A transcription activator-like effector toolbox for genome engineering (original) (raw)

References

  1. Boch, J. et al. Breaking the code of DNA binding specificity of TAL-type III effectors. Science 326, 1509–1512 (2009).
    Article CAS Google Scholar
  2. Moscou, M.J. & Bogdanove, A.J. A simple cipher governs DNA recognition by TAL effectors. Science 326, 1501 (2009).
    Article CAS Google Scholar
  3. Zhang, F. et al. Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. Nat. Biotechnol. 29, 149–153 (2011).
    Article Google Scholar
  4. Miller, J.C. et al. A TALE nuclease architecture for efficient genome editing. Nat. Biotechnol. 29, 143–148 (2011).
    Article CAS Google Scholar
  5. Morbitzer, R., Romer, P., Boch, J. & Lahaye, T. Regulation of selected genome loci using _de novo_-engineered transcription activator-like effector (TALE)-type transcription factors. Proc. Natl. Acad. Sci. USA 107, 21617–21622 (2010).
    Article CAS Google Scholar
  6. Weber, E., Gruetzner, R., Werner, S., Engler, C. & Marillonnet, S. Assembly of designer TAL effectors by golden gate cloning. PLoS ONE 6, e19722 (2011).
    Article CAS Google Scholar
  7. Cermak, T. et al. Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res. 39, e82 (2011).
    Article CAS Google Scholar
  8. Geissler, R. et al. Transcriptional activators of human genes with programmable DNA-specificity. PLoS ONE 6, e19509 (2011).
    Article CAS Google Scholar
  9. Li, T. et al. Modularly assembled designer TAL effector nucleases for targeted gene knockout and gene replacement in eukaryotes. Nucleic Acids Res. 39, 6315–6325 (2011).
    Article CAS Google Scholar
  10. Morbitzer, R., Elsaesser, J., Hausner, J. & Lahaye, T. Assembly of custom TALE-type DNA binding domains by modular cloning. Nucleic Acids Res. 39, 5790–5799 (2011).
    Article CAS Google Scholar
  11. Wood, A.J. et al. Targeted genome editing across species using ZFNs and TALENs. Science 333, 307 (2011).
    Article CAS Google Scholar
  12. Christian, M. et al. Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186, 757–761 (2010).
    Article CAS Google Scholar
  13. Hockemeyer, D. et al. Genetic engineering of human pluripotent cells using TALE nucleases. Nat. Biotechnol. 29, 731–734 (2011).
    Article CAS Google Scholar
  14. Li, T. et al. TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain. Nucleic Acids Res. 39, 359–372 (2011).
    Article Google Scholar
  15. Mahfouz, M.M. et al. _De novo_-engineered transcription activator-like effector (TALE) hybrid nuclease with novel DNA binding specificity creates double-strand breaks. Proc. Natl. Acad. Sci. USA 108, 2623–2628 (2011).
    Article CAS Google Scholar
  16. Boch, J. & Bonas, U. Xanthomonas AvrBs3 family-type III effectors: discovery and function. Annu. Rev. Phytopathol. 48, 419–436 (2010).
    Article CAS Google Scholar
  17. Bogdanove, A.J., Schornack, S. & Lahaye, T. TAL effectors: finding plant genes for disease and defense. Curr. Opin. Plant Biol. 13, 394–401 (2010).
    Article CAS Google Scholar
  18. Romer, P. et al. Plant pathogen recognition mediated by promoter activation of the pepper Bs3 resistance gene. Science 318, 645–648 (2007).
    Article Google Scholar
  19. Kay, S., Hahn, S., Marois, E., Hause, G. & Bonas, U. A bacterial effector acts as a plant transcription factor and induces a cell size regulator. Science 318, 648–651 (2007).
    Article CAS Google Scholar
  20. Kay, S., Hahn, S., Marois, E., Wieduwild, R. & Bonas, U. Detailed analysis of the DNA recognition motifs of the Xanthomonas type III effectors AvrBs3 and AvrBs3Deltarep16. Plant J. 59, 859–871 (2009).
    Article CAS Google Scholar
  21. Romer, P. et al. Recognition of AvrBs3-like proteins is mediated by specific binding to promoters of matching pepper Bs3 alleles. Plant Physiol. 150, 1697–1712 (2009).
    Article Google Scholar
  22. Hinnen, A., Hicks, J.B. & Fink, G.R. Transformation of yeast. Proc. Natl. Acad. Sci. USA 75, 1929–1933 (1978).
    Article CAS Google Scholar
  23. Szostak, J.W., Orr-Weaver, T.L., Rothstein, R.J. & Stahl, F.W. The double-strand-break repair model for recombination. Cell 33, 25–35 (1983).
    Article CAS Google Scholar
  24. Thomas, K.R., Folger, K.R. & Capecchi, M.R. High frequency targeting of genes to specific sites in the mammalian genome. Cell 44, 419–428 (1986).
    Article CAS Google Scholar
  25. Ivics, Z., Hackett, P.B., Plasterk, R.H. & Izsvak, Z. Molecular reconstruction of Sleeping Beauty, a _Tc1_-like transposon from fish, and its transposition in human cells. Cell 91, 501–510 (1997).
    Article CAS Google Scholar
  26. Kawakami, K., Shima, A. & Kawakami, N. Identification of a functional transposase of the Tol2 element, an Ac-like element from the Japanese medaka fish, and its transposition in the zebrafish germ lineage. Proc. Natl. Acad. Sci. USA 97, 11403–11408 (2000).
    Article CAS Google Scholar
  27. Akagi, K. et al. Cre-mediated somatic site-specific recombination in mice. Nucleic Acids Res. 25, 1766–1773 (1997).
    Article CAS Google Scholar
  28. Epinat, J.C. et al. A novel engineered meganuclease induces homologous recombination in yeast and mammalian cells. Nucleic Acids Res. 31, 2952–2962 (2003).
    Article CAS Google Scholar
  29. Lois, C., Hong, E.J., Pease, S., Brown, E.J. & Baltimore, D. Germline transmission and tissue-specific expression of transgenes delivered by lentiviral vectors. Science 295, 868–872 (2002).
    Article CAS Google Scholar
  30. Khan, I.F., Hirata, R.K. & Russell, D.W. AAV-mediated gene targeting methods for human cells. Nat. Protoc. 6, 482–501 (2011).
    Article CAS Google Scholar
  31. Pavletich, N.P. & Pabo, C.O. Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A. Science 252, 809–817 (1991).
    Article CAS Google Scholar
  32. Klug, A. The discovery of zinc fingers and their development for practical applications in gene regulation and genome manipulation. Q. Rev. Biophys. 43, 1–21 (2010).
    Article CAS Google Scholar
  33. 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. 4, 1471–1501 (2009).
    Article CAS Google Scholar
  34. Kim, J.S., Lee, H.J. & Carroll, D. Genome editing with modularly assembled zinc-finger nucleases. Nat. Methods 7, 91; author reply 91–92 (2010).
    Article CAS Google Scholar
  35. Sander, J.D. et al. Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA). Nat. Methods 8, 67–69 (2011).
    Article CAS Google Scholar
  36. Perez, E.E. et al. Establishment of HIV-1 resistance in CD4+ T cells by genome editing using zinc-finger nucleases. Nat. Biotechnol. 26, 808–816 (2008).
    Article CAS Google Scholar
  37. Keenholtz, R.A., Rowland, S.J., Boocock, M.R., Stark, W.M. & Rice, P.A. Structural basis for catalytic activation of a serine recombinase. Structure 19, 799–809 (2011).
    Article CAS Google Scholar
  38. Gersbach, C.A., Gaj, T., Gordley, R.M., Mercer, A.C. & Barbas, C.F. III. Targeted plasmid integration into the human genome by an engineered zinc-finger recombinase. Nucleic Acids Res. 39, 7868–7878 (2011).
    Article CAS Google Scholar
  39. Gaj, T., Mercer, A.C., Gersbach, C.A., Gordley, R.M. & Barbas, C.F. III. Structure-guided reprogramming of serine recombinase DNA sequence specificity. Proc. Natl. Acad. Sci. USA 108, 498–503 (2011).
    Article Google Scholar
  40. Urnov, F.D. et al. Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature 435, 646–651 (2005).
    Article CAS Google Scholar
  41. Wilson, M.H., Kaminski, J.M. & George, A.L. Jr. Functional zinc finger/sleeping beauty transposase chimeras exhibit attenuated overproduction inhibition. FEBS Lett. 579, 6205–6209 (2005).
    Article CAS Google Scholar
  42. Engler, C., Kandzia, R. & Marillonnet, S. A one pot, one step, precision cloning method with high throughput capability. PLoS ONE 3, e3647 (2008).
    Article Google Scholar
  43. Engler, C., Gruetzner, R., Kandzia, R. & Marillonnet, S. Golden gate shuffling: a one-pot DNA shuffling method based on type IIs restriction enzymes. PLoS ONE 4, e5553 (2009).
    Article Google Scholar
  44. Weber, E., Engler, C., Gruetzner, R., Werner, S. & Marillonnet, S. A modular cloning system for standardized assembly of multigene constructs. PLoS ONE 6, e16765 (2011).
    Article CAS Google Scholar
  45. Huertas, P. DNA resection in eukaryotes: deciding how to fix the break. Nat. Struct. Mol. Biol. 17, 11–16 (2010).
    Article CAS Google Scholar
  46. Nolan, T., Hands, R.E. & Bustin, S.A. Quantification of mRNA using real-time RT-PCR. Nat. Protoc. 1, 1559–1582 (2006).
    Article CAS Google Scholar
  47. Guschin, D.Y. et al. A rapid and general assay for monitoring endogenous gene modification. Methods Mol. Biol. 649, 247–256 (2010).
    Article CAS Google Scholar
  48. Zhang, F. et al. High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases. Proc. Natl. Acad. Sci. USA 107, 12028–12033 (2010).
    Article CAS Google Scholar
  49. Buzdin, A.A. in Nucleic Acids Hybridization (eds. Buzdin, A., Lukyanov, S.) 211–239 (Springer, 2007).
  50. Till, B.J., Burtner, C., Comai, L. & Henikoff, S. Mismatch cleavage by single-strand specific nucleases. Nucleic Acids Res. 32, 2632–2641 (2004).
    Article CAS Google Scholar
  51. Babon, J.J., McKenzie, M. & Cotton, R.G. The use of resolvases T4 endonuclease VII and T7 endonuclease I in mutation detection. Mol. Biotechnol. 23, 73–81 (2003).
    Article CAS Google Scholar
  52. Yang, B. et al. Purification, cloning, and characterization of the CEL I nuclease. Biochemistry 39, 3533–3541 (2000).
    Article CAS Google Scholar
  53. Kulinski, J., Besack, D., Oleykowski, C.A., Godwin, A.K. & Yeung, A.T. CEL I enzymatic mutation detection assay. Biotechniques 29, 44–46, 48 (2000).
    Article CAS Google Scholar
  54. Oleykowski, C.A., Bronson Mullins, C.R., Godwin, A.K. & Yeung, A.T. Mutation detection using a novel plant endonuclease. Nucleic Acids Res. 26, 4597–4602 (1998).
    Article CAS Google Scholar
  55. Pfaffl, M.W. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 29, e45 (2001).
    Article CAS Google Scholar
  56. Murakami, M.T. et al. The repeat domain of the type III effector protein PthA shows a TPR-like structure and undergoes conformational changes upon DNA interaction. Proteins 78, 3386–3395 (2010).
    Article CAS Google Scholar
  57. Scholze, H. & Boch, J. TAL effectors are remote controls for gene activation. Curr. Opin. Microbiol. 14, 47–53 (2011).
    Article CAS Google Scholar
  58. Huang, P. et al. Heritable gene targeting in zebrafish using customized TALENs. Nat. Biotechnol. 29, 699–700 (2011).
    Article Google Scholar
  59. Sander, J.D. et al. Targeted gene disruption in somatic zebrafish cells using engineered TALENs. Nat. Biotechnol. 29, 697–698 (2011).
    Article CAS Google Scholar
  60. Tesson, L. et al. Knockout rats generated by embryo microinjection of TALENs. Nat. Biotechnol. 29, 695–696 (2011).
    Article CAS Google Scholar

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