Functional genetics for all: Engineered nucleases, CRISPR and the gene editing revolution

EvoDevo

Volumn 5, Issue 1, 2014, Pages

  Gilles, Anna F ^a,b   Averof, Michalis ^a,c  

^a UNIVERSITÉ DE LYON   (France)

^b UNIVERSITÉ LYON 1   (France)

^c CNRS   (France)

Author keywords

Comparative developmental biology; CRISPR; Gene targeting; Gene editing nucleases; Homologous recombination; Model organisms

Indexed keywords

EID: 84924528187     PISSN: None     EISSN: 20419139     Source Type: Journal    
DOI: 10.1186/2041-9139-5-43     Document Type: Article

References (144)

1. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC: Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 1998, 391:806-811. 10.1038/35888.
2. Hamilton AJ: A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 1999, 286:950-952. 10.1126/science.286.5441.950.
3. Tuschl T, Zamore PD, Lehmann R, Bartel DP, Sharp PA: Targeted mRNA degradation by double-stranded RNA in vitro. Genesand Development 1999, 13:3191-3197. 10.1101/gad.13.24.3191.
4. Tijsterman M, Ketting RF, Plasterk RHA: The genetics of RNA silencing. Annual Review Of Genetics 2002, 36:489-519. 10.1146/annurev.genet.36.043002.091619.
5. Nasevicius A, Ekker SC: Effective targeted gene "knockdown" in zebrafish. Nat Genet 2000, 26:216-220. 10.1038/79951.
6. Wahlestedt C, Salmi P, Good L, Kela J, Johnsson T, Hokfelt T, Broberger C, Porreca F, Lai J, Ren K, Ossipov M, Koshkin A, Jakobsen N, Skouv J, Oerum H, Jacobsen MH, Wengel J: Potent and nontoxic antisense oligonucleotides containing locked nucleic acids. Proc Natl Acad Sci USA 2000, 97:5633-5638. 10.1073/pnas.97.10.5633.
7. Heasman J: Morpholino oligos: making sense of antisense? Dev Biol 2002, 243:209-214. 10.1006/dbio.2001.0565.
8. Krutzfeldt J, Rajewsky N, Braich R, Rajeev KG, Tuschl T, Manoharan M, Stoffel M: Silencing of microRNAs in vivo with "antagomirs.". Nature 2005, 438:685-689. 10.1038/nature04303.
9. Sanchez Alvarado A, Newmark PA: Double-stranded RNA specifically disrupts gene expression during planarian regeneration. Proc Natl Acad Sci USA 1999, 96:5049-5054. 10.1073/pnas.96.9.5049.
10. Bucher G, Scholten J, Klingler M: Parental RNAi in Tribolium (Coleoptera). Curr Biol 2002, 12:R85-R86. 10.1016/S0960-9822(02)00666-8.
11. Layden MJ, Röttinger E, Wolenski FS, Gilmore TD, Martindale MQ: Microinjection of mRNA or morpholinos for reverse genetic analysis in the starlet sea anemone, Nematostella vectensis. Nat Protoc 2013, 8:924-934. 10.1038/nprot.2013.009.
12. Conzelmann M, Williams EA, Tunaru S, Randel N, Shahidi R, Asadulina A, Berger J, Offermanns S, Jékely G: Conserved MIP receptor-ligand pair regulates Platynereis larval settlement. Proc Natl Acad Sci USA 2013, 110:8224-8229. 10.1073/pnas.1220285110.
13. Yamada L: Morpholino-based gene knockdown screen of novel genes with developmental function in Ciona intestinalis. Development 2003, 130:6485-6495. 10.1242/dev.00847.
14. Reddien PW, Bermange AL, Murfitt KJ, Jennings JR, Sanchez Alvarado A: Identification of genes needed for regeneration, stem cell function, and tissue homeostasis by systematic gene perturbation in planaria. Dev Cell 2005, 8:635-649. 10.1016/j.devcel.2005.02.014.
15. Oates AC, Bruce AEE, Ho RK: Too much interference: injection of double-stranded RNA has nonspecific effects in the zebrafish embryo. Dev Biol 2000, 224:20-28. 10.1006/dbio.2000.9761.
16. Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, Tuschl T: Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 2001, 411:494-498. 10.1038/35078107.
17. Echeverri CJ, Beachy PA, Baum B, Boutros M, Buchholz F, Chanda SK, Downward J, Ellenberg J, Fraser AG, Hacohen N, Hahn WC, Jackson AL, Kiger A, Linsley PS, Lum L, Ma Y, Mathey-Prevot B, Root DE, Sabatini DM, Taipale J, Perrimon N, Bernards R: Minimizing the risk of reporting false positives in large-scale RNAi screens. Nat Methods 2006, 3:777-779. 10.1038/nmeth1006-777.
18. Berghammer AJ, Klingler M, Wimmer EA: A universal marker for transgenic insects. Nature 1999, 402:370-371. 10.1038/46463.
19. Sasakura Y, Awazu S, Chiba S, Satoh N: Germ-line transgenesis of the Tc1/mariner superfamily transposon Minos in Ciona intestinalis. Proc Natl Acad Sci USA 2003, 100:7726-7730. 10.1073/pnas.1230736100.
20. Pavlopoulos A, Averof M: Establishing genetic transformation for comparative developmental studies in the crustacean Parhyale hawaiensis. Proc Natl Acad Sci USA 2005, 102:7888-7893. 10.1073/pnas.0501101102.
21. Sobkow L, Epperlein HH, Herklotz S, Straube WL, Tanaka EM: A germline GFP transgenic axolotl and its use to track cell fate: Dual origin of the fin mesenchyme during development and the fate of blood cells during regeneration. Dev Biol 2006, 290:386-397. 10.1016/j.ydbio.2005.11.037.
22. Wittlieb J, Khalturin K, Lohmann JU, Anton-Erxleben F, Bosch TCG: Transgenic Hydra allow in vivo tracking of individual stem cells during morphogenesis. Proc Natl Acad Sci USA 2006, 103:6208-6211. 10.1073/pnas.0510163103.
23. Renfer E, Amon-Hassenzahl A, Steinmetz PR, Technau U: A muscle-specific transgenic reporter line of the sea anemone, Nematostella vectensis. Proc Natl Acad Sci USA 2010, 107:104-108. 10.1073/pnas.0909148107.
24. Backfisch B, Rajan VBV, Fischer RM, Lohs C, Arboleda E, Tessmar-Raible K, Raible F: Stable transgenesis in the marine annelid Platynereis dumerilii sheds new light on photoreceptor evolution. Proc Natl Acad Sci USA 2013, 110:193-198. 10.1073/pnas.1209657109.
25. Blair SS: Genetic mosaic techniques for studying Drosophila development. Development 2003, 130:5065-5072. 10.1242/dev.00774.
26. Kragl M, Knapp D, Nacu E, Khattak S, Maden M, Epperlein HH, Tanaka EM: Cells keep a memory of their tissue origin during axolotl limb regeneration. Nature 2009, 460:60-65. 10.1038/nature08152.
27. Konstantinides N, Averof M: A common cellular basis for muscle regeneration in arthropods and vertebrates. Science 2014, 343:788-791. 10.1126/science.1243529.
28. Yeh J-RJ, Crews CM: Chemical genetics adding to the developmental biology toolbox. Dev Cell 2003, 5:11-19. 10.1016/S1534-5807(03)00200-4.
29. Capecchi MR: Gene targeting in mice: functional analysis of the mammalian genome for the twenty-first century. Nat Rev Genet 2005, 6:507-512. 10.1038/nrg1619.
30. Deng C, Capecchi MR: Reexamination of gene targeting frequency as a function of the extent of homology between the targeting vector and the target locus. Mol Cell Biol 1992, 12:3365-3371.
31. Hinnen A, Hicks JB, Fink GR: Transformation of yeast. Proc Natl Acad Sci USA 1978, 75:1929-1933. 10.1073/pnas.75.4.1929.
32. Smithies O, Gregg RG, Boggs SS, Koralewski MA, Kucherlapati RS: Insertion of DNA sequences into the human chromosomal beta-globin locus by homologous recombination. Nature 1985, 317:230-234. 10.1038/317230a0.
33. Thomas KR, Folger KR, Capecchi MR: High frequency targeting of genes to specific sites in the mammalian genome. Cell 1986, 44:419-428. 10.1016/0092-8674(86)90463-0.
34. Szostak JW, Orr-Weaver TL, Rothstein RJ, Stahl FW: The double-strand-break repair model for recombination. Cell 1983, 33:25-35. 10.1016/0092-8674(83)90331-8.
35. Rouet P, Smih F, Jasin M: Introduction of double-strand breaks into the genome of mouse cells by expression of a rare-cutting endonuclease. Mol Cell Biol 1994, 14:8096-8106.
36. Choulika A, Perrin A, Dujon B, Nicolas JF: Induction of homologous recombination in mammalian chromosomes by using the I-SceI system of Saccharomyces cerevisiae. Mol Cell Biol 1995, 15:1968-1973.
37. Donoho G, Jasin M, Berg P: Analysis of gene targeting and intrachromosomal homologous recombination stimulated by genomic double-strand breaks in mouse embryonic stem cells. Mol Cell Biol 1998, 18:4070-4078.
38. Taghian DG, Nickoloff JA: Chromosomal double-strand breaks induce gene conversion at high frequency in mammalian cells. Mol Cell Biol 1997, 17:6386-6393.
39. Gloor GB, Nassif NA, Johnson-Schlitz DM, Preston CR, Engels WR: Targeted gene replacement in Drosophila via P element-induced gap repair. Science 1991, 253:1110-1117. 10.1126/science.1653452.
40. Robert V, Bessereau J-L: Targeted engineering of the Caenorhabditis elegans genome following Mos1-triggered chromosomal breaks. Embo J 2007, 26:170-183. 10.1038/sj.emboj.7601463.
41. Krebs JE, Kilpatrick ST, Goldstein SE: Lewin's Genes XI. Burlington, MA: Jones & Bartlett Publishers; 2014.
42. Maresca M, Lin VG, Guo N, Yang Y: Obligate ligation-gated recombination (ObLiGaRe): custom-designed nuclease-mediated targeted integration through nonhomologous end joining. Genome Res 2013, 23:539-546. 10.1101/gr.145441.112.
43. Cristea S, Freyvert Y, Santiago Y, Holmes MC, Urnov FD, Gregory PD, Cost GJ: In vivo cleavage of transgene donors promotes nuclease-mediated targeted integration. Biotechnol Bioeng 2013, 110:871-880. 10.1002/bit.24733.
44. Ran FA, Hsu PD, Lin C-Y, Gootenberg JS, Konermann S, Trevino AE, Scott DA, Inoue A, Matoba S, Zhang Y, Zhang F: Double nicking by RNA-Guided CRISPR Cas9 for enhanced genome editing specificity. Cell 2013, 154:1380-1389. 10.1016/j.cell.2013.08.021.
45. Auer TO, Duroure K, De Cian A, Concordet JP, Del Bene F: Highly efficient CRISPR/Cas9-mediated knock-in in zebrafish by homology-independent DNA repair. Genome Res 2014, 24:142-153. 10.1101/gr.161638.113.
46. Dickinson DJ, Ward JD, Reiner DJ, Goldstein B: Engineering the Caenorhabditis elegans genome using Cas9-triggered homologous recombination. Nat Meth 2013, 10:1028-1034. 10.1038/nmeth.2641.
47. Gratz SJ, Ukken FP, Rubinstein CD, Thiede G, Donohue LK, Cummings AM, O'Connor-Giles KM: Highly Specific and Efficient CRISPR/Cas9-Catalyzed Homology-Directed Repair in Drosophila. Genetics 2014, 196:961-971. 10.1534/genetics.113.160713.
48. Port F, Chen HM, Lee T, Bullock SL: Optimized CRISPR/Cas tools for efficient germline and somatic genome engineering in Drosophila. Proc Natl Acad Sci USA 2014, 111:E2967-E2976. 10.1073/pnas.1405500111.
49. Beumer KJ, Trautman JK, Bozas A, Liu JL, Rutter J, Gall JG, Carroll D: Efficient gene targeting in Drosophila by direct embryo injection with zinc-finger nucleases. Proc Natl Acad Sci USA 2008, 105:19821-19826. 10.1073/pnas.0810475105.
50. Beumer KJ, Trautman JK, Mukherjee K, Carroll D: Donor DNA Utilization during Gene Targeting with Zinc-finger Nucleases. G3 (Bethesda) 2013. doi:10.1534/g3.112.005439
51. Hwang WY, Fu Y, Reyon D, Maeder ML, Kaini P, Sander JD, Joung JK, Peterson RT, Yeh J-RJ: Heritable and precise zebrafish genome editing using a CRISPR-Cas system. PLoS ONE 2013, 8:e68708. 10.1371/journal.pone.0068708.
52. Chen F, Pruett-Miller SM, Huang Y, Gjoka M, Duda K, Taunton J, Collingwood TN, Frodin M, Davis GD: High-frequency genome editing using ssDNA oligonucleotides with zinc-finger nucleases. Nat Meth 2011, 8:753-755. 10.1038/nmeth.1653.
53. Takeuchi R, Lambert AR, Mak AN-S, Jacoby K, Dickson RJ, Gloor GB, Scharenberg AM, Edgell DR, Stoddard BL: Tapping natural reservoirs of homing endonucleases for targeted gene modification. Proc Natl Acad Sci USA 2011, 108:13077-13082. 10.1073/pnas.1107719108.
54. Majumdar A, Muniandy PA, Liu J, Liu JL, Liu ST, Cuenoud B, Seidman MM: Targeted gene knock in and sequence modulation mediated by a psoralen-linked triplex-forming oligonucleotide. J Biol Chem 2008, 283:11244-11252. 10.1074/jbc. M800607200.
55. Pei D, Corey DR, Schultz PG: Site-specific cleavage of duplex DNA by a semisynthetic nuclease via triple-helix formation. Proc Natl Acad Sci USA 1990, 87:9858-9862. 10.1073/pnas.87.24.9858.
56. Kim YG, Cha J, Chandrasegaran S: Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proc Natl Acad Sci USA 1996, 93:1156-1160. 10.1073/pnas.93.3.1156.
57. Carroll D: Genome engineering with zinc-finger nucleases. Genetics 2011, 188:773-782. 10.1534/genetics.111.131433.
58. Miller JC, Holmes MC, Wang J, Guschin DY, Lee Y-L, Rupniewski I, Beausejour CM, Waite AJ, Wang NS, Kim KA, Gregory PD, Pabo CO, Rebar EJ: An improved zinc-finger nuclease architecture for highly specific genome editing. Nat Biotechnol 2007, 25:778-785. 10.1038/nbt1319.
59. Maeder ML, Thibodeau-Beganny S, Osiak A, Wright DA, Anthony RM, Eichtinger M, Jiang T, Foley JE, Winfrey RJ, Townsend JA, Unger-Wallace E, Sander JD, Müller-Lerch F, Fu F, Pearlberg J, Göbel C, Dassie JP, Pruett-Miller SM, Porteus MH, Sgroi DC, Iafrate AJ, Dobbs D, McCray PB, Cathomen T, Voytas DF, Joung JK: Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification. Mol Cell 2008, 31:294-301. 10.1016/j.molcel.2008.06.016.
60. Isalan M, Choo Y, Klug A: Synergy between adjacent zinc fingers in sequence-specific DNA recognition. Proc Natl Acad Sci USA 1997, 94:5617-5621. 10.1073/pnas.94.11.5617.
61. Sander JD, Dahlborg EJ, Goodwin MJ, Cade L, Zhang F, Cifuentes D, Curtin SJ, Blackburn JS, Thibodeau-Beganny S, Qi Y, Pierick CJ, Hoffman E, Maeder ML, Khayter C, Reyon D, Dobbs D, Langenau DM, Stupar RM, Giraldez AJ, Voytas DF, Peterson RT, Yeh J-RJ, Joung JK: Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA). Nat Meth 2010, 8:67-69.
62. Ramirez CL, Foley JE, Wright DA, Müller-Lerch F, Rahman SH, Cornu TI, Winfrey RJ, Sander JD, Fu F, Townsend JA, Cathomen T, Voytas DF, Joung JK: Unexpected failure rates for modular assembly of engineered zinc fingers. Nat Meth 2008, 5:374-375. 10.1038/nmeth0508-374.
63. Boch J, Scholze H, Schornack S, Landgraf A, Hahn S, Kay S, Lahaye T, Nickstadt A, Bonas U: Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors. Science 2009, 326:1509-1512. 10.1126/science.1178811.
64. Moscou MJ, Bogdanove AJ: A simple cipher governs DNA recognition by TAL effectors. Science 2009, 326:1501. 10.1126/science.1178817.
65. Guilinger JP, Pattanayak V, Reyon D, Tsai SQ, Sander JD, Joung JK, Liu DR: Broad specificity profiling of TALENs results in engineered nucleases with improved DNA-cleavage specificity. Nat Meth 2014, 11:429-435. 10.1038/nmeth.2845.
66. Christian M, Cermak T, Doyle EL, Schmidt C, Zhang F, Hummel A, Bogdanove AJ, Voytas DF: Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 2010, 186:757-761. 10.1534/genetics.110.120717.
67. Li T, Huang S, Jiang WZ, Wright D, Spalding MH, Weeks DP, Yang B: TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain. Nucleic Acids Res 2011, 39:359-372. 10.1093/nar/gkq704.
68. Miller JC, Tan S, Qiao G, Barlow KA, Wang J, Xia DF, Meng X, Paschon DE, Leung E, Hinkley SJ, Dulay GP, Hua KL, Ankoudinova I, Cost GJ, Urnov FD, Zhang HS, Holmes MC, Zhang L, Gregory PD, Rebar EJ: A TALE nuclease architecture for efficient genome editing. Nat Biotechnol 2011, 29:143-148. 10.1038/nbt.1755.
69. Bedell VM, Wang Y, Campbell JM, Poshusta TL, Starker CG, Krug RG II, Tan W, Penheiter SG, Ma AC, Leung AYH, Fahrenkrug SC, Carlson DF, Voytas DF, Clark KJ, Essner JJ, Ekker SC: In vivo genome editing using a high-efficiency TALEN system. Nature 2012, 491:114-118. 10.1038/nature11537.
70. Watanabe T, Ochiai H, Sakuma T, Horch HW, Hamaguchi N, Nakamura T, Bando T, Ohuchi H, Yamamoto T, Noji S, Mito T: Non-transgenic genome modifications in a hemimetabolous insect using zinc-finger and TAL effector nucleases. Nat Commun 2012, 3:1017-1018.
71. Beumer KJ, Trautman JK, Christian M, Dahlem TJ, Lake CM, Hawley RS, Grunwald DJ, Voytas DF, Carroll D: Comparing Zinc Finger Nucleases and Transcription Activator-Like Effector Nucleases for Gene Targeting in Drosophila. G3 (Bethesda) 2013, 3:1717-1725. 2013
72. Takasu Y, Sajwan S, Daimon T, Osanai-Futahashi M, Uchino K, Sezutsu H, Tamura T, Zurovec M: Efficient TALEN construction for Bombyx mori gene targeting. PLoS ONE 2013, 8:e73458. 10.1371/journal.pone.0073458.
73. Lo T-W, Pickle CS, Lin S, Ralston EJ, Gurling M, Schartner CM, Bian Q, Doudna JA, Meyer BJ: Precise and heritable genome editing in evolutionarily diverse nematodes using TALENs and CRISPR/Cas9 to engineer insertions and deletions. Genetics 2013, 195:331-348. 10.1534/genetics.113.155382.
74. Bannister S, Antonova O, Polo A, Lohs C, Hallay N, Valinciute A, Raible F, Tessmar-Raible K: TALENs mediate efficient and heritable mutation of endogenous genes in the marine annelid Platynereis dumerilii. Genetics 2014, 197:77-89. 10.1534/genetics.113.161091.
75. Yoshida K, Treen N, Hozumi A, Sakuma T, Yamamoto T, Sasakura Y: Germ cell mutations of the ascidian Ciona intestinalis with TALE nucleases. Genesis 2014, 52:431-439. 10.1002/dvg.22770.
76. Carroll D: Genome engineering with targetable nucleases. Annu Rev Biochem 2014, 83:409-439. 10.1146/annurev-biochem-060713-035418.
77. Cermak T, Doyle EL, Christian M, Wang L, Zhang Y, Schmidt C, Baller JA, Somia NV, Bogdanove AJ, Voytas DF: Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res 2011, 39:e82. 10.1093/nar/gkr218.
78. Reyon D, Tsai SQ, Khayter C, Foden JA, Sander JD, Joung JK: FLASH assembly of TALENs for high-throughput genome editing. Nat Biotechnol 2012, 30:460-465. 10.1038/nbt.2170.
79. Sakuma T, Ochiai H, Kaneko T, Mashimo T, Tokumasu D, Sakane Y, Suzuki K-I, Miyamoto T, Sakamoto N, Matsuura S, Yamamoto T: Repeating pattern of non-RVD variations in DNA-binding modules enhances TALEN activity. Sci Rep 2013, 3:3379.
80. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P: CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes. Science 2007, 315:1709-1712. 10.1126/science.1138140.
81. Garneau JE, Dupuis M-È, Villion M, Romero DA, Barrangou R, Boyaval P, Fremaux C, Horvath P, Magadán AH, Moineau S: The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 2010, 468:67-71. 10.1038/nature09523.
82. 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 USA 2012, 109:E2579-E2586. 10.1073/pnas.1208507109.
83. Wiedenheft B, Sternberg SH, Doudna JA: RNA-guided genetic silencing systems in bacteria and archaea. Nature 2012, 482:331-338. 10.1038/nature10886.
84. 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, 60:174-182. 10.1007/s00239-004-0046-3.
85. Bolotin A, Quinquis B, Sorokin A, Ehrlich SD: Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology 2005, 151:2551-2561. 10.1099/mic.0.28048-0.
86. Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EV: 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 2006, 1:7. 10.1186/1745-6150-1-7.
87. 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, 337:816-821. 10.1126/science.1225829.
88. Fu Y, Sander JD, Reyon D, Cascio VM, Joung JK: Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat Biotechnol 2014, 32:279-284. 10.1038/nbt.2808.
89. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F: Multiplex genome engineering using CRISPR/Cas systems. Science 2013, 339:819-823. 10.1126/science.1231143.
90. Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM: RNA-Guided human genome engineering via Cas9. Science 2013, 339:823-826. 10.1126/science.1232033.
91. Jinek M, East A, Cheng A, Lin S, Ma E, Doudna J, Weigel D: RNA-programmed genome editing in human cells. Elife 2013, 2:e00471.
92. Hwang WY, Fu Y, Reyon D, Maeder ML, Tsai SQ, Sander JD, Peterson RT, Yeh J-RJ, Joung JK: Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol 2013, 31:227-229. 10.1038/nbt.2501.
93. Cho SW, Kim S, Kim JM, Kim J-S: Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat Biotechnol 2013, 31:230-232. 10.1038/nbt.2507.
94. Sander JD, Joung JK: CRISPR-Cas systems for editing, regulating and targeting genomes. Nat Biotechnol 2014, 32:347-355. 10.1038/nbt.2842.
95. Belhaj K, Chaparro-Garcia A, Kamoun S, Nekrasov V: Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system. Plant Methods 2013, 9:39. 10.1186/1746-4811-9-39.
96. Kondo S, Ueda R: Highly improved gene targeting by germline-specific Cas9 expression in Drosophila. Genetics 2013, 195:715-721. 10.1534/genetics.113.156737.
97. Daimon T, Kiuchi T, Takasu Y: Recent progress in genome engineering techniques in the silkworm, Bombyx mori. Develop Growth Differ 2013, 56:14-25.
98. Flowers GP, Timberlake AT, Mclean KC, Monaghan JR, Crews CM: Highly efficient targeted mutagenesis in axolotl using Cas9 RNA-guided nuclease. Development 2014, 141:2165-2171. 10.1242/dev.105072.
99. Guo X, Zhang T, Hu Z, Zhang Y, Shi Z, Wang Q, Cui Y, Wang F, Zhao H, Chen Y: Efficient RNA/Cas9-mediated genome editing in Xenopus tropicalis. Development 2014, 141:707-714. 10.1242/dev.099853.
100. Niu Y, Shen B, Cui Y, Chen Y, Wang J, Wang L, Kang Y, Zhao X, Si W, Li W, Xiang AP, Zhou J, Guo X, Bi Y, Si C, Hu B, Dong G, Wang H, Zhou Z, Li T, Tan T, Pu X, Wang F, Ji S, Zhou Q, Huang X, Ji W, Sha J: Generation of Gene-Modified Cynomolgus Monkey via Cas9/RNA-Mediated Gene Targeting in One-Cell Embryos - 1-s2.0-S0092867414000798-main.pdf. Cell 2014, 156:836-843. 10.1016/j.cell.2014.01.027.
101. Valton J, Dupuy A, Daboussi F, Thomas S, Maréchal A, Macmaster R, Melliand K, Juillerat A, Duchateau P: Overcoming TALE DNA binding domain's inability to bind methylcytosine: overcoming transcription activator-like effector (TALE) DNA binding domain sensitivity to cytosine methylation. J Biol Chem 2012, 287:38433.
102. Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O, Cradick TJ, Marraffini LA, Bao G, Zhang F: DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol 2013, 31:827-832. 10.1038/nbt.2647.
103. Kim H, Kim J-S: A guide to genome engineering with programmable nucleases. Nat Rev Genet 2014, 15:321-334. 10.1038/nrg3686.
104. Lee J-S, Kwak S-J, Kim J, Kim A-K, Noh HM, Kim J-S, Yu K: CRISPR/Cas9 mediated genome engineering in Drosophila. G3 (Bethesda) 2014, 4:1291-1295. 2014
105. Cho SW, Lee J, Carroll D, Kim J-S, Lee J: Heritable gene knockout in Caenorhabditis elegans by direct injection of Cas9-sgRNA ribonucleoproteins. Genetics 2013, 195:1177-1180. 10.1534/genetics.113.155853.
106. Imburgio D, Rong M, Ma K, McAllister WT: Studies of promoter recognition and start site selection by T7 RNA polymerase using a comprehensive collection of promoter variants. Biochemistry 2000, 39:10419-10430. 10.1021/bi000365w.
107. Ren X, Sun J, Housden BE, Hu Y, Roesel C, Lin S, Liu L-P, Yang Z, Mao D, Sun L, Wu Q, Ji J-Y, Xi J, Mohr SE, Xu J, Perrimon N, Ni J-Q: Optimized gene editing technology for Drosophila melanogaster using germ line-specific Cas9. Proc Natl Acad Sci USA 2013, 110:19012-19017. 10.1073/pnas.1318481110.
108. Nissim L, Perli SD, Fridkin A, Perez-Pinera P, Lu TK: Multiplexed and programmable regulation of gene networks with an integrated RNA and CRISPR/Cas toolkit in human cells. Mol Cell 2014, 54:698-710. 10.1016/j.molcel.2014.04.022.
109. Tsai SQ, Wyvekens N, Khayter C, Foden JA, Thapar V, Reyon D, Goodwin MJ, Aryee MJ, Joung JK: Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing. Nat Biotechnol 2014, 32:569-576. 10.1038/nbt.2908.
110. Ranganathan V, Wahlin K, Maruotti J, Zack DJ: Expansion of the CRISPR-Cas9 genome targeting space through the use of H1 promoter-expressed guide RNAs. Nat Commun 2014, 5:4516.
111. Sternberg SH, Redding S, Jinek M, Greene EC, Doudna JA: DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 2014, 507:62-67. 10.1038/nature13011.
112. Esvelt KM, Mali P, Braff JL, Moosburner M, Yaung SJ, Church GM: Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat Meth 2013, 10:1116-1121. 10.1038/nmeth.2681.
113. Hou Z, Zhang Y, Propson NE, Howden SE, Chu L-F, Sontheimer EJ, Thomson JA: Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis. Proc Natl Acad Sci USA 2013, 110:15644-15649. 10.1073/pnas.1313587110.
114. Fonfara I, Le Rhun A, Chylinski K, Makarova KS, Lecrivain AL, Bzdrenga J, Koonin EV, Charpentier E: Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems. Nucleic Acids Res 2014, 42:2577-2590. 10.1093/nar/gkt1074.
115. Jiang W, Bikard D, Cox D, Zhang F, Marraffini LA: RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol 2013, 31:233-239. 10.1038/nbt.2508.
116. Fu Y, Foden JA, Khayter C, Maeder ML, Reyon D, Joung JK, Sander JD: High-frequency off-target mutagenesis induced by CrIsPr-Cas nucleases in human cells. Nat Biotechnol 2013, 31:822-826. 10.1038/nbt.2623.
117. Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M, Kosuri S, Yang L, Church GM: CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol 2013, 31:833-838. 10.1038/nbt.2675.
118. Pattanayak V, Lin S, Guilinger JP, Ma E, Doudna JA, Liu DR: High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat Biotechnol 2013, 31:839-843. 10.1038/nbt.2673.
119. Cho SW, Kim S, Kim Y, Kweon J, Kim HS, Bae S, Kim J-S: Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Res 2014, 24:132-141. 10.1101/gr.162339.113.
120. Wu X, Scott DA, Kriz AJ, Chiu AC, Hsu PD, Dadon DB, Cheng AW, Trevino AE, Konermann S, Chen S, Jaenisch R, Zhang F, Sharp PA: Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat Biotechnol 2014, 32:670-676. 10.1038/nbt.2889.
121. Kuscu C, Arslan S, Singh R, Thorpe J, Adli M: Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease. Nat Biotechnol 2014, 32:677-683. 10.1038/nbt.2916.
122. Blitz IL, Biesinger J, Xie X, Cho KWY: Biallelic genome modification in F0 Xenopus tropicalis embryos using the CRISPR/Cas system. Genesis 2013, 51:827-834. 10.1002/dvg.22719.
123. Sebo ZL, Lee HB, Peng Y, Guo Y: A simplified and efficient germline-specific CRISPR/Cas9 system for Drosophila genomic engineering. Fly (Austin) 2014, 8:52-57. 10.4161/fly.26828.
124. Shen B, Zhang W, Zhang J, Zhou J, Wang J, Chen L, Wang L, Hodgkins A, Iyer V, Huang X, Skarnes WC: Efficient genome modification by CRISPR-Cas9 nickase with minimal off-target effects. Nat Meth 2014, 11:399-402. 10.1038/nmeth.2857.
125. Guilinger JP, Thompson DB, Liu DR: Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification. Nat Biotechnol 2014, 32:577-582. 10.1038/nbt.2909.
126. Qiu P, Shandilya H, D'Alessio JM, O'Connor K, Durocher J, Gerard GF: Mutation detection using Surveyor nuclease. Biotechniques 2004, 36:702-707.
127. Kim HJ, Lee HJ, Kim H, Cho SW, Kim JS: Targeted genome editing in human cells with zinc finger nucleases constructed via modular assembly. Genome Res 2009, 19:1279-1288. 10.1101/gr.089417.108.
128. Bassett AR, Tibbit C, Ponting CP, Liu J-L: Highly efficient targeted mutagenesis of Drosophila with the CRISPR/Cas9 system. Cell Rep 2013, 4:220-228. 10.1016/j.celrep.2013.06.020.
129. Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA, Zhang F: Genome engineering using the CRISPR-Cas9 system. Nat Protoc 2013, 8:2281-2308. 10.1038/nprot.2013.143.
130. Jao LE, Wente SR, Chen W: Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system. Proc Natl Acad Sci USA 2013, 110:13904. 10.1073/pnas.1308335110.
131. Treen N, Yoshida K, Sakuma T, Sasaki H, Kawai N, Yamamoto T, Sasakura Y: Tissue-specific and ubiquitous gene knockouts by TALEN electroporation provide new approaches to investigating gene function in Ciona. Development 2014, 141:481-487. 10.1242/dev.099572.
132. Qi Y, Zhang Y, Zhang F, Baller JA, Cleland SC, Ryu Y, Starker CG, Voytas DF: Increasing frequencies of site-specific mutagenesis and gene targeting in Arabidopsis by manipulating DNA repair pathways. Genome Res 2013, 23:547-554. 10.1101/gr.145557.112.
133. Greenspan RJ: Fly Pushing: The Theory and Practice of Drosophila Genetics. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press; 2004.
134. Xiao A, Wang Z, Hu Y, Wu Y, Luo Z, Yang Z, Zu Y, Li W, Huang P, Tong X, Zhu Z, Lin S, Zhang B: Chromosomal deletions and inversions mediated by TALENs and CRISPR/Cas in zebrafish. Nucleic Acids Res 2013, 41:e141. 10.1093/nar/gkt464.
135. Choi PS, Meyerson M: Targeted genomic rearrangements using CRISPR/Cas technology. Nat Commun 2014, 5:3728.
136. Park C-Y, Kim J, Kweon J, Son JS, Lee JS, Yoo J-E, Cho S-R, Kim J-H, Kim J-S, Kim D-W: Targeted inversion and reversion of the blood coagulation factor 8 gene in human iPS cells using TALENs. Proc Natl Acad Sci USA 2014, 111:9253-9258. 10.1073/pnas.1323941111.
137. Mali P, Esvelt KM, Church GM: Cas9 as a versatile tool for engineering biology. Nat Meth 2013, 10:957-963. 10.1038/nmeth.2649.
138. Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA: Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 2013, 152:1173-1183. 10.1016/j.cell.2013.02.022.
139. Gilbert LA, Larson MH, Morsut L, Liu Z, Brar GA, Torres SE, Stern-Ginossar N, Brandman O, Whitehead EH, Doudna JA, Lim WA, Weissman JS, Qi LS: CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 2013, 154:442-451. 10.1016/j.cell.2013.06.044.
140. Maeder ML, Linder SJ, Reyon D, Angstman JF, Fu Y, Sander JD, Joung JK: Robust, synergistic regulation of human gene expression using TALE activators. Nat Meth 2013, 10:243-245. 10.1038/nmeth.2366.
141. Crocker J, Stern DL: TALE-mediated modulation of transcriptional enhancers in vivo. Nat Meth 2013, 10:762-767. 10.1038/nmeth.2543.
142. Perez-Pinera P, Kocak DD, Vockley CM, Adler AF, Kabadi AM, Polstein LR, Thakore PI, Glass KA, Ousterout DG, Leong KW, Guilak F, Crawford GE, Reddy TE, Gersbach CA: RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nat Meth 2013, 10:973-976. 10.1038/nmeth.2600.
143. Cheng AW, Wang H, Yang H, Shi L, Katz Y, Theunissen TW, Rangarajan S, Shivalila CS, Dadon DB, Jaenisch R: Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system. Cell Research 2013, 23:1163-1171. 10.1038/cr.2013.122.
144. Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W, Li G-W, Park J, Blackburn EH, Weissman JS, Qi LS, Huang B: Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 2013, 155:1479-1491. 10.1016/j.cell.2013.12.001.