A TALE nuclease architecture for efficient genome editing (original) (raw)

• Urnov, F.D., Rebar, E.J., Holmes, M.C., Zhang, H.S. & Gregory, P.D. Genome editing with engineered zinc finger nucleases. Nat. Rev. Genet. 11, 636–646 (2010).
  Article CAS PubMed Google Scholar
• Davis, D. & Stokoe, D. Zinc finger nucleases as tools to understand and treat human diseases. BMC Med. 8, 42 (2010).
  Article PubMed PubMed Central Google Scholar
• Camenisch, T.D., Brilliant, M.H. & Segal, D.J. Critical parameters for genome editing using zinc finger nucleases. Mini Rev. Med. Chem. 8, 669–676 (2008).
  Article CAS PubMed Google Scholar
• Carroll, D. Progress and prospects: zinc-finger nucleases as gene therapy agents. Gene Ther. 15, 1463–1468 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Cathomen, T. & Joung, J.K. Zinc-finger nucleases: the next generation emerges. Mol. Ther. 16, 1200–1207 (2008).
  Article CAS PubMed Google Scholar
• Galetto, R., Duchateau, P. & Paques, F. Targeted approaches for gene therapy and the emergence of engineered meganucleases. Expert Opin. Biol. Ther. 9, 1289–1303 (2009).
  Article CAS PubMed Google Scholar
• Hoeijmakers, J.H. Genome maintenance mechanisms for preventing cancer. Nature 411, 366–374 (2001).
  Article CAS PubMed Google Scholar
• Ochiai, H. et al. Targeted mutagenesis in the sea urchin embryo using zinc-finger nucleases. Genes Cells 15, 875–885 (2010).
  CAS PubMed Google Scholar
• Takasu, Y. et al. Targeted mutagenesis in the silkworm Bombyx mori using zinc finger nuclease mRNA injection. Insect Biochem. Mol. Biol. 40, 759–765 (2010).
  Article CAS PubMed Google Scholar
• Morton, J., Davis, M.W., Jorgensen, E.M. & Carroll, D. Induction and repair of zinc-finger nuclease-targeted double-strand breaks in Caenorhabditis elegans somatic cells. Proc. Natl. Acad. Sci. USA 103, 16370–16375 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Holt, N. et al. Human hematopoietic stem/progenitor cells modified by zinc-finger nucleases targeted to CCR5 control HIV-1 in vivo. Nat. Biotechnol. 28, 839–847 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Benabdallah, B.F. et al. Targeted gene addition to human mesenchymal stromal cells as a cell-based plasma-soluble protein delivery platform. Cytotherapy 12, 394–399 (2010).
  Article CAS PubMed Google Scholar
• Zou, J. et al. Gene targeting of a disease-related gene in human induced pluripotent stem and embryonic stem cells. Cell Stem Cell 5, 97–110 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Hockemeyer, D. et al. Efficient targeting of expressed and silent genes in human ESCs and iPSCs using zinc-finger nucleases. Nat. Biotechnol. 27, 851–857 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Lombardo, A. et al. Gene editing in human stem cells using zinc finger nucleases and integrase-defective lentiviral vector delivery. Nat. Biotechnol. 25, 1298–1306 (2007).
  Article CAS PubMed Google Scholar
• 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 PubMed PubMed Central Google Scholar
• Urnov, F.D. et al. Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature 435, 646–651 (2005).
  Article CAS PubMed Google Scholar
• 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).
  CAS PubMed PubMed Central Google Scholar
• Porteus, M.H. & Baltimore, D. Chimeric nucleases stimulate gene targeting in human cells. Science 300, 763 (2003).
  Article PubMed Google Scholar
• Maeder, M.L. et al. Rapid “open-source” engineering of customized zinc-finger nucleases for highly efficient gene modification. Mol. Cell 31, 294–301 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• 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. 19, 1279–1288 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• 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).
  Article CAS PubMed PubMed Central Google Scholar
• Boch, J. et al. Breaking the code of DNA binding specificity of TAL-type III effectors. Science 326, 1509–1512 (2009).
  Article CAS PubMed Google Scholar
• Moscou, M.J. & Bogdanove, A.J. A simple cipher governs DNA recognition by TAL effectors. Science 326, 1501 (2009).
  Article CAS PubMed Google Scholar
• Römer, P. et al. Plant pathogen recognition mediated by promoter activation of the pepper Bs3 resistance gene. Science 318, 645–648 (2007).
  Article PubMed Google Scholar
• 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 PubMed Google Scholar
• Kay, S. & Bonas, U. How Xanthomonas type III effectors manipulate the host plant. Curr. Opin. Microbiol. 12, 37–43 (2009).
  Article CAS PubMed Google Scholar
• 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 PubMed Google Scholar
• Boch, J. & Bonas, U. Xanthomonas AvrBs3 family-type III effectors: discovery and function. Annu. Rev. Phytopathol. 48, 419–436 (2010).
  Article CAS PubMed Google Scholar
• Christian, M. et al. Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186, 757–761 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Li, T. et al. TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain. Nucleic Acids Res. published online, doi:10.1093/nar/gkq704 (10 August 2010).
• Szurek, B., Rossier, O., Hause, G. & Bonas, U. Type III-dependent translocation of the Xanthomonas AvrBs3 protein into the plant cell. Mol. Microbiol. 46, 13–23 (2002).
  Article CAS PubMed Google Scholar
• Chao, M.V., Rajagopal, R. & Lee, F.S. Neurotrophin signalling in health and disease. Clin. Sci. (Lond.) 110, 167–173 (2006).
  Article CAS Google Scholar
• 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 PubMed Google Scholar
• Miller, J.C. et al. An improved zinc-finger nuclease architecture for highly specific genome editing. Nat. Biotechnol. 25, 778–785 (2007).
  Article CAS PubMed Google Scholar
• Guschin, D.Y. et al. A rapid and general assay for monitoring endogenous gene modification. Methods Mol. Biol. 649, 247–256 (2010).
  Article CAS PubMed Google Scholar
• Doyon, Y. et al. Transient cold shock enhances zinc-finger nuclease-mediated gene disruption. Nat. Methods 7, 459–460 (2010).
  Article CAS PubMed Google Scholar
• Jeggo, P.A. DNA breakage and repair. Adv. Genet. 38, 185–218 (1998).
  Article CAS PubMed Google Scholar
• Orlando, S.J. et al. Zinc-finger nuclease-driven targeted integration into mammalian genomes using donors with limited chromosomal homology. Nucleic Acids Res. 38, e152 (2010).
  Article PubMed PubMed Central Google Scholar
• Liu, R. et al. Homozygous defect in HIV-1 coreceptor accounts for resistance of some multiply-exposed individuals to HIV-1 infection. Cell 86, 367–377 (1996).
  Article CAS PubMed Google Scholar
• Townsend, J.A. et al. High-frequency modification of plant genes using engineered zinc-finger nucleases. Nature 459, 442–445 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Redondo, P. et al. Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases. Nature 456, 107–111 (2008).
  Article CAS PubMed Google Scholar
• DeKelver, R.C. et al. Functional genomics, proteomics, and regulatory DNA analysis in isogenic settings using zinc finger nuclease-driven transgenesis into a safe harbor locus in the human genome. Genome Res. 20, 1133–1142 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Doyon, Y. et al. Enhancing zinc-finger-nuclease activity with improved obligate heterodimeric architectures. Nat. Methods published online, doi: 10.1038/nmeth.1539 (5 December 2010).
• Cuthbert, G.L. et al. Histone deimination antagonizes arginine methylation. Cell 118, 545–553 (2004).
  Article CAS PubMed Google Scholar
• Reik, A. et al. Enhanced protein production by engineered zinc finger proteins. Biotechnol. Bioeng. 97, 1180–1189 (2007).
  Article CAS PubMed Google Scholar
• Liu, P.Q. et al. Isogenic human cell lines for drug discovery: regulation of target gene expression by engineered zinc-finger protein transcription factors. J. Biomol. Screen. 10, 304–313 (2005).
  Article CAS PubMed Google Scholar
• Whitlock, P.R., Hackett, N.R., Leopold, P.L., Rosengart, T.K. & Crystal, R.G. Adenovirus-mediated transfer of a minigene expressing multiple isoforms of VEGF is more effective at inducing angiogenesis than comparable vectors expressing individual VEGF cDNAs. Mol. Ther. 9, 67–75 (2004).
  Article CAS PubMed Google Scholar
• Ozawa, C.R. et al. Microenvironmental VEGF concentration, not total dose, determines a threshold between normal and aberrant angiogenesis. J. Clin. Invest. 113, 516–527 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Tan, S. et al. Zinc-finger protein-targeted gene regulation: genomewide single-gene specificity. Proc. Natl. Acad. Sci. USA 100, 11997–12002 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Morbitzer, R., Römer, 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 (2010).
• Hoover, D.M. & Lubkowski, J. DNAWorks: an automated method for designing oligonucleotides for PCR-based gene synthesis. Nucleic Acids Res. 30, e43 (2002).
  Article PubMed PubMed Central Google Scholar