Methods for targeted mutagenesis in zebrafish using TALENs

Methods

Volumn 69, Issue 1, 2014, Pages 76-84

  Hwang, Woong Y ^a,b   Peterson, Randall T ^a,b,c   Yeh, Jing Ruey Joanna ^a,b  

^a MASSACHUSETTS GENERAL HOSPITAL   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c BROAD INSTITUTE OF MIT AND HARVARD   (United States)

Author keywords

Gene disruption; Gene targeting; Genome engineering; Knockout; Site specific nuclease; Transcription activator like effector nuclease; Zebrafish

Indexed keywords

DNA FRAGMENT; DNA POLYMERASE; GENOMIC DNA; PLASMID DNA; TRANSCRIPTION ACTIVATOR LIKE EFFECTOR NUCLEASE; DEOXYRIBONUCLEASE;

ARTICLE; BAMHI GENE; CLONING VECTOR; COMPUTER PROGRAM; DNA BINDING; DNA CLEAVAGE; DNA DETERMINATION; DNA METHYLATION; DNA SEQUENCE; DNA VECTOR; DOUBLE STRANDED DNA BREAK; ENZYME ACTIVITY; ENZYME ASSAY; FOKI GENE; GENE CONSTRUCT; GENE EXPRESSION; GENE LOCUS; GENE MUTATION; GENETIC ENGINEERING; GENOMICS; HUMAN; MOLECULAR CLONING; MUTAGENESIS; MUTATIONAL ANALYSIS; NHEI GENE; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN DOMAIN; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RESTRICTION MAPPING; SEQUENCE ANALYSIS; T7 ENDONUCLEASE I ASSAY; TALEN GENE; TRANSGENOMICS; ZEBRA FISH; ANIMAL; CHEMISTRY; GENETICS; PROCEDURES; PROTEIN ENGINEERING; SITE DIRECTED MUTAGENESIS;

DANIO RERIO;

ANIMALS; DEOXYRIBONUCLEASES; MUTAGENESIS, SITE-DIRECTED; PROTEIN ENGINEERING; ZEBRAFISH;

EID: 84929506439     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2014.04.009     Document Type: Article

References (56)

1. Gaj T., Gersbach C.A., Barbas C.F. Trends Biotechnol. 2013, 31:397-405.
2. Joung J.K., Sander J.D. Mol. Cell Biol. 2013, 14:49-55.
3. Mali P., Esvelt K.M., Church G.M. Nat. Methods 2013, 10:957-963.
4. Urnov F.D., Rebar E.J., Holmes M.C., Zhang H.S., Gregory P.D. Genetics 2010, 11:636-646.
5. Doyon Y., McCammon J.M., Miller J.C., Faraji F., Ngo C., Katibah G.E., Amora R., Hocking T.D., Zhang L., Rebar E.J., et al. Nat. Biotechnol. 2008, 26:702-708.
6. Foley J.E., Yeh J.R., Maeder M.L., Reyon D., Sander J.D., Peterson R.T., Joung J.K. PLoS One 2009, 4:e4348.
7. Hockemeyer D., Soldner F., Beard C., Gao Q., Mitalipova M., DeKelver R.C., Katibah G.E., Amora R., Boydston E.A., Zeitler B., et al. Nat. Biotechnol. 2009, 27:851-857.
8. Meng X., Noyes M.B., Zhu L.J., Lawson N.D., Wolfe S.A. Nat. Biotechnol. 2008, 26:695-701.
9. Sander J.D., Dahlborg E.J., Goodwin M.J., Cade L., Zhang F., Cifuentes D., Curtin S.J., Blackburn J.S., Thibodeau-Beganny S., Qi Y., et al. Nat. Methods 2011, 8:67-69.
10. Wood A.J., Lo T.W., Zeitler B., Pickle C.S., Ralston E.J., Lee A.H., Amora R., Miller J.C., Leung E., Meng X., et al. Science 2011, 333:307.
11. Wright D.A., Townsend J.A., Winfrey R.J., Irwin P.A., Rajagopal J., Lonosky P.M., Hall B.D., Jondle M.D., Voytas D.F. Plant J. Cell Mol. Biol. 2005, 44:693-705.
12. Zou J., Maeder M.L., Mali P., Pruett-Miller S.M., Thibodeau-Beganny S., Chou B.K., Chen G., Ye Z., Park I.H., Daley G.Q., et al. Cell Stem Cell 2009, 5:97-110.
13. Beumer K.J., Trautman J.K., Bozas A., Liu J.L., Rutter J., Gall J.G., Carroll D. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:19821-19826.
14. Bedell V.M., Wang Y., Campbell J.M., Poshusta T.L., Starker C.G., Krug R.G., Tan W., Penheiter S.G., Ma A.C., Leung A.Y., et al. Nature 2012, 491:114-118.
15. Christian M., Qi Y., Zhang Y., Voytas D.F. G3 (Bethesda) 2013, 3:1697-1705.
16. Hockemeyer D., Wang H., Kiani S., Lai C.S., Gao Q., Cassady J.P., Cost G.J., Zhang L., Santiago Y., Miller J.C., et al. Nat. Biotechnol. 2011, 29:731-734.
17. Huang P., Xiao A., Zhou M., Zhu Z., Lin S., Zhang B. Nat. Biotechnol. 2011, 29:699-700.
18. Reyon D., Tsai S.Q., Khayter C., Foden J.A., Sander J.D., Joung J.K. Nat. Biotechnol. 2012, 30:460-465.
19. Sander J.D., Cade L., Khayter C., Reyon D., Peterson R.T., Joung J.K., Yeh J.R. Nat. Biotechnol. 2011, 29:697-698.
20. Tesson L., Usal C., Menoret S., Leung E., Niles B.J., Remy S., Santiago Y., Vincent A.I., Meng X., Zhang L., et al. Nat. Biotechnol. 2011, 29:695-696.
21. Miller J.C., Tan S., Qiao G., Barlow K.A., Wang J., Xia D.F., Meng X., Paschon D.E., Leung E., Hinkley S.J., et al. Nat. Biotechnol. 2011, 29:143-148.
22. Bassett A.R., Tibbit C., Ponting C.P., Liu J.L. Cell Rep. 2013, 4:220-228.
23. Cho S.W., Kim S., Kim J.M., Kim J.S. Nat. Biotechnol. 2013, 31:230-232.
24. Cong L., Ran F.A., Cox D., Lin S., Barretto R., Habib N., Hsu P.D., Wu X., Jiang W., Marraffini L.A., et al. Science 2013, 339:819-823.
25. Dicarlo J.E., Norville J.E., Mali P., Rios X., Aach J., Church G.M. Nucleic Acids Res. 2013, 41:4336-4343.
26. Friedland A.E., Tzur Y.B., Esvelt K.M., Colaiacovo M.P., Church G.M., Calarco J.A. Nat. Methods 2013, 10:741-743.
27. Hwang W.Y., Fu Y., Reyon D., Maeder M.L., Tsai S.Q., Sander J.D., Peterson R.T., Yeh J.R., Joung J.K. Nat. Biotechnol. 2013, 31:227-229.
28. Jinek M., East A., Cheng A., Lin S., Ma E., Doudna J. eLife 2013, 2:e00471.
29. Li D., Qiu Z., Shao Y., Chen Y., Guan Y., Liu M., Li Y., Gao N., Wang L., Lu X., et al. Nat. Biotechnol. 2013, 31:681-683.
30. Li W., Teng F., Li T., Zhou Q. Nat. Biotechnol. 2013, 31:684-686.
31. Mali P., Yang L., Esvelt K.M., Aach J., Guell M., DiCarlo J.E., Norville J.E., Church G.M. Science 2013, 339:823-826.
32. Wang H., Yang H., Shivalila C.S., Dawlaty M.M., Cheng A.W., Zhang F., Jaenisch R. Cell 2013, 153:910-918.
33. Cade L., Reyon D., Hwang W.Y., Tsai S.Q., Patel S., Khayter C., Joung J.K., Sander J.D., Peterson R.T., Yeh J.R. Nucleic Acids Res. 2012, 40:8001-8010.
34. Hwang W.Y., Fu Y., Reyon D., Maeder M.L., Kaini P., Sander J.D., Joung J.K., Peterson R.T., Yeh J.R. PLoS One 2013, 8:e68708.
35. Moore F.E., Reyon D., Sander J.D., Martinez S.A., Blackburn J.S., Khayter C., Ramirez C.L., Joung J.K., Langenau D.M. PLoS One 2012, 7:e37877.
36. Chen S., Oikonomou G., Chiu C.N., Niles B.J., Liu J., Lee D.A., Antoshechkin I., Prober D.A. Nucleic Acids Res. 2013, 41:2769-2778.
37. Jao L.E., Wente S.R., Chen W. Proc. Natl. Acad. Sci. U.S.A. 2013, 110:13904-13909.
38. Chang N., Sun C., Gao L., Zhu D., Xu X., Zhu X., Xiong J.W., Xi J.J. Cell Res. 2013, 23:465-472.
39. Sood R., Carrington B., Bishop K., Jones M., Rissone A., Candotti F., Chandrasekharappa S.C., Liu P. PLoS One 2013, 8:e57239.
40. Fu Y., Foden J.A., Khayter C., Maeder M.L., Reyon D., Joung J.K., Sander J.D. Nat. Biotechnol. 2013, 31:822-826.
41. Hsu P.D., Scott D.A., Weinstein J.A., Ran F.A., Konermann S., Agarwala V., Li Y., Fine E.J., Wu X., Shalem O., et al. Nat. Biotechnol. 2013, 31:827-832.
42. Mali P., Aach J., Stranges P.B., Esvelt K.M., Moosburner M., Kosuri S., Yang L., Church G.M. Nat. Biotechnol. 2013, 31:833-838.
43. Pattanayak V., Lin S., Guilinger J.P., Ma E., Doudna J.A., Liu D.R. Nat. Biotechnol. 2013, 31:839-843.
44. D. Reyon, C. Khayter, M.R. Regan, J.K. Joung, J.D. Sander, in: Frederick M. Ausubel, et al. (Eds.), Current Protocols in Molecular Biology, 2012 (Chapter 12, Unit 12 15).
45. D. Reyon, M.L. Maeder, C. Khayter, S.Q. Tsai, J.E. Foley, J.D. Sander, J.K. Joung, in: Frederick M. Ausubel, et al. (Eds.), Current Protocols in Molecular Biology, 2013 (Chapter 12, Unit 12 16).
46. Sander J.D., Maeder M.L., Reyon D., Voytas D.F., Joung J.K., Dobbs D. Nucleic Acids Res. 2010, 38:W462-W468.
47. Boch J., Scholze H., Schornack S., Landgraf A., Hahn S., Kay S., Lahaye T., Nickstadt A., Bonas U. Science 2009, 326:1509-1512.
48. Moscou M.J., Bogdanove A.J. Science 2009, 326:1501.
49. Deng D., Yan C., Pan X., Mahfouz M., Wang J., Zhu J.K., Shi Y., Yan N. Science 2012, 335:720-723.
50. Mak A.N., Bradley P., Cernadas R.A., Bogdanove A.J., Stoddard B.L. Science 2012, 335:716-719.
51. Valton J., Dupuy A., Daboussi F., Thomas S., Marechal A., Macmaster R., Melliand K., Juillerat A., Duchateau P. J. Biol. Chem. 2012, 287:38427-38432.
52. Cermak T., Doyle E.L., Christian M., Wang L., Zhang Y., Schmidt C., Baller J.A., Somia N.V., Bogdanove A.J., Voytas D.F. Nucleic Acids Res. 2011, 39:e82.
53. Doyon Y., Vo T.D., Mendel M.C., Greenberg S.G., Wang J., Xia D.F., Miller J.C., Urnov F.D., Gregory P.D., Holmes M.C. Nat. Methods 2011, 8:74-79.
54. Zu Y., Tong X., Wang Z., Liu D., Pan R., Li Z., Hu Y., Luo Z., Huang P., Wu Q., et al. Nat. Methods 2013, 10:329-331.
55. Foley J.E., Maeder M.L., Pearlberg J., Joung J.K., Peterson R.T., Yeh J.R. Nat. Protoc. 2009, 4:1855-1867.
56. Guschin D.Y., Waite A.J., Katibah G.E., Miller J.C., Holmes M.C., Rebar E.J. Methods Mol. Biol. 2010, 649:247-256.