatics. 2014;30(8):1180-2. [Link] [DOI:10.1093/bioinformatics/btt764]
135. Bell CC, Magor GW, Gillinder KR, Perkins AC. A high-throughput screening strategy for detecting CRISPR-Cas9 induced mutations using next-generation sequencing. BMC Genom. 2014;15:1002. [Link] [DOI:10.1186/1471-2164-15-1002]
136. Wang X, Tilford C, Neuhaus I, Mintier G, Guo Q, Feder JN, et al. CRISPR-DAV: CRISPR NGS data analysis and visualization pipeline. Bioinformatics. 2017;33(23):3811-2. [Link] [DOI:10.1093/bioinformatics/btx518]
137. Shi J, Gao H, Wang H, Lafitte HR, Archibald RL, Yang M, et al. ARGOS8 variants generated by CRISPR-Cas9 improve maize grain yield under field drought stress conditions. Plant Biotechnol J. 2017;15(2):207-16. [Link] [DOI:10.1111/pbi.12603]
138. Shan-e-Ali Zaidi S, Tashkandi M, Mansoor Sh, Mahfouz MM. Engineering plant immunity: Using CRISPR/Cas9 to generate virus resistance. Front Plant Sci. 2016;7:1673. [Link] [DOI:10.3389/fpls.2016.01673]
139. Chandrasekaran J, Brumin M, Wolf D, Leibman D, Klap C, Pearlsman M, et al. Development of broad virus resistance in non-transgenic cucumber using CRISPR/Cas9 technology. Mol Plant Pathol. 2016;17(7):1140-53. [Link] [DOI:10.1111/mpp.12375]
140. Chen L, Wang G, Zhu YN, Xiang H, Wang W. Advances and perspectives in the application of CRISPR/Cas9 in insects. Zool Res. 2016;37(4):220-8. [Link]
141. Perkin LC, Adrianos SL, Oppert B. Gene disruption technologies have the potential to transform stored product insect pest control. Insects. 2016;7(3).pii:E46. [Link] [DOI:10.3390/insects7030046]
142. Leitão AL, Costa MC, Enguita FJ. Applications of genome editing by programmable nucleases to the metabolic engineering of secondary metabolites. J Biotechnol. 2017;241:50-60. [Link] [DOI:10.1016/j.jbiotec.2016.11.009]
143. Andersson HC, Arpaia S, Bartsch D, Casacuberta J, Davies HV, Du Jardin P, et al. Scientific opinion addressing the safety assessment of plants developed through cisgenesis and intragenesis. EFSA J. 2012;10(2):2561. [Link] [DOI:10.2903/j.efsa.2012.2561]
144. Hartung F, Schiemann J. Precise plant breeding using new genome editing techniques: Opportunities, safety and regulation in the EU. Plant J. 2014;78(5):742-52. [Link] [DOI:10.1111/tpj.12413]
145. Araki M, Ishii T. Towards social acceptance of plant breeding by genome editing. Trends Plant Sci. 2015;20(3):145-9. [Link] [DOI:10.1016/j.tplants.2015.01.010]
146. Waltz E. Gene-edited CRISPR mushroom escapes US regulation. Nature. 2016;532(7599):293. [Link] [DOI:10.1038/nature.2016.19754]
147. Liang P, Xu Y, Zhang X, Ding C, Huang R, Zhang Z, et al. CRISPR/Cas9-mediated gene editing in human tripronuclear zygotes. Protein Cell. 2015;6(5):363-72. [Link] [DOI:10.1007/s13238-015-0153-5]
148. Zhang Q, Ye Y. Not all predicted CRISPR-Cas systems are equal: Isolated cas genes and classes of CRISPR like elements. BMC Bioinform. 2017;18:92. [Link] [DOI:10.1186/s12859-017-1512-4]
149. Zhu H, Richmond E, Liang C. CRISPR-RT: A web service for designing CRISPR-C2c2 crRNA with improved target specificity. BioRxiv. 2017 Jan. [Link] [DOI:10.1101/099895]
150. Garst AD, Bassalo MC, Pines G, Lynch SA, Halweg-Edwards AL, Liu R, et al. Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering. Nat Biotechnol. 2017;35(1):48-55. [Link] [DOI:10.1038/nbt.3718]
151. Cao Q, Ma J, Chen CH, Xu H, Chen Z, Li W, et al. CRISPR-FOCUS: A web server for designing focused CRISPR screening experiments. PLoS One. 2017;12(9):e0184281. [Link] [DOI:10.1371/journal.pone.0184281]
152. Wang K, Liang C. CRF: Detection of CRISPR arrays using random forest. PeerJ. 2017;5:e3219. [Link] [DOI:10.7717/peerj.3219]
153. Park J, Lim K, Kim JS, Bae S. Cas-analyzer: An online tool for assessing genome editing results using NGS data. Bioinformatics. 2017;33(2):286-8. [Link] [DOI:10.1093/bioinformatics/btw561]
154. Hough SH, Kancleris K, Brody L, Humphryes-Kirilov N, Wolanski J, Dunaway K, et al. Guide Picker is a comprehensive design tool for visualizing and selecting guides for CRISPR experiments. BMC Bioinform. 2017;18:167. [Link] [DOI:10.1186/s12859-017-1581-4]
155. Winter J, Schwering M, Pelz O, Rauscher B, Zhan T, Heigwer F, et al. CRISPRAnalyzeR: Interactive analysis, annotation and documentation of pooled CRISPR screens. BioRxiv. 2017 Feb. [Link] [DOI:10.1101/109967]
156. Peterson KA, Beane GL, Goodwin LO, Kutny PM, Reinholdt LG, Murray SA. CRISPRtools: A flexible computational platform for performing CRISPR/Cas9 experiments in the mouse. Mamm Genome. 2017;28(7-8):283-90. [Link] [DOI:10.1007/s00335-017-9681-z]
157. Yu SH, Vogel J, Förstner KU. ANNOgesic: A pipeline to translate bacterial/archaeal RNA-Seq data into high-resolution genome annotations. BioRxiv. 2017 May. [Link]
158. Jeong HH, Kim SY, WC Rosseaux M, Zoghbi HY, Liu Z. SAVE: A secure cloud-based pipeline for CRISPR pooled screen deconvolution. BioRxiv. 2017 Feb. [Link] [DOI:10.1101/110262]
159. Ahmed M, He HH. SgTiler: A fast method to design tiling sgRNAs for CRISPR/Cas9 mediated screening. BioRxiv. 2017 Nov. [Link] [DOI:10.1101/217166]
160. Rastogi A, Murik O, Bowler C, Tirichine L. PhytoCRISP-Ex: A web-based and stand-alone application to find specific target sequences for CRISPR/CAS editing. BMC Bioinform. 2016;17:261. [Link] [DOI:10.1186/s12859-016-1143-1]
161. Haeussler M, Schönig K, Eckert H, Eschstruth A, Mianné J, Renaud JB, et al. Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biol. 2016;17(1):148. [Link] [DOI:10.1186/s13059-016-1012-2]
162. Ge R, Mai G, Wang P, Zhou M, Luo Y, Cai Y, et al. CRISPRdigger: Detecting CRISPRs with better direct repeat annotations. Sci Rep. 2016;6:32942. [Link] [DOI:10.1038/srep32942]
163. Boel A, Steyaert W, De Rocker N, Menten B, Callewaert B, De Paepe A, et al. BATCH-GE: Batch analysis of next-generation sequencing data for genome editing assessment. Sci Rep. 2016;6:30330. [Link] [DOI:10.1038/srep30330]
164. Alkhnbashi OS, Shah SA, Garrett RA, Saunders SJ, Costa F, Backofen R. Characterizing leader sequences of CRISPR loci. Bioinformatics. 2016;32(17):i576-85. [Link] [DOI:10.1093/bioinformatics/btw454]
165. Ma J, Köster J, Qin Q, Hu S, Li W, Chen C, et al. CRISPR-DO for genome-wide CRISPR design and optimization. Bioinformatics. 2016;32(21):3336-8. [Link] [DOI:10.1093/bioinformatics/btw476]
166. Oliveros JC, Franch M, Tabas-Madrid D, San-León D, Montoliu L, Cubas P, et al. Breaking-Cas-interactive design of guide RNAs for CRISPR-Cas experiments for ENSEMBL genomes. Nucleic Acids Res. 2016;44(W1):W267-71. [Link] [DOI:10.1093/nar/gkw407]
167. Zhu H, Misel L, Graham M, Robinson ML, Liang C. CT-Finder: A web service for CRISPR optimal target prediction and visualization. Sci Rep. 2016;6:25516. [Link] [DOI:10.1038/srep25516]
168. Pulido-Quetglas C, Aparicio-Prat E, Arnan C, Polidori T, Hermoso T, Palumbo E, et al. Scalable design of paired CRISPR guide RNAs for genomic deletion. BioRxiv. 2016 May. [Link] [DOI:10.1101/052795]
169. Heigwer F, Zhan T, Breinig M, Winter J, Brügemann D, Leible S, et al. CRISPR Library Designer (CLD): Software for multispecies design of single guide RNA libraries. Genome Biol. 2016;17:55. [Link] [DOI:10.1186/s13059-016-0915-2]
170. Blin K, Pedersen LE, Weber T, Lee SY. CRISPy-web: An online resource to design sgRNAs for CRISPR applications. Synthetic Syst Biotechnol. 2016;1(2):118-21. [Link] [DOI:10.1016/j.synbio.2016.01.003]
171. Biswas A, Staals RHJ, Morales SE, Fineran PC, Brown CM. CRISPRDetect: A flexible algorithm to define CRISPR arrays. BMC Genomics. 2016;17:356. [Link] [DOI:10.1186/s12864-016-2627-0]
172. Peng D, Tarleton R. EuPaGDT: A web tool tailored to design CRISPR guide RNAs for eukaryotic pathogens. Microb Genom. 2015;1(4):e000033. [Link] [DOI:10.1099/mgen.0.000033]
173. Xu H, Xiao T, Chen CH, Li W, Meyer CA, Wu Q, et al. Sequence determinants of improved CRISPR sgRNA design. Genome Res. 2015;25(8):1147-57. [Link] [DOI:10.1101/gr.191452.115]
174. Park J, Bae S, Kim JS. Cas-Designer: A web-based tool for choice of CRISPR-Cas9 target sites. Bioinformatics. 2015;31(24):4014-6. [Link] [DOI:10.1093/bioinformatics/btv537]
175. Prykhozhij SV, Rajan V, Gaston D, Berman JN. CRISPR multitargeter: A web tool to find common and unique CRISPR single guide RNA targets in a set of similar sequences. PLoS One. 2015;10(3):e0119372. [Link] [DOI:10.1371/journal.pone.0119372]
176. Liu H, Wei Z, Dominguez A, Li Y, Wang X, Qi LS. CRISPR-ERA: A comprehensive design tool for CRISPR-mediated gene editing, repression and activation. Bioinformatics. 2015;31(22):3676-8. [Link] [DOI:10.1093/bioinformatics/btv423]
177. Stemmer M, Thumberger T, Del Sol Keyer M, Wittbrodt J, Mateo JL. CCTop: An intuitive, flexible and reliable CRISPR/Cas9 target prediction tool. PLoS One. 2015;10(4):e0124633. [Link] [DOI:10.1371/journal.pone.0124633]
178. Pinello L, Canver MC, Hoban MD, Orkin SH, Kohn DB, Bauer DE, et al. CRISPResso: Sequencing analysis toolbox for CRISPR-Cas9 genome editing. BioRxiv. 2015 Nov. [Link] [DOI:10.1101/031203]
179. Moreno-Mateos MA, Vejnar CE, Beaudoin JD, Fernandez JP, Mis EK, Khokha MK, et al. CRISPRscan: Designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo. Nat Methods. 2015;12(10):982-8. [Link] [DOI:10.1038/nmeth.3543]
180. Mac Pherson CR, Scherf A. Flexible guide-RNA design for CRISPR applications using protospacer workbench. Nat Biotechnol. 2015;33(8):805-6. [Link] [DOI:10.1038/nbt.3291]
181. Lei Y, Lu L, Liu HY, Li S, Xing F, Chen LL. CRISPR-P: A web tool for synthetic single-guide RNA design of CRISPR-system in plants. Mol Plant. 2014;7(9):1494-6. [Link] [DOI:10.1093/mp/ssu044]
182. Liu H, Ding Y, Zhou Y, Jin W, Xie K, Chen LL. CRISPR-P 2.0: An improved CRISPR-Cas9 tool for genome editing in plants. Mol Plant. 2017;10(3):530-2. [Link] [DOI:10.1016/j.molp.2017.01.003]
183. Naito Y, Hino K, Bono H, Ui-Tei K. CRISPRdirect: Software for designing CRISPR/Cas guide RNA with reduced off-target sites. Bioinformatics. 2015;31(7):1120-3. [Link] [DOI:10.1093/bioinformatics/btu743]
184. Gratz SJ, Ukken FP, Dustin Rubinstein C, Thiede G, Donohue LK, Cummings AM, et al. Highly specific and efficient CRISPR/Cas9-catalyzed homology-directed repair in Drosophila. Genetics. 2014;196(4):961-71. [Link] [DOI:10.1534/genetics.113.160713]
185. O'Brien A, Bailey TL. GT-Scan: Identifying unique genomic targets. Bioinformatics. 2014;30(18):2673-5. [Link] [DOI:10.1093/bioinformatics/btu354]
186. Xie S, Shen B, Zhang C, Huang X, Zhang Y. sgRNAcas9: A software package for designing CRISPR sgRNA and evaluating potential off-target cleavage sites. PLoS One. 2014;9(6):e100448. [Link] [DOI:10.1371/journal.pone.0100448]
187. Upadhyay SK, Sharma S. SSFinder: High throughput CRISPR-Cas target sites prediction tool. Biomed Res Int. 2014;2014:742482. [Link] [DOI:10.1155/2014/742482]
188. Güell M, Yang L, Church GM. Genome editing assessment using CRISPR Genome Analyzer (CRISPR-GA). Bioinformatics. 2014;30(20):2968-70. [Link] [DOI:10.1093/bioinformatics/btu427]
189. Brinkman EK, Chen T, Amendola M, Van Steensel B. Easy quantitative assessment of genome editing by sequence trace decomposition. Nucleic Acids Res. 2014;42(22):e168. [Link] [DOI:10.1093/nar/gku936]
190. Skennerton CT, Imelfort M, Tyson GW. Crass: Identification and reconstruction of CRISPR from unassembled metagenomic data. Nucleic Acids Res. 2013;41(10):e105. [Link] [DOI:10.1093/nar/gkt183]
191. Ma M, Ye AY, Zheng W, Kong L. A guide RNA sequence design platform for the CRISPR/Cas9 system for model organism genomes. Biomed Res Int. 2013;2013:270805. [Link] [DOI:10.1155/2013/270805]
192. Park J, Bae S. Cpf1-Database: Web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cpf1. Bioinformatics. 2018;34(6):1077-9. [Link] [DOI:10.1093/bioinformatics/btx695]
193. Dong C, Hao GF, Hua HL, Liu S, Labena AA, Chai G, et al. Anti-CRISPRdb: A comprehensive online resource for anti-CRISPR proteins. Nucleic Acids Res. 2018;46(D1):D393-8. [Link] [DOI:10.1093/nar/gkx835]
194. Rauscher B, Heigwer F, Breinig M, Winter J, Boutros M. GenomeCRISPR - a database for high-throughput CRISPR/Cas9 screens. Nucleic Acids Res. 2017;45(Database issue):D679-86. [Link] [DOI:10.1093/nar/gkw997]
195. Lenoir WF, Lim TL, Hart T. PICKLES: The database of pooled in-vitro CRISPR knockout library essentiality screens. Nucleic Acids Res. 2018;46(D1):D776-80. [Link] [DOI:10.1093/nar/gkx993]
196. Chen IA, Markowitz VM, Chu K, Palaniappan K, Szeto E, Pillay M, et al. IMG/M: Integrated genome and metagenome comparative data analysis system. Nucleic Acids Res. 2017;45(D1):D507-16. [Link] [DOI:10.1093/nar/gkw929]
197. Park J, Kim JS, Bae S. Cas-Database: Web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cas9. Bioinformatics. 2016;32(13):2017-23. [Link] [DOI:10.1093/bioinformatics/btw103]
198. Wang Y, Liu X, Ren C, Zhong GY, Yang L, Li Sh, et al. Identification of genomic sites for CRISPR/Cas9-based genome editing in the Vitis vinifera genome. BMC Plant Boil. 2016;16:96. [Link] [DOI:10.1186/s12870-016-0787-3]
199. Jaskula-Ranga V, Zack DJ. grID: A CRISPR-Cas9 guide RNA database and resource for genome-editing. BioRxiv. 2016 Dec. [Link] [DOI:10.1101/097352]
200. Varshney GK, Zhang S, Pei W, Adomako-Ankomah A, Fohtung J, Schaffer K, et al. CRISPRz: A database of zebrafish validated sgRNAs. Nucleic Acids Res. 2016;44(Database issue):D822-6. [Link] [DOI:10.1093/nar/gkv998]
201. Hodgkins A, Farne A, Perera S, Grego T, Parry-Smith DJ, Skarnes WC, et al. WGE: A CRISPR database for genome engineering. Bioinformatics. 2015;31(18):3078-80. [Link] [DOI:10.1093/bioinformatics/btv308]
202. Kaur K, Tandon H, Gupta AK, Kumar M. CrisprGE: A central hub of CRISPR/Cas-based genome editing. Database (Oxford). 2015;2015:bav055. [Link] [DOI:10.1093/database/bav055]
203. Xiao A, Wu Y, Yang Z, Hu Y, Wang W, Zhang Y, et al. EENdb: A database and knowledge base of ZFNs and TALENs for endonuclease engineering. Nucleic Acids Res. 2013;41(Database issue):D415-22. [Link] [DOI:10.1093/nar/gks1144]
204. Rousseau C, Gonnet M, Le Romancer M, Nicolas J. CRISPI: A CRISPR interactive database. Bioinformatics. 2009;25(24):3317-8. [Link] [DOI:10.1093/bioinformatics/btp586]
205. Lin Y, Fine EJ, Zheng Z, Antico CJ, Voit RA, Porteus MH, et al. SAPTA: A new design tool for improving TALE nuclease activity. Nucleic Acids Res. 2014;42(6):e47. [Link] [DOI:10.1093/nar/gkt1363]
206. Grau J, Boch J, Posch S. TALENoffer: Genome-wide TALEN off-target prediction. Bioinformatics. 2013;29(22):2931-2. [Link] [DOI:10.1093/bioinformatics/btt501]
207. Heigwer F, Kerr G, Walther N, Glaeser K, Pelz O, Breinig M, et al. E-TALEN: A web tool to design TALENs for genome engineering. Nucleic Acids Res. 2013;41(20):e190. [Link] [DOI:10.1093/nar/gkt789]
208. Neff KL, Argue DP, Ma AC, Lee HB, Clark KJ, Ekker SC. Mojo Hand, a TALEN design tool for genome editing applications. BMC Bioinform. 2013;14:1. [Link] [DOI:10.1186/1471-2105-14-1]
209. Li L, Piatek MJ, Atef A, Piatek A, Wibowo A, Fang X, et al. Rapid and highly efficient construction of TALE-based transcriptional regulators and nucleases for genome modification. Plant Mol Biol. 2012;78(4-5):407-16. [Link] [DOI:10.1007/s11103-012-9875-4]
210. Kim Y, Kweon J, Kim A, Chon JK, Yoo JY, Kim HJ, et al. A library of TAL effector nucleases spanning the human genome. Nat Biotechnol. 2013;31:251-8. [Link] [DOI:10.1038/nbt.2517]
211. Cradick TJ, Ambrosini G, Iseli C, Bucher P, Mc Caffrey AP. ZFN-site searches genomes for zinc finger nuclease target sites and off-target sites. BMC Bioinform. 2011;12:152. [Link] [DOI:10.1186/1471-2105-12-152]
212. Mandell JG, Barbas III CF. Zinc finger tools: Custom DNA-binding domains for transcription factors and nucleases. Nucleic Acids Res. 2006;34(Web Server issue):W516-23. [Link] [DOI:10.1093/nar/gkl209]
213. Jayakanthan M, Muthukumaran J, Chandrasekar S, Chawla K, Punetha A, Sundar D. ZifBASE: A database of zinc finger proteins and associated resources. BMC Genomics. 2009;10:421. [Link] [DOI:10.1186/1471-2164-10-421]
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