Validation and expression of zinc finger nucleases in plant cells

Methods in Molecular Biology

Volumn 649, Issue , 2010, Pages 315-336

  Tovkach, Andriy ^a   Zeevi, Vardit ^a   Tzfira, Tzvi ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

binary vectors; Gene targeting; multigene vectors; plant transformation

Indexed keywords

MAMMALIA;

CERIUM; ENDONUCLEASE; PEPTIDE; ZINC FINGER PROTEIN;

ARTICLE; GENE TARGETING; GENETICS; METABOLISM; PLANT; SITE DIRECTED MUTAGENESIS;

CERIUM; ENDONUCLEASES; GENE TARGETING; MUTAGENESIS, SITE-DIRECTED; PEPTIDES; PLANTS; ZINC FINGERS;

EID: 78249250940     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-60761-753-2_20     Document Type: Article

References (45)

1. Britt, A.B. and May, G.D. (2003) Reengineering plant gene targeting. Trends Plant Sci. 8, 90-95.
2. Siebert, R. and Puchta, H. (2002) Efficient repair of genomic double-strand breaks by homologous recombination between directly repeated sequences in the plant genome. Plant Cell. 14, 1121-1131.
3. Tzfira, T., Li, J., Lacroix, B., and Citovsky, V. (2004) Agrobacterium T-DNA integration: Molecules and models. Trends Genet. 20, 375-383.
4. Terada, R., Urawa, H., Inagaki, Y., Tsugane, K., and Iida, S. (2002) Efficient gene targeting by homologous recombination in rice. Nat Biotechnol. 20, 1030-1034.
5. Terada, R., Johzuka-Hisatomi, Y., Saitoh, M., Asao, H., and Iida, S. (2007) Gene targeting by homologous recombination as a biotechnological tool for rice functional genomics. Plant Physiol. 144, 846-856.
6. Shaked, H., Melamed-Bessudo, C., and Levy, A.A. (2005) High frequency gene targeting in Arabidopsis plants expressing the yeast RAD54 gene. Proc Natl Acad Sci USA. 102, 12265-12269.
7. Puchta, H. (2002) Gene replacement by homologous recombination in plants. Plant Mol Biol. 48, 173-182.
8. Puchta, H., Dujon, B., and Hohn, B. (1993) Homologous recombination in plant cells is enhanced by in vivo induction of double strand breaks into DNA by a sitespecific endonuclease. Nucleic Acids Res. 21, 5034-5040.
9. Puchta, H., Dujon, B., and Hohn, B. (1996) Two different but related mechanisms are used in plants for the repair of genomic double-strand breaks by homologous recombination. Proc Natl Acad Sci USA. 93, 5055-5060.
10. Chiurazzi, M., Ray, A., Viret, J.F., Perera, R., Wang, X.H., Lloyd, A.M., and Signer, E.R. (1996) Enhancement of somatic intrachromosomal homologous recombination in Arabidopsis by theHOendonuclease. Plant Cell. 8, 2057-2066.
11. Chilton, M.-D.M. and Que, Q. (2003) Targeted integration of T-DNA into the tobacco genome at double-strand breaks: New insights on the mechanism of T-DNA integration. Plant Physiol. 133, 956-965.
12. Tzfira, T., Frankmen, L., Vaidya, M., and Citovsky, V. (2003) Site-specific integration of Agrobacterium tumefaciens T-DNA via double-stranded intermediates. Plant Physiol. 133, 1011-1023.
13. Salomon, S. and Puchta, H. (1998) Capture of genomic and T-DNA sequences during double-strand break repair in somatic plant cells. EMBO J. 17, 6086-6095.
14. Porteus, M.H. and Carroll, D. (2005) Gene targeting using zinc finger nucleases. Nat Biotechnol. 23, 967-973.
15. Durai, S., Mani, M., Kandavelou, K., Wu, J., Porteus, M.H., and Chandrasegaran, S. (2005) Zinc finger nucleases: Customdesigned molecular scissors for genome engineering of plant and mammalian cells. Nucleic Acids Res. 33, 5978-5990.
16. Carroll, D., Morton, J.J., Beumer, K.J., and Segal, D.J. (2006) Design, construction and in vitro testing of zinc finger nucleases. Nat Protoc. 1, 1329-1341.
17. Bibikova, M., Carroll, D., Segal, D.J., Trautman, J.K., Smith, J., Kim, Y.G., and Chandrasegaran, S. (2001) Stimulation of homologous recombination through targeted cleavage by chimeric nucleases. Mol Cell Biol. 21, 289-297.
18. Urnov, F.D., Miller, J.C., Lee, Y.L., Beausejour, C.M., Rock, J.M., Augustus, S., Jamieson, A.C., Porteus, M.H., Gregory, P.D., and Holmes, M.C. (2005) Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature. 435, 646-651.
19. Porteus, M.H. and Baltimore, D. (2003) Chimeric nucleases stimulate gene targeting in human cells. Science. 300, 763.
20. Beumer, K., Bhattacharyya, G., Bibikova, M., Trautman, J.K., and Carroll, D. (2006) Efficient gene targeting in Drosophila with zinc-finger nucleases. Genetics. 172, 2391-2403.
21. Moehle, E.A., Rock, J.M., Lee, Y.L., Jouvenot, Y., Dekelver, R.C., Gregory, P.D., Urnov, F.D., and Holmes, M.C. (2007) Targeted gene addition into a specified location in the human genome using designed zinc finger nucleases. Proc Natl Acad Sci USA. 104, 3055-3060.
22. Santiago, Y., Chan, E., Liu, P.Q., Orlando, S., Zhang, L., Urnov, F.D., Holmes, M.C., Guschin, D., Waite, A., Miller, J.C., Rebar, E.J., Gregory, P.D., Klug, A., and Collingwood, T.N. (2008) Targeted gene knockout in mammalian cells by using engineered zincfinger nucleases. Proc Natl Acad Sci USA. 105, 5809-5814.
23. Wright, D.A., Townsend, J.A., Winfrey, R.J., Jr., Irwin, P.A., Rajagopal, J., Lonosky, P.M., Hall, B.D., Jondle, M.D., and Voytas, D.F. (2005) High-frequency homologous recombination in plants mediated by zincfinger nucleases. Plant J. 44, 693-705.
24. Perez, E.E., Wang, J., Miller, J.C., Jouvenot, Y., Kim, K.A., Liu, O., Wang, N., Lee, G., Bartsevich, V.V., Lee, Y.L., Guschin, D.Y., Rupniewski, I., Waite, A.J., Carpenito, C., Carroll, R.G., Orange, J.S., Urnov, F.D., Rebar, E.J., Ando, D., Gregory, P.D., Riley, J.L., Holmes, M.C., and June, C.H. (2008) Establishment of HIV-1 resistance in CD4+ T cells by genome editing using zinc-finger nucleases. Nat Biotechnol. 26, 808-816.
25. Lloyd, A., Plaisier, C.L., Carroll, D., and Drews, G.N. (2005) Targeted mutagenesis using zinc-finger nucleases in Arabidopsis. Proc Natl Acad Sci USA. 102, 2232-2237.
26. 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., Jr., Cathomen, T., Voytas, D.F., and Joung, J.K. (2008) Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification. Mol Cell. 31, 294-301.
27. 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., and Joung, J.K. (2006) Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly. Nat Protoc. 1, 1637-1652.
28. Porteus, M. (2008) Design and testing of zinc finger nucleases for use in mammalian cells. Methods Mol Biol. 435, 47-61.
29. Mani, M., Kandavelou, K., Dy, F.J., Durai, S., and Chandrasegaran, S. (2005) Design, engineering, and characterization of zinc finger nucleases. Biochem Biophys Res Commun. 335, 447-457.
30. Tzfira, T., Tian, G.-W., Lacroix, B., Vyas, S., Li, J., Leitner-Dagan, Y., Krichevsky, A., Taylor, T., Vainstein, A., and Citovsky, V. (2005) pSAT vectors: A modular series of plasmids for autofluorescent protein tagging and expression of multiple genes in plants. Plant Mol Biol. 57, 503-516.
31. Chung, S.M., Frankman, E.L., and Tzfira, T. (2005) A versatile vector system for multiple gene expression in plants. Trends Plant Sci. 10, 357-361.
32. Dafny-Yelin, M. and Tzfira, T. (2007) Delivery of multiple transgenes to plant cells. Plant Physiol. 145, 1118-1128.
33. Carrington, J.C., Freed, D.D., and Leinicke, A.J. (1991) Bipartite signal sequence mediates nuclear translocation of the plant potyviral NIa protein. Plant Cell. 3, 953-962.
34. Mandell, J.G. and Barbas, C.F., 3rd (2006) Zinc Finger Tools: Custom DNA-binding domains for transcription factors and nucleases. Nucleic Acids Res. 34, W516-W523.
35. Sander, J.D., Zaback, P., Joung, J.K., Voytas, D.F., and Dobbs, D. (2007) Zinc Finger Targeter (ZiFiT): An engineered zinc finger/ target site design tool. Nucleic Acids Res. 35, W599-W605.
36. Liu, Q., Xia, Z., Zhong, X., and Case, C.C. (2002) Validated zinc finger protein designs for all 16 GNN DNA triplet targets. J Biol Chem. 277, 3850-3856.
37. Zeevi, V., Tovkach, A., and Tzfira, T. (2010) Artificial zinc finger nucleases for DNA cloning. Methods Mol Biol. (in press).
38. Zeevi, V., Tovkach, A., and Tzfira, T. (2008) Increasing cloning possibilities using artificial zinc finger nucleases. Proc Natl Acad Sci USA. 105, 12785-12790.
39. Tovkach, A., Zeevi, V., and Tzfira, T. (2009) A toolbox and procedural notes for characterizing novel zinc finger nucleases for genome editing in plant cells. Plant J. 57, 747-757.
40. Takahashi, T. and Komeda, Y. (1989) Characterization of two genes encoding small heat-shock proteins in Arabidopsis thaliana. Mol Gen Genet. 219, 365-372.
41. Zhang, X., Henriques, R., Lin, S.S., Niu, Q.W., and Chua, N.H. (2006) Agrobacterium-mediated transformation of Arabidopsis thaliana using the floral dip method. Nat Protoc. 1, 641-646.
42. Lee, M.W. and Yang, Y. (2006) Transient expression assay by agroinfiltration of leaves. Methods Mol Biol. 323, 225-229.
43. Goderis, I.J., De Bolle, M.F., Francois, I.E., Wouters, P.F., Broekaert, W.F., and Cammue, B.P. (2002) A set of modular plant transformation vectors allowing flexible insertion of up to six expression units. Plant Mol Biol. 50, 17-27.
44. Cathomen, T., Segal, D.J., Brondani, V., and Muller-Lerch, F. (2008) Generation and functional analysis of zinc finger nucleases. Methods Mol Biol. 434, 277-290.
45. Tzfira, T., Jensen, C.S., Wangxia, W., Zuker, A., Altman, A., and Vainstein, A. (1997) Transgenic Populus: A step-by-step protocol for its Agrobacterium-mediated transformation. Plant Mol Biol Rep. 15, 219-235.