Targeted gene inactivation in zebrafish using engineered zinc-finger nucleases

Nature Biotechnology

Volumn 26, Issue 6, 2008, Pages 695-701

  Meng, Xiangdong ^a,b   Noyes, Marcus B ^a   Zhu, Lihua J ^a   Lawson, Nathan D ^a   Wolfe, Scot A ^a  

^a UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

^b SANGAMO BIOSCIENCES INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL CULTURE; COBALT; COBALT COMPOUNDS; COMPUTER NETWORKS; RADIATION PROTECTION; TECHNOLOGY; ZINC; ZINC SULFIDE;

(OTDR) TECHNOLOGY; ANIMAL SPECIES; CELL LINES; CO INJECTION; EMBRYONIC STEM (ES) CELLS; GENE INACTIVATION; GERM LINES; HERITABLE MUTATIONS; HIGH-FREQUENCY (HF); ORTHOLOG; RECEPTOR (IR); VASCULAR ENDOTHELIAL GROWTH FACTOR (VEGF); VERTEBRATE MODEL; ZEBRA FISH; ZEBRAFISH EMBRYOS; ZINC FINGER NUCLEASES;

ANIMAL CELL CULTURE;

MESSENGER RNA; NUCLEASE; PLASMID DNA; ZINC FINGER PROTEIN;

ANIMAL EXPERIMENT; ARTICLE; EMBRYO; EMBRYO DEVELOPMENT; GENE INACTIVATION; GENE MUTATION; GENE TARGETING; GENOMICS; GERM LINE; MUTAGENESIS; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; ZEBRA FISH;

ANIMALS; ANIMALS, GENETICALLY MODIFIED; DEOXYRIBONUCLEASES; GENE SILENCING; GENE TARGETING; GENETIC ENGINEERING; MUTAGENESIS, SITE-DIRECTED; PROTEIN ENGINEERING; ZEBRAFISH; ZEBRAFISH PROTEINS; ZINC FINGERS;

ANIMALIA; DANIO RERIO; VERTEBRATA;

EID: 44949162060     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt1398     Document Type: Article

References (32)

1. Porteus, M.H. & Carroll, D. Gene targeting using zinc finger nucleases. Nat. Biotechnol. 23, 967-973 (2005).
2. Urnov, F.D. et al. Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature 435, 646-651 (2005).
3. Porteus, M.H. & Baltimore, D. Chimeric nucleases stimulate gene targeting in human cells. Science 300, 763 (2003).
4. Koller, B.H. & Smithies, O. Inactivating the beta 2-microglobulin locus in mouse embryonic stem cells by homologous recombination. Proc. Natl. Acad. Sci. USA 86, 8932-8935 (1989).
5. Zijlstra, M., Li, E., Sajjadi, F., Subramani, S. & Jaenisch, R. Germ-line transmission of a disrupted beta 2-microglobulin gene produced by homologous recombination in embryonic stem cells. Nature 342, 435-438 (1989).
6. Kim, Y.G., Cha, J. & Chandrasegaran, S. Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proc. Natl. Acad. Sci. USA 93, 1156-1160 (1996).
7. Lloyd, A., Plaisier, C.L., Carroll, D. & Drews, G.N. Targeted mutagenesis using zincfinger nucleases in Arabidopsis. Proc. Natl. Acad. Sci. USA 102, 2232-2237 (2005).
8. Wright, D.A. et al. High-frequency homologous recombination in plants mediated by zinc-finger nucleases. Plant J. 44, 693-705 (2005).
9. Bibikova, M., Beumer, K., Trautman, J.K. & Carroll, D. Enhancing gene targeting with designed zinc finger nucleases. Science 300, 764 (2003).
10. Beumer, K., Bhattacharyya, G., Bibikova, M., Trautman, J.K. & Carroll, D. Efficient gene targeting in Drosophila with zinc-finger nucleases. Genetics 172, 2391-2403 (2006).
11. Alwin, S. et al. Custom zinc-finger nucleases for use in human cells. Mol. Ther. 12, 610-617 (2005).
12. Wright, D.A. et al. Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly. Nat. Protoc. 1, 1637-1652 (2006).
13. Carroll, D., Morton, J.J., Beumer, K.J. & Segal, D.J. Design, construction and in vitro testing of zinc finger nucleases. Nat. Protoc. 1, 1329-1341 (2006).
14. Liu, Q., Xia, Z. & Case, C.C. Validated zinc finger protein designs for all 16 GNN DNA triplet targets. J. Biol. Chem. 277, 3850-3856 (2002).
15. 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. USA 100, 12271-12276 (2003).
16. Bibikova, M. et al. Stimulation of homologous recombination through targeted cleavage by chimeric nucleases. Mol. Cell. Biol. 21, 289-297 (2001).
17. Bibikova, M., Golic, M., Golic, K.G. & Carroll, D. Targeted chromosomal cleavage and mutagenesis in Drosophila using zinc-finger nucleases. Genetics 161, 1169-1175 (2002).
18. Covassin, L.D., Villefranc, J.A., Kacergis, M.C., Weinstein, B.M. & Lawson, N.D. Distinct genetic interactions between multiple Vegf receptors are required for development of different blood vessel types in zebrafish. Proc. Natl. Acad. Sci. USA 103, 6554-6559 (2006).
19. Turner, D.L. & Weintraub, H. Expression of achaete-scute homolog 3 in Xenopus embryos converts ectodermal cells to a neural fate. Genes Dev. 8, 1434-1447 (1994).
20. Miller, J.C. et al. An improved zinc-finger nuclease architecture for highly specific genome editing. Nat. Biotechnol. 25, 778-785 (2007).
21. Szczepek, M. et al. Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases. Nat. Biotechnol. 25, 786-793 (2007).
22. Lawson, N.D. & Weinstein, B.M. In vivo imaging of embryonic vascular development using transgenic zebrafish. Dev. Biol. 248, 307-318 (2002).
23. Qiu, P. et al. Mutation detection using Surveyor nuclease. Biotechniques 36, 702-707 (2004).
24. Mandell, J.G. & Barbas, C.F. III. Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases. Nucleic Acids Res. 34, W516-W523 (2006).
25. Cornu, T.I. et al. DNA-binding specificity is a major determinant of the activity and toxicity of zinc-finger nucleases. Mol. Ther. 16, 352-358 (2008).
26. Westerfield, M. The Zebrafish Book. (University of Oregon Press, Eugene, OR, 1993).
27. Xu, Q. Microinjection into zebrafish embryos. in Molecular Methods in Developmental Biology Vol. 127. (ed. M. Guille) 125-132 (Humana Press, Inc., Totowa, NJ, 1999).
28. Meng, X. & Wolfe, S.A. Identifying DNA sequences recognized by a transcription factor using a bacterial one-hybrid system. Nat. Protoc. 1, 30-45 (2006).
29. Noyes, M.B. et al. A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. Nucleic Acids Res. published online, doi:10.1093/nar/gkn048 (10 March 2008).
30. Bailey, T.L. & Elkan, C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2, 28-36 (1994).
31. Schneider, T.D. & Stephens, R.M. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. 18, 6097-6100 (1990).
32. Crooks, G.E., Hon, G., Chandonia, J.M. & Brenner, S.E. WebLogo: a sequence logo generator. Genome Res. 14, 1188-1190 (2004).