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Tailor-Made Mutations in Arabidopsis Using Zinc Finger Nucleases

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Arabidopsis Protocols

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1062))

Abstract

Zinc finger nucleases (ZFNs) are proteins engineered to make site-specific double-strand breaks (DSBs) in a DNA sequence of interest. Imprecise repair of the ZFN-induced DSBs by the nonhomologous end-joining (NHEJ) pathway results in a spectrum of mutations, such as nucleotide substitutions, insertions, and deletions. Here we describe a method for targeted mutagenesis in Arabidopsis with ZFNs, which are engineered by context-dependent assembly (CoDA). This ZFN-induced mutagenesis method is an alternative to other currently available gene knockout or knockdown technologies and is useful for reverse genetic studies.

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References

  1. Alonso JM, Ecker JR (2006) Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis. Nat Rev Genet 7:524–536

    Article  PubMed  CAS  Google Scholar 

  2. Alonso JM et al (2003) Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301:653–657

    Article  PubMed  Google Scholar 

  3. Sessions A et al (2002) A high-throughput Arabidopsis reverse genetics system. Plant Cell 14:2985–2994

    Article  PubMed  CAS  Google Scholar 

  4. Woody ST et al (2007) The WiscDsLox T-DNA collection: an arabidopsis community resource generated by using an improved high-throughput T-DNA sequencing pipeline. J Plant Res 120:157–165

    Article  PubMed  CAS  Google Scholar 

  5. McCallum CM et al (2000) Targeted screening for induced mutations. Nat Biotechnol 18:455–457

    Article  PubMed  CAS  Google Scholar 

  6. Bush SM, Krysan PJ (2011) iTILLING: a personalized approach to the identification of induced mutations in Arabidopsis. Plant Physiol 154:25–35

    Article  Google Scholar 

  7. Kim YG, Cha J, Chandrasegaran S (1996) Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proc Natl Acad Sci U S A 93:1156–1160

    Article  PubMed  CAS  Google Scholar 

  8. Bibikova M et al (2001) Stimulation of homologous recombination through targeted cleavage by chimeric nucleases. Mol Cell Biol 21:289–297

    Article  PubMed  CAS  Google Scholar 

  9. Bitinaite J et al (1998) FokI dimerization is required for DNA cleavage. Proc Natl Acad Sci U S A 95:10570–10575

    Article  PubMed  CAS  Google Scholar 

  10. Townsend JA et al (2009) High-frequency modification of plant genes using engineered zinc-finger nucleases. Nature 459:442–445

    Article  PubMed  CAS  Google Scholar 

  11. Carroll D (2011) Genome engineering with zinc-finger nucleases. Genetics 188:773–782

    Article  PubMed  CAS  Google Scholar 

  12. Zhang F et al (2010) High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases. Proc Natl Acad Sci U S A 107:12028–12033

    Article  PubMed  CAS  Google Scholar 

  13. Shukla VK et al (2009) Precise genome modification in the crop species Zea mays using zinc-finger nucleases. Nature 459:437–441

    Article  PubMed  CAS  Google Scholar 

  14. Osakabe K, Osakabe Y, Toki S (2010) Site-directed mutagenesis in Arabidopsis using custom-designed zinc finger nucleases. Proc Natl Acad Sci U S A 107:12034–12039

    Article  PubMed  CAS  Google Scholar 

  15. Doyon Y et al (2008) Heritable targeted gene disruption in zebrafish using designed zinc-finger nucleases. Nat Biotechnol 26:702–708

    Article  PubMed  CAS  Google Scholar 

  16. Kim S et al (2011) Preassembled zinc-finger arrays for rapid construction of ZFNs. Nat Methods 8:7

    Article  PubMed  CAS  Google Scholar 

  17. Ramirez CL et al (2008) Unexpected failure rates for modular assembly of engineered zinc fingers. Nat Methods 5:374–375

    Article  PubMed  CAS  Google Scholar 

  18. Maeder ML et al (2008) Rapid “open-source” engineering of customized zinc-finger nucleases for highly efficient gene modification. Mol Cell 31:294–301

    Article  PubMed  CAS  Google Scholar 

  19. Sander JD et al (2011) Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA). Nat Methods 8:67–69

    Article  PubMed  CAS  Google Scholar 

  20. Curtin SJ et al (2011) Targeted mutagenesis of duplicated genes in soybean with zinc-finger nucleases. Plant Physiol 156:466–473

    Article  PubMed  CAS  Google Scholar 

  21. Sander JD, Maeder ML, Joung JK (2011) Engineering designer nucleases with customized cleavage specificities. Curr Protoc Mol Biol Chapter 12, Unit12 13. doi: 10.1002/0471142727.mb1213s96

    Google Scholar 

  22. Osborn MJ et al (2011) Synthetic zinc finger nuclease design and rapid assembly. Hum Gene Ther 22:1155–1165

    Article  PubMed  CAS  Google Scholar 

  23. Curtis MD, Grossniklaus U (2003) A gateway cloning vector set for high-throughput functional analysis of genes in planta. Plant Physiol 133:462–469

    Article  PubMed  CAS  Google Scholar 

  24. Koncz C et al (1989) High-frequency T-DNA-mediated gene tagging in plants. Proc Natl Acad Sci U S A 86:8467–8471

    Article  PubMed  CAS  Google Scholar 

  25. Wright DA et al (2006) Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly. Nat Protoc 1:1637–1652

    Article  PubMed  Google Scholar 

  26. Sander JD et al (2010) ZiFiT (zinc finger targeter): an updated zinc finger engineering tool. Nucleic Acids Res 38:W462–W468

    Article  PubMed  CAS  Google Scholar 

  27. Clough SJ, Bent AF (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J 16:735–743

    Article  PubMed  CAS  Google Scholar 

  28. Miller JC et al (2007) An improved zinc-finger nuclease architecture for highly specific genome editing. Nat Biotechnol 25:778–785

    Article  PubMed  CAS  Google Scholar 

  29. Szymczak AL et al (2004) Correction of multi-gene deficiency in vivo using a single “self-cleaving” 2A peptide-based retroviral vector. Nat Biotechnol 22:589–594

    Article  PubMed  CAS  Google Scholar 

  30. Guschin DY et al (2010) A rapid and general assay for monitoring endogenous gene modification. Methods Mol Biol 649:247–256

    Article  PubMed  CAS  Google Scholar 

  31. Herrmann F et al (2011) p53 Gene repair with zinc finger nucleases optimised by yeast 1-hybrid and validated by Solexa sequencing. PLoS One 6:e20913

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

This work is supported by grants from the National Science Foundation to D.F.V. (DBI 0923827 and MCB 0209818).

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Qi, Y., Starker, C.G., Zhang, F., Baltes, N.J., Voytas, D.F. (2014). Tailor-Made Mutations in Arabidopsis Using Zinc Finger Nucleases. In: Sanchez-Serrano, J., Salinas, J. (eds) Arabidopsis Protocols. Methods in Molecular Biology, vol 1062. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-580-4_10

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  • DOI: https://doi.org/10.1007/978-1-62703-580-4_10

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-579-8

  • Online ISBN: 978-1-62703-580-4

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