Engineering zinc finger nucleases for targeted mutagenesis of zebrafish

Methods in Cell Biology

Volumn 104, Issue , 2011, Pages 51-58

  Sander, Jeffry D ^a,b   Yeh, J R Joanna ^a,b   Peterson, Randall T ^a,b,c   Joung, J Keith ^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

Protein engineering; Reverse genetics; Targeted mutagenesis; Zinc finger nucleases

Indexed keywords

EID: 80052806758     PISSN: 0091679X     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-374814-0.00003-3     Document Type: Chapter

References (28)

1. Carroll D., Morton J.J., Beumer K.J., Segal D.J. Design, construction and in vitro testing of zinc finger nucleases. Nat. Protoc. 2006, 1:1329-1341.
2. Cifuentes D., Xue H., Taylor D.W., Patnode H., Mishima Y., Cheloufi S., Ma E., Mane S., Hannon G.J., Lawson N., Wolfe S., Giraldez A.J. A novel miRNA processing pathway independent of dicer requires Argonaute2 catalytic activity. Science 2010, 328:1694-1698.
3. Dove S.L., Joung J.K., Hochschild A. Activation of prokaryotic transcription through arbitrary protein-protein contacts. Nature 1997, 386:627-630.
4. 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., Gregory P.D., Urnov F.D., Amacher S.L. Heritable targeted gene disruption in zebrafish using designed zinc-finger nucleases. Nat. Biotechnol. 2008, 26:702-708.
5. Elrod-Erickson M., Rould M.A., Nekludova L., Pabo C.O. Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions. Structure 1996, 4:1171-1180.
6. Foley J.E., Yeh J.R., Maeder M.L., Reyon D., Sander J.D., Peterson R.T., Joung J.K. Rapid mutation of endogenous zebrafish genes using zinc finger nucleases made by Oligomerized Pool ENgineering (OPEN). PLoS ONE 2009, 4:e4348.
7. Fu F., Sander J.D., Maeder M., Thibodeau-Beganny S., Joung J.K., Dobbs D., Miller L., Voytas D.F. Zinc Finger Database (ZiFDB): a repository for information on C2H2 zinc fingers and engineered zinc-finger arrays. Nucleic Acids Res. 2009, 37:D279-D283.
8. Hurt J.A., Thibodeau S.A., Hirsh A.S., Pabo C.O., Joung J.K. Highly specific zinc finger proteins obtained by directed domain shuffling and cell-based selection. Proc. Natl Acad. Sci. U. S. A. 2003, 100:12271-12276.
9. Isalan M., Choo Y., Klug A. Synergy between adjacent zinc fingers in sequence-specific DNA recognition. Proc. Natl Acad. Sci. U. S. A. 1997, 94:5617-5621.
10. Isalan M., Klug A., Choo Y. Comprehensive DNA recognition through concerted interactions from adjacent zinc fingers. Biochemistry 1998, 37:12026-12033.
11. Joung J.K., Ramm E.I., Pabo C.O. A bacterial two-hybrid selection system for studying protein-DNA and protein-protein interactions. Proc. Natl Acad. Sci. U. S. A. 2000, 97:7382-7387.
12. Joung J.K., Voytas D.F., Cathomen T. Reply to " Genome editing with modularly assembled zinc-finger nucleases" Nat. Methods 2010, 7:91-92.
13. Kim H.J., Lee H.J., Kim H., Cho S.W., Kim J.S. Targeted genome editing in human cells with zinc finger nucleases constructed via modular assembly. Genome Res. 2009, 19:1279-1288.
14. Maeder M.L., Thibodeau-Beganny S., Osiak A., Wright D.A., Anthony R.M., Eichtinger M., Jiang T., Foley J.E., Winfrey R.J., Townsend J.A., Unger-Wallace E., Sander J.D., Muller-Lerch F., Fu F., Pearlberg J., Gobel C., Dassie J.P., Pruett-Miller S.M., Porteus M.H., Sgroi D.C., Iafrate A.J., Dobbs D., McCray P.B., Cathomen T., Voytas D.F., Joung J.K. Rapid 'open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification. Mol. Cell 2008, 31:294-301.
15. Maeder M.L., Thibodeau-Beganny S., Sander J.D., Voytas D.F., Joung J.K. Oligomerized pool engineering (OPEN): an 'open-source' protocol for making customized zinc-finger arrays. Nat. Protoc. 2009, 4:1471-1501.
16. Mandell J.G., Barbas C.F. Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases. Nucleic Acids Res. 2006, 34:W516-W523.
17. Meng X., Noyes M.B., Zhu L.J., Lawson N.D., Wolfe S.A. Targeted gene inactivation in zebrafish using engineered zinc-finger nucleases. Nat. Biotechnol. 2008, 26:695-701.
18. Miller J.C., Holmes M.C., Wang J., Guschin D.Y., Lee Y.L., Rupniewski I., Beausejour C.M., Waite A.J., Wang N.S., Kim K.A., Gregory P.D., Pabo C.O., Rebar E.J. An improved zinc-finger nuclease architecture for highly specific genome editing. Nat. Biotechnol. 2007, 25:778-785.
19. Pearson H. The fate of fingers. Nature 2008, 455:160-164.
20. Ramirez C.L., Foley J.E., Wright D.A., Muller-Lerch F., Rahman S.H., Cornu T.I., Winfrey R.J., Sander J.D., Fu F., Townsend J.A., Cathomen T., Voytas D.F., Joung J.K. Unexpected failure rates for modular assembly of engineered zinc-fingers. Nat. Methods. 2008, 5:374-375.
21. Reyon D., Kirkpatrick J.R., Sander J.D., Zhang F., Voytas D.F., Joung J.K., Dobbs D., Coffman C.R. ZFNGenome: a comprehensive resource for locating zinc finger nuclease target sites in model organisms. BMC Genomics 2011, 12:83.
22. 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., Pierick C.J., Hoffman E., Maeder M.L., Khayter C., Reyon D., Dobbs D., Langenau D.M., Stupar R.M., Giraldez A.J., Voytas D.F., Peterson R.T., Yeh J.R., Joung J.K. Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA). Nat. Methods 2011, 8:67-69.
23. Sander J.D., Maeder M.L., Reyon D., Voytas D.F., Joung J.K., Dobbs D. ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool. Nucleic Acids Res. 2010, 38(Suppl.):W462-W468.
24. Sander J.D., Zaback P., Joung J.K., Voytas D.F., Dobbs D. Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool. Nucleic Acids Res. 2007, 35:W599-W605.
25. Siekmann A.F., Standley C., Fogarty K.E., Wolfe S.A., Lawson N.D. Chemokine signaling guides regional patterning of the first embryonic artery. Genes Dev. 2009, 23:2272-2277.
26. Wolfe S.A., Grant R.A., Elrod-Erickson M., Pabo C.O. Beyond the " recognition code": structures of two Cys2His2 zinc finger/TATA box complexes. Structure (Camb) 2001, 9:717-723.
27. Wolfe S.A., Greisman H.A., Ramm E.I., Pabo C.O. Analysis of zinc fingers optimized via phage display: evaluating the utility of a recognition code. J. Mol. Biol. 1999, 285:1917-1934.
28. Wright D.A., Thibodeau-Beganny S., Sander J.D., Winfrey R.J., Hirsh A.S., Eichtinger M., Fu F., Porteus M.H., Dobbs D., Voytas D.F., Joung J.K. Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly. Nat. Protoc. 2006, 1:1637-1652.