SEARCH

SEARCH BY CITATION

References

  • Acevedo-Arozena, A., Wells, S., Potter, P., Kelly, M., Cox, R. D. & Brown, S. D. 2008. ENU mutagenesis, a way forward to understand gene function. Annu. Rev. Genomics Hum. Genet. 9, 4969.
  • Ansai, S., Ochiai, H., Kanie, Y., Kamei, Y., Gou, Y., Kitano, T., Yamamoto, T. & Kinoshita, M. 2012. Targeted disruption of exogenous EGFP gene in medaka using zinc-finger nucleases. Dev. Growth Differ. 54, 546556.
  • Ansai, S., Sakuma, T., Yamamoto, T., Ariga, H., Uemura, N., Takahashi, R. & Kinoshita, M. 2013. Efficient targeted mutagenesis in medaka using custom-designed transcription activator-like effector nucleases. Genetics 193, 739749.
  • Aryan, A., Anderson, M. A., Myles, K. M. & Adelman, Z. N. 2013. TALEN-based gene disruption in the dengue vector Aedes aegypti. PLoS ONE 8, e60082.
  • Bedell, V. M., Wang, Y., Campbell, J. M., Poshusta, T. L., Starker, C. G., Krug, R. G. 2nd, Tan, W., Penheiter, S. G., Ma, A. C., Leung, A. Y., Fahrenkrug, S. C., Carlson, D. F., Voytas, D. F., Clark, K. J., Essner, J. J. & Ekker, S. C. 2012. In vivo genome editing using a high-efficiency TALEN system. Nature 491, 114118.
  • Beumer, K. J., Trautman, J. K., Bozas, A., Liu, J. L., Rutter, J., Gall, J. G. & Carroll, D. 2008. Efficient gene targeting in Drosophila by direct embryo injection with zinc-finger nucleases. Proc. Natl Acad. Sci. USA 105, 1982119826.
  • Beurdeley, M., Bietz, F., Li, J., Thomas, S., Stoddard, T., Juillerat, A., Zhang, F., Voytas, D. F., Duchateau, P. & Silva, G. H. 2013. Compact designer TALENs for efficient genome engineering. Nat. Commun. 4, 1762.
  • Bibikova, M., Golic, M., Golic, K. G. & Carroll, D. 2002. Targeted chromosomal cleavage and mutagenesis in Drosophila using zinc-finger nucleases. Genetics 161, 11691175.
  • Boch, J., Scholze, H., Schornack, S., Landgraf, A., Hahn, S., Kay, S., Lahaye, T., Nickstadt, A. & Bonas, U. 2009. Breaking the code of DNA binding specificity of TAL-type III effectors. Science 326, 15091512.
  • Bogdanove, A. J., Schornack, S. & Lahaye, T. 2010. TAL effectors: finding plant genes for disease and defense. Curr. Opin. Plant Biol. 13, 394401.
  • Brown, A. J., Fisher, D. A., Kouranova, E., McCoy, A., Forbes, K., Wu, Y., Henry, R., Ji, D., Chambers, A., Warren, J., Shu, W., Weinstein, E. J. & Cui, X. 2013. Whole-rat conditional gene knockout via genome editing. Nat. Methods 10, 638640.
  • Cade, L., Reyon, D., Hwang, W. Y., Tsai, S. Q., Patel, S., Khayter, C., Joung, J. K., Sander, J. D., Peterson, R. T. & Yeh, J. R. 2012. Highly efficient generation of heritable zebrafish gene mutations using homo- and heterodimeric TALENs. Nucleic Acids Res. 40, 80018010.
  • Capecchi, M. R. 2005. Gene targeting in mice: functional analysis of the mammalian genome for the twenty-first century. Nat. Rev. Genet. 6, 507512.
  • Carbery, I. D., Ji, D., Harrington, A., Brown, V., Weinstein, E. J., Liaw, L. & Cui, X. 2010. Targeted genome modification in mice using zinc-finger nucleases. Genetics 186, 451459.
  • Carlson, D. F., Tan, W., Lillico, S. G., Stverakova, D., Proudfoot, C., Christian, M., Voytas, D. F., Long, C. R., Whitelaw, C. B. & Fahrenkrug, S. C. 2012. Efficient TALEN-mediated gene knockout in livestock. Proc. Natl Acad. Sci. USA 109, 1738217387.
  • Cermak, T., Doyle, E. L., Christian, M., Wang, L., Zhang, Y., Schmidt, C., Baller, J. A., Somia, N. V., Bogdanove, A. J. & Voytas, D. F. 2011. Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res. 39, e82.
  • Chen, F., Pruett-Miller, S. M., Huang, Y., Gjoka, M., Duda, K., Taunton, J., Collingwood, T. N., Frodin, M. & Davis, G. D. 2011. High-frequency genome editing using ssDNA oligonucleotides with zinc-finger nucleases. Nat. Methods 8, 753755.
  • Chen, C., Fenk, L. A. & de Bono, M. 2013. Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination. Nucleic Acids Res. 41, e193.
  • Cheng, A. W., Wang, H., Yang, H., Shi, L., Katz, Y., Theunissen, T. W., Rangarajan, S., Shivalila, C. S., Dadon, D. B. & Jaenisch, R. 2013. Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system. Cell Res. 23, 11631171.
  • Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., Marraffini, L. A. & Zhang, F. 2013. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819823.
  • Cradick, T. J., Ambrosini, G., Iseli, C., Bucher, P. & McCaffrey, A. P. 2011. ZFN-site searches genomes for zinc finger nuclease target sites and off-target sites. BMC Bioinformatics 12, 152.
  • Cradick, T. J., Fine, E. J., Antico, C. J. & Bao, G. 2013. CRISPR/Cas9 systems targeting β-globin and CCR5 genes have substantial off-target activity. Nucleic Acids Res. 41, 95849592.
  • Crocker, J. & Stern, D. L. 2013. TALE-mediated modulation of transcriptional enhancers in vivo. Nat. Methods 10, 762767.
  • Cui, X., Ji, D., Fisher, D. A., Wu, Y., Briner, D. M. & Weinstein, E. J. 2011. Targeted integration in rat and mouse embryos with zinc-finger nucleases. Nat. Biotechnol. 29, 6467.
  • Coluccio, A., Miselli, F., Lombardo, A., Marconi, A., Malagoli Tagliazucchi, G., Gonçalves, M. A., Pincelli, C., Maruggi, G., Del Rio, M., Naldini, L., Larcher, F., Mavilio, F. & Recchia, A. 2013. Targeted gene addition in human epithelial stem cells by zinc-finger nuclease-mediated homologous recombination. Mol. Ther. 21, 16951704.
  • Dahlem, T. J., Hoshijima, K., Jurynec, M. J., Gunther, D., Starker, C. G., Locke, A. S., Weis, A. M., Voytas, D. F. & Grunwald, D. J. 2012. Simple methods for generating and detecting locus-specific mutations induced with TALENs in the zebrafish genome. PLoS Genet. 8, e1002861.
  • Dickinson, D. J., Ward, J. D., Reiner, D. J. & Goldstein, B. 2013. Engineering the Caenorhabditis elegans genome using Cas9-triggered homologous recombination. Nat. Methods 10, 10281034.
  • Doyle, E. L., Booher, N. J., Standage, D. S., Voytas, D. F., Brendel, V. P., Vandyk, J. K. & Bogdanove, A. J. 2012. TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction. Nucleic Acids Res. 40, W117W122.
  • Doyon, Y., McCammon, J. M., Miller, J. C., Faraji, F., Ngo, C., Katibah, G. E., Amora, R., Hocking, T. D., Zhang, L., Rebar, E. J., Gregory, P. D., Urnov, F. D. & Amacher, S. L. 2008. Heritable targeted gene disruption in zebrafish using designed zinc-finger nucleases. Nat. Biotechnol. 26, 702708.
  • Ebina, H., Misawa, N., Kanemura, Y. & Koyanagi, Y. 2013. Harnessing the CRISPR/Cas9 system to disrupt latent HIV-1 provirus. Sci. Rep. 3, 2510.
  • Esvelt, K. M., Mali, P., Braff, J. L., Moosburner, M., Yaung, S. J. & Church, G. M. 2013. Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat. Methods 10, 11161121.
  • Fu, Y., Foden, J. A., Khayter, C., Maeder, M. L., Reyon, D., Joung, J. K. & Sander, J. D. 2013. High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat. Biotechnol. 31, 822826.
  • Fujii, W., Kawasaki, K., Sugiura, K. & Naito, K. 2013. Efficient generation of large-scale genome-modified mice using gRNA and CAS9 endonuclease. Nucleic Acids Res. 41, e187.
  • Gaj, T., Guo, J., Kato, Y., Sirk, S. J. & Barbas, C. F. 3rd 2012. Targeted gene knockout by direct delivery of zinc-finger nuclease proteins. Nat. Methods 9, 805807.
  • Gaj, T., Mercer, A. C., Sirk, S. J., Smith, H. L. & Barbas, C. F. 3rd 2013. A comprehensive approach to zinc-finger recombinase customization enables genomic targeting in human cells. Nucleic Acids Res. 41, 39373946.
  • Gersbach, C. A., Gaj, T., Gordley, R. M., Mercer, A. C. & Barbas, C. F. 3rd 2011. Targeted plasmid integration into the human genome by an engineered zinc-finger recombinase. Nucleic Acids Res. 39, 78687878.
  • Gilbert, L. A., Larson, M. H., Morsut, L., Liu, Z., Brar, G. A., Torres, S. E., Stern-Ginossar, N., Brandman, O., Whitehead, E. H., Doudna, J. A., Lim, W. A., Weissman, J. S. & Qi, L. S. 2013. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154, 442451.
  • Gordley, R. M., Smith, J. D., Graslund, T. & Barbas, C. F. 3rd 2007. Evolution of programmable zinc finger-recombinases with activity in human cells. J. Mol. Biol. 367, 802813.
  • Gratz, S. J., Cummings, A. M., Nguyen, J. N., Hamm, D. C., Donohue, L. K., Harrison, M. M., Wildonger, J. & O'Connor-Giles, K. M. 2013. Genome engineering of Drosophila with the CRISPR RNA-guided Cas9 nuclease. Genetics 194, 10291035.
  • Grizot, S., Smith, J., Daboussi, F., Prieto, J., Redondo, P., Merino, N., Villate, M., Thomas, S., Lemaire, L., Montoya, G., Blanco, F. J., Paques, F. & Duchateau, P. 2009. Efficient targeting of a SCID gene by an engineered single-chain homing endonuclease. Nucleic Acids Res. 37, 54055419.
  • Guo, J., Gaj, T. & Barbas, C. F. 3rd 2010. Directed evolution of an enhanced and highly efficient FokI cleavage domain for zinc finger nucleases. J. Mol. Biol. 400, 96107.
  • Gupta, A., Hall, V. L., Kok, F. O., Shin, M., McNulty, J. C., Lawson, N. D. & Wolfe, S. A. 2013. Targeted chromosomal deletions and inversions in zebrafish. Genome Res. 23, 10081017.
  • Guschin, D. Y., Waite, A. J., Katibah, G. E., Miller, J. C., Holmes, M. C. & Rebar, E. J. 2010. A rapid and general assay for monitoring endogenous gene modification. Methods Mol. Biol. 649, 247256.
  • Hauschild, J., Petersen, B., Santiago, Y., Queisser, A. L., Carnwath, J. W., Lucas-Hahn, A., Zhang, L., Meng, X., Gregory, P. D., Schwinzer, R., Cost, G. J. & Niemann, H. 2011. Efficient generation of a biallelic knockout in pigs using zinc-finger nucleases. Proc. Natl Acad. Sci. USA 108, 1201312017.
  • Hayashi, T., Sakamoto, K., Sakuma, T., Yokotani, N., Inoue, T., Kawaguchi, E., Agata, K., Yamamoto, T. & Takeuchi, T. 2013. TALENs efficiently disrupt the target gene in Iberian ribbed newts (Pleurodeles waltl), an experimental model animal for regeneration. Dev. Growth Differ. 56, 115121.
  • Heigwer, F., Kerr, G., Walther, N., Glaeser, K., Pelz, O., Breinig, M. & Boutros, M. 2013. E-TALEN: a web tool to design TALENs for genome engineering. Nucleic Acids Res. 41, e190.
  • Hisano, Y., Ota, S., Arakawa, K., Muraki, M., Kono, N., Oshita, K., Sakuma, T., Tomita, M., Yamamoto, T., Okada, Y. & Kawahara, A. 2013. Quantitative assay for TALEN activity at endogenous genomic loci. Biol. Open 2, 363367.
  • Hockemeyer, D., Soldner, F., Beard, C., Gao, Q., Mitalipova, M., Dekelver, R. C., Katibah, G. E., Amora, R., Boydston, E. A., Zeitler, B., Meng, X., Miller, J. C., Zhang, L., Rebar, E. J., Gregory, P. D., Urnov, F. D. & Jaenisch, R. 2009. Efficient targeting of expressed and silent genes in human ESCs and iPSCs using zinc-finger nucleases. Nat. Biotechnol. 27, 851857.
  • Hockemeyer, D., Wang, H., Kiani, S., Lai, C. S., Gao, Q., Cassady, J. P., Cost, G. J., Zhang, L., Santiago, Y., Miller, J. C., Zeitler, B., Cherone, J. M., Meng, X., Hinkley, S. J., Rebar, E. J., Gregory, P. D., Urnov, F. D. & Jaenisch, R. 2011. Genetic engineering of human pluripotent cells using TALE nucleases. Nat. Biotechnol. 29, 731734.
  • Holt, N., Wang, J., Kim, K., Friedman, G., Wang, X., Taupin, V., Crooks, G. M., Kohn, D. B., Gregory, P. D., Holmes, M. C. & Cannon, P. M. 2010. Human hematopoietic stem/progenitor cells modified by zinc-finger nuclease targeted to CCR5 control HIV-1 in vivo. Nat. Biotechnol. 28, 839847.
  • Hosoi, S., Sakuma, T., Sakamoto, N. & Yamamoto, T. 2013. Targeted mutagenesis in sea urchin embryos using TALENs. Dev. Growth Differ. 56, 9297.
  • Hou, Z., Zhang, Y., Propson, N. E., Howden, S. E., Chu, L. F., Sontheimer, E. J. & Thomson, J. A. 2013. Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis. Proc. Natl Acad. Sci. USA 110, 1564415649.
  • Hsu, P. D., Scott, D. A., Weinstein, J. A., Ran, F. A., Konermann, S., Agarwala, V., Li, Y., Fine, E. J., Wu, X., Shalem, O., Cradick, T. J., Marraffini, L. A., Bao, G. & Zhang, F. 2013. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat. Biotechnol. 31, 827832.
  • Hwang, W. Y., Fu, Y., Reyon, D., Maeder, M. L., Kaini, P., Sander, J. D., Joung, J. K., Peterson, R. T. & Yeh, J. R. 2013. Heritable and precise zebrafish genome editing using a CRISPR-Cas system. PLoS ONE 8, e68708.
  • Jao, L. E., Wente, S. R. & Chen, W. 2013. Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system. Proc. Natl Acad. Sci. USA 110, 1390413909.
  • Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A. & Charpentier, E. 2012. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816821.
  • Jones, J. M. & Meisler, M. H. 2013. Modeling human epilepsy by TALEN targeting of mouse sodium channel Scn8a. Genesis (in press, doi: 10.1002/dvg.22731)
  • Joung, J. K. & Sander, J. D. 2013. TALENs: a widely applicable technology for targeted genome editing. Nat. Rev. Mol. Cell Biol. 14, 4955.
  • Kawai, N., Ochiai, H., Sakuma, T., Yamada, L., Sawada, H., Yamamoto, T. & Sasakura, Y. 2012. Efficient targeted mutagenesis of the chordate Ciona intestinalis genome with zinc-finger nucleases. Dev. Growth Differ. 54, 535545.
  • Kim, H., Um, E., Cho, S. R., Jung, C., Kim, H. & Kim, J. S. 2011. Surrogate reporters for enrichment of cells with nuclease-induced mutations. Nat. Methods 8, 941943.
  • Kim, E., Kim, S., Kim, D. H., Choi, B. S., Choi, I. Y. & Kim, J. S. 2012. Precision genome engineering with programmable DNA-nicking enzymes. Genome Res. 22, 13271333.
  • Kim, Y. G., Cha, J. & Chandrasegaran, S. 1996. Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proc. Natl Acad. Sci. USA 93, 11561160.
  • Kleinstiver, B. P., Wolfs, J. M., Kolaczyk, T., Roberts, A. K., Hu, S. X. & Edgell, D. R. 2012. Monomeric site-specific nucleases for genome editing. Proc. Natl Acad. Sci. USA 109, 80618066.
  • Komiyama, M. 2013. Cut-and-Paste of DNA Using an Artificial Restriction DNA Cutter. Int. J. Mol. Sci. 14, 33433357.
  • Konermann, S., Brigham, M. D., Trevino, A. E., Hsu, P. D., Heidenreich, M., Cong, L., Platt, R. J., Scott, D. A., Church, G. M. & Zhang, F. 2013. Optical control of mammalian endogenous transcription and epigenetic states. Nature 500, 472476.
  • Lancaster, M. A., Renner, M., Martin, C.-A., Wenzel, D., Bicknell, L. S., Hurles, M. E., Homfray, T., Penninger, J. M., Jackson, A. P. & Knoblich, J. A. 2013. Cerebral organoids model human brain development and microcephaly. Nature 501, 373379.
  • Lee, H. J., Kim, E. & Kim, J. S. 2010. Targeted chromosomal deletions in human cells using zinc finger nucleases. Genome Res. 20, 8189.
  • Lee, H. J., Kweon, J., Kim, E., Kim, S. & Kim, J. S. 2012. Targeted chromosomal duplications and inversions in the human genome using zinc finger nucleases. Genome Res. 22, 539548.
  • Li, L., Piatek, M. J., Atef, A., Piatek, A., Wibowo, A., Fang, X., Sabir, J. S., Zhu, J. K. & Mahfouz, M. M. 2012. Rapid and highly efficient construction of TALE-based transcriptional regulators and nucleases for genome modification. Plant Mol. Biol. 78, 407416.
  • Li, W., Teng, F., Li, T. & Zhou, Q. 2013a. Simultaneous generation and germline transmission of multiple gene mutations in rat using CRISPR-Cas systems. Nat. Biotechnol. 31, 684686.
  • Li, X., Burnight, E. R., Cooney, A. L., Malani, N., Brady, T., Sander, J. D., Staber, J., Wheelan, S. J., Joung, J. K., McCray, P. B. Jr, Bushman, F. D., Sinn, P. L. & Craig, N. L. 2013b. piggyBac transposase tools for genome engineering. Proc. Natl Acad. Sci. USA 110, E2279E2287.
  • Liu, P. Q., Tan, S., Mendel, M. C., Murrills, R. J., Bhat, B. M., Schlag, B., Samuel, R., Matteo, J. J., de la Rosa, R., Howes, K., Reik, A., Case, C. C., Bex, F. J., Young, K. & Gregory, P. D. 2005. Isogenic human cell lines for drug discovery: regulation of target gene expression by engineered zinc-finger protein transcription factors. J. Biomol. Screen. 10, 304313.
  • Liu, J., Li, C., Yu, Z., Huang, P., Wu, H., Wei, C., Zhu, N., Shen, Y., Chen, Y., Zhang, B., Deng, W. M. & Jiao, R. 2012. Efficient and specific modifications of the Drosophila genome by means of an easy TALEN strategy. J. Genet. Genomics 39, 209215.
  • Lo, T. W., Pickle, C. S., Lin, S., Ralston, E. J., Gurling, M., Schartner, C. M., Bian, Q., Doudna, J. A. & Meyer, B. J. 2013. Precise and heritable genome editing in evolutionarily diverse nematodes using TALENs and CRISPR/Cas9 to engineer insertions and deletions. Genetics 195, 331348.
  • Ma, S., Zhang, S., Wang, F., Liu, Y., Liu, Y., Xu, H., Liu, C., Lin, Y., Zhao, P. & Xia, Q. 2012. Highly efficient and specific genome editing in silkworm using custom TALENs. PLoS ONE 7, e45035.
  • Maeder, M. L., Thibodeau-Beganny, S., Sander, J. D., Voytas, D. F. & Joung, J. K. 2009. Oligomerized pool engineering (OPEN): an ‘open-source’ protocol for making customized zinc-finger arrays. Nat. Protoc. 4, 14711501.
  • Maeder, M. L., Linder, S. J., Reyon, D., Angstman, J. F., Fu, Y., Sander, J. D. & Joung, J. K. 2013. Robust, synergistic regulation of human gene expression using TALE activators. Nat. Methods 10, 243245.
  • Mali, P., Yang, L., Esvelt, K. M., Aach, J., Guell, M., DiCarlo, J. E., Norville, J. E. & Church, G. M. 2013a. RNA-guided human genome engineering via Cas9. Science 339, 823826.
  • Mali, P., Aach, J., Stranges, P. B., Esvelt, K. M., Moosburner, M., Kosuri, S., Yang, L. & Church, G. M. 2013b. CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat. Biotechnol. 31, 833838.
  • Mashimo, T., Takizawa, A., Voigt, B., Yoshimi, K., Hiai, H., Kuramoto, T. & Serikawa, T. 2010. Generation of knockout rats with X-linked severe combined immunodeficiency (X-SCID) using zinc-finger nucleases. PLoS ONE 5, e8870.
  • Mashimo, T., Kaneko, T., Sakuma, T., Kobayashi, J., Kunihiro, Y., Voigt, B., Yamamoto, T. & Serikawa, T. 2013. Efficient gene targeting by TAL effector nucleases coinjected with exonucleases in zygotes. Sci. Rep. 3, 1253.
  • Meng, X., Noyes, M. B., Zhu, L. J., Lawson, N. D. & Wolfe, S. A. 2008. Targeted gene inactivation in zebrafish using engineered zinc-finger nucleases. Nat. Biotechnol. 26, 695701.
  • Menoret, S., Fontaniere, S., Jantz, D., Tesson, L., Thinard, R., Remy, S., Usal, C., Ouisse, L. H., Fraichard, A. & Anegon, I. 2013. Generation of Rag1-knockout immunodeficient rats and mice using engineered meganucleases. FASEB J. 27, 703711.
  • Mercer, A. C., Gaj, T., Fuller, R. P. & Barbas, C. F. 3rd 2012. Chimeric TALE recombinases with programmable DNA sequence specificity. Nucleic Acids Res. 40, 1116311172.
  • Merlin, C., Beaver, L. E., Taylor, O. R., Wolfe, S. A. & Reppert, S. M. 2013. Efficient targeted mutagenesis in the monarch butterfly using zinc-finger nucleases. Genome Res. 23, 159168.
  • Meyer, M., de Angelis, M. H., Wurst, W. & Kühn, R. 2010. Gene targeting by homologous recombination in mouse zygotes mediated by zinc-finger nucleases. Proc. Natl Acad. Sci. USA 107, 1502215026.
  • Meyer, M., Ortiz, O., Hrabé de Angelis, M., Wurst, W. & Kühn, R. 2012. Modeling disease mutations by gene targeting in one-cell mouse embryos. Proc. Natl Acad. Sci. USA 109, 93549359.
  • Miller, J. C., Holmes, M. C., Wang, J., Guschin, D. Y., Lee, Y. L., Rupniewski, I., Beausejour, C. M., Waite, A. J., Wang, N. S., Kim, K. A., Gregory, P. D., Pabo, C. O. & Rebar, E. J. 2007. An improved zinc-finger nuclease architecture for highly specific genome editing. Nat. Biotechnol. 25, 778785.
  • Minczuk, M., Papworth, M. A., Miller, J. C., Murphy, M. P. & Klug, A. 2008. Development of a single-chain, quasi-dimeric zinc-finger nuclease for the selective degradation of mutated human mitochondrial DNA. Nucleic Acids Res. 36, 39263938.
  • Mino, T., Aoyama, Y. & Sera, T. 2009. Efficient double-stranded DNA cleavage by artificial zinc-finger nucleases composed of one zinc-finger protein and a single-chain FokI dimer. J. Biotechnol. 140, 156161.
  • Mori, T., Kagatsume, I., Shinomiya, K., Aoyama, Y. & Sera, T. 2009. Sandwiched zinc-finger nucleases harboring a single-chain FokI dimer as a DNA-cleavage domain. Biochem. Biophys. Res. Commun. 390, 694697.
  • Moscou, M. J. & Bogdanove, A. J. 2009. A simple cipher governs DNA recognition by TAL effectors. Science 326, 1501.
  • Munoz, I. G., Prieto, J., Subramanian, S., Coloma, J., Redondo, P., Villate, M., Merino, N., Marenchino, M., D'Abramo, M., Gervasio, F. L., Grizot, S., Daboussi, F., Smith, J., Chion-Sotinel, I., Paques, F., Duchateau, P., Alibes, A., Stricher, F., Serrano, L., Blanco, F. J. & Montoya, G. 2011. Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus. Nucleic Acids Res. 39, 729743.
  • Mussolino, C. & Cathomen, T. 2012. TALE nucleases: tailored genome engineering made easy. Curr. Opin. Biotechnol. 23, 644650.
  • Nakagawa, Y., Yamamoto, T., Suzuki, K., Araki, K., Takeda, N., Ohmuraya, M. & Sakuma, T. 2013. Screening methods to identify TALEN-mediated knockout mice. Exp. Anim. 63, 7984 (in press).
  • Neff, K. L., Argue, D. P., Ma, A. C., Lee, H. B., Clark, K. J. & Ekker, S. C. 2013. Mojo Hand, a TALEN design tool for genome editing applications. BMC Bioinformatics 14, 1.
  • Ochiai, H., Fujita, K., Suzuki, K., Nishikawa, M., Shibata, T., Sakamoto, N. & Yamamoto, T. 2010. Targeted mutagenesis in the sea urchin embryo using zinc-finger nucleases. Genes Cells 15, 875885.
  • Ochiai, H., Sakamoto, N., Fujita, K., Nishikawa, M., Suzuki, K., Matsuura, S., Miyamoto, T., Sakuma, T., Shibata, T. & Yamamoto, T. 2012. Zinc-finger nuclease-mediated targeted insertion of reporter genes for quantitative imaging of gene expression in sea urchin embryos. Proc. Natl Acad. Sci. USA 109, 1091510920.
  • Ousterout, D. G., Perez-Pinera, P., Thakore, P. I., Kabadi, A. M., Brown, M. T., Qin, X., Fedrigo, O., Mouly, V., Tremblay, J. P. & Gersbach, C. A. 2013. Reading frame correction by targeted genome editing restores dystrophin expression in cells from duchenne muscular dystrophy patients. Mol. Ther. 21, 17181726.
  • Ota, S., Hisano, Y., Muraki, M., Hoshijima, K., Dahlem, T. J., Grunwald, D. J., Okada, Y. & Kawahara, A. 2013. Efficient identification of TALEN-mediated genome modifications using heteroduplex mobility assays. Genes Cells 18, 450458.
  • Owens, J. B., Mauro, D., Stoytchev, I., Bhakta, M. S., Kim, M. S., Segal, D. J. & Moisyadi, S. 2013. Transcription activator like effector (TALE)-directed piggyBac transposition in human cells. Nucleic Acids Res. 41, 91979207.
  • Pattanayak, V., Lin, S., Guilinger, J. P., Ma, E., Doudna, J. A. & Liu, D. R. 2013. High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat. Biotechnol. 31, 839843.
  • Pauwels, K., Podevin, N., Breyer, D., Carroll, D. & Herman, P. 2013. Engineering nucleases for gene targeting: safety and regulatory considerations. N. Biotechnol. 31, 1827.
  • 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. & June, C. H. 2008. Establishment of HIV-1 resistance in CD4 +  T cells by genome editing using zinc-finger nucleases. Nat. Biotechnol. 26, 808816.
  • Perez-Pinera, P., Ousterout, D. G., Brunger, J. M., Farin, A. M., Glass, K. A., Guilak, F., Crawford, G. E., Hartemink, A. J. & Gersbach, C. A. 2013. Synergistic and tunable human gene activation by combinations of synthetic transcription factors. Nat. Methods 10, 239242.
  • Piganeau, M., Ghezraoui, H., De Cian, A., Guittat, L., Tomishima, M., Perrouault, L., Rene, O., Katibah, G. E., Zhang, L., Holmes, M. C., Doyon, Y., Concordet, J. P., Giovannangeli, C., Jasin, M. & Brunet, E. 2013. Cancer translocations in human cells induced by zinc finger and TALE nucleases. Genome Res. 23, 11821193.
  • Pillay, L. M., Selland, L. G., Fleisch, V. C., Leighton, P. L., Cheng, C. S., Famulski, J. K., Ritzel, R. G., March, L. D., Wang, H., Allison, W. T. & Waskiewicz, A. J. 2013. Evaluating the mutagenic activity of targeted endonucleases containing a Sharkey FokI cleavage domain variant in zebrafish. Zebrafish 10, 353364.
  • Podevin, N., Davies, H. V., Hartung, F., Nogue, F. & Casacuberta, J. M. 2013. Site-directed nucleases: a paradigm shift in predictable, knowledge-based plant breeding. Trends Biotechnol. 31, 375383.
  • Qi, L. S., Larson, M. H., Gilbert, L. A., Doudna, J. A., Weissman, J. S., Arkin, A. P. & Lim, W. A. 2013. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152, 11731183.
  • Ramalingam, S., Kandavelou, K., Rajenderan, R. & Chandrasegaran, S. 2011. Creating designed zinc-finger nucleases with minimal cytotoxicity. J. Mol. Biol. 405, 630641.
  • Ramirez, C. L., Foley, J. E., Wright, D. A., Muller-Lerch, F., Rahman, S. H., Cornu, T. I., Winfrey, R. J., Sander, J. D., Fu, F., Townsend, J. A., Cathomen, T., Voytas, D. F. & Joung, J. K. 2008. Unexpected failure rates for modular assembly of engineered zinc fingers. Nat. Methods 5, 374375.
  • Ramirez, C. L., Certo, M. T., Mussolino, C., Goodwin, M. J., Cradick, T. J., McCaffrey, A. P., Cathomen, T., Scharenberg, A. M. & Joung, J. K. 2012. Engineered zinc finger nickases induce homology-directed repair with reduced mutagenic effects. Nucleic Acids Res. 40, 55605568.
  • Ran, F. A., Hsu, P. D., Lin, C. Y., Gootenberg, J. S., Konermann, S., Trevino, A. E., Scott, D. A., Inoue, A., Matoba, S., Zhang, Y. & Zhang, F. 2013a. Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity. Cell 154, 13801389.
  • Ran, F. A., Hsu, P. D., Wright, J., Agarwala, V., Scott, D. A. & Zhang, F. 2013b. Genome engineering using the CRISPR-Cas9 system. Nat. Protoc. 8, 22812308.
  • Raya, A., Rodríguez-Pizà, I., Navarro, S., Richaud-Patin, Y., Guenechea, G., Sánchez-Danés, A., Consiglio, A., Bueren, J. & Izpisúa Belmonte, J. C. 2010. A protocol describing the genetic correction of somatic human cells and subsequent generation of iPS cells. Nat. Protoc. 5, 647660.
  • Reyon, D., Tsai, S. Q., Khayter, C., Foden, J. A., Sander, J. D. & Joung, J. K. 2012. FLASH assembly of TALENs for high-throughput genome editing. Nat. Biotechnol. 30, 460465.
  • Sakane, Y., Sakuma, T., Kashiwagi, K., Kashiwagi, A., Yamamoto, T. & Suzuki, K. 2013. Targeted mutagenesis of multiple and paralogous genes in Xenopus laevis using two pairs of transcription activator-like effector nucleases. Dev. Growth Differ. 56, 108114.
  • Sakuma, T., Hosoi, S., Woltjen, K., Suzuki, K., Kashiwagi, K., Wada, H., Ochiai, H., Miyamoto, T., Kawai, N., Sasakura, Y., Matsuura, S., Okada, Y., Kawahara, A., Hayashi, S. & Yamamoto, T. 2013a. Efficient TALEN construction and evaluation methods for human cell and animal applications. Genes Cells 18, 315326.
  • Sakuma, T., Ochiai, H., Kaneko, T., Mashimo, T., Tokumasu, D., Sakane, Y., Suzuki, K., Miyamoto, T., Sakamoto, N., Matsuura, S. & Yamamoto, T. 2013b. Repeating pattern of non-RVD variations in DNA-binding modules enhances TALEN activity. Sci. Rep. 3, 3379.
  • Sanchez, J. P., Ullman, C., Moore, M., Choo, Y. & Chua, N. H. 2002. Regulation of gene expression in Arabidopsis thaliana by artificial zinc finger chimeras. Plant Cell Physiol. 43, 14651472.
  • Sander, J. D., Maeder, M. L., Reyon, D., Voytas, D. F., Joung, J. K. & Dobbs, D. 2010. ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool. Nucleic Acids Res. 38, W462W468.
  • Smidler, A. L., Terenzi, O., Soichot, J., Levashina, E. A. & Marois, E. 2013. Targeted mutagenesis in the malaria mosquito using TALE nucleases. PLoS ONE 8, e74511.
  • Stanford, W. L., Cohn, J. B. & Cordes, S. P. 2001. Gene-trap mutagenesis: past, present and beyond. Nat. Rev. Genet. 2, 756768.
  • Sugi, T., Sakuma, T., Ohtani, T. & Yamamoto, T. 2013. Versatile strategy for isolating TALEN-mediated knockout mutants in Caenorhabditis elegans. Dev. Growth Differ. 56, 7885.
  • Sung, Y. H., Baek, I. J., Kim, D. H., Jeon, J., Lee, J., Lee, K., Jeong, D., Kim, J. S. & Lee, H. W. 2013. Knockout mice created by TALEN-mediated gene targeting. Nat. Biotechnol. 31, 2324.
  • Suzuki, K. T., Isoyama, Y., Kashiwagi, K., Sakuma, T., Ochiai, H., Sakamoto, N., Furuno, N., Kashiwagi, A. & Yamamoto, T. 2013. High efficiency TALENs enable F0 functional analysis by targeted gene disruption in Xenopus laevis embryos. Biol. Open 2, 448452.
  • Tan, W., Carlson, D. F., Lancto, C. A., Garbe, J. R., Webster, D. A., Hackett, P. B. & Fahrenkrug, S. C. 2013. Efficient nonmeiotic allele introgression in livestock using custom endonucleases. Proc. Natl Acad. Sci. USA 110, 1652616531.
  • Tesson, L., Usal, C., Menoret, S., Leung, E., Niles, B. J., Remy, S., Santiago, Y., Vincent, A. I., Meng, X., Zhang, L., Gregory, P. D., Anegon, I. & Cost, G. J. 2011. Knockout rats generated by embryo microinjection of TALENs. Nat. Biotechnol. 29, 695696.
  • Tiscornia, G., Vivas, E. L. & Belmonte, J. C. I. 2011. Diseases in a dish: modeling human genetic disorders using induced pluripotent cells. Nat. Med. 17, 15701576.
  • Toscano, M. G., Anderson, P., Muñoz, P., Lucena, G., Cobo, M., Benabdellah, K., Gregory, P. D., Holmes, M. C. & Martin, F. 2013. Use of zinc-finger nucleases to knock out the WAS gene in K562 cells: a human cellular model for Wiskott-Aldrich syndrome. Dis. Model Mech. 6, 544554.
  • Treen, N., Yoshida, K., Sakuma, T., Sasaki, H., Kawai, N., Yamamoto, T. & Sasakura, Y. 2013. Tissue-specific and ubiquitous gene knockouts by TALEN electroporation provide new approaches to investigating gene function in Ciona. Development DOI: 10.1242/dev.099572.
  • Tremblay, J. P., Chapdelaine, P., Coulombe, Z. & Rousseau, J. 2012. Transcription activator-like effector proteins induce the expression of the frataxin gene. Hum. Gene Ther. 23, 883890.
  • Urnov, F. D., Rebar, E. J., Holmes, M. C., Zhang, H. S. & Gregory, P. D. 2010. Genome editing with engineered zinc finger nucleases. Nat. Rev. Genet. 11, 636646.
  • 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. & Holmes, M. C. 2005. Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature 435, 646651.
  • Voytas, D. F. 2013. Plant genome engineering with sequence-specific nucleases. Annu. Rev. Plant Biol. 64, 327350.
  • Wang, H., Yang, H., Shivalila, C. S., Dawlaty, M. M., Cheng, A. W., Zhang, F. & Jaenisch, R. 2013. One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell 153, 910918.
  • Wang, J., Friedman, G., Doyon, Y., Wang, N. S., Li, C. J., Miller, J. C., Hua, K. L., Yan, J. J., Babiarz, J. E., Gregory, P. D. & Holmes, M. C. 2012. Targeted gene addition to a predetermined site in the human genome using a ZFN-based nicking enzyme. Genome Res. 22, 13161326.
  • Watanabe, T., Ochiai, H., Sakuma, T., Horch, H. W., Hamaguchi, N., Nakamura, T., Bando, T., Ohuchi, H., Yamamoto, T., Noji, S. & Mito, T. 2012. Non-transgenic genome modifications in a hemimetabolous insect using zinc-finger and TAL effector nucleases. Nat. Commun. 3, 1017.
  • Wefers, B., Meyer, M., Ortiz, O., Hrabé de Angelis, M., Hansen, J., Wurst, W. & Kühn, R. 2013. Direct production of mouse disease models by embryo microinjection of TALENs and oligodeoxynucleotides. Proc. Natl Acad. Sci. USA 110, 37823787.
  • Wood, A. J., Lo, T. W., Zeitler, B., Pickle, C. S., Ralston, E. J., Lee, A. H., Amora, R., Miller, J. C., Leung, E., Meng, X., Zhang, L., Rebar, E. J., Gregory, P. D., Urnov, F. D. & Meyer, B. J. 2011. Targeted genome editing across species using ZFNs and TALENs. Science 333, 307.
  • 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. & Joung, J. K. 2006. Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly. Nat. Protoc. 1, 16371652.
  • Xiao, A., Wu, Y., Yang, Z., Hu, Y., Wang, W., Zhang, Y., Kong, L., Gao, G., Zhu, Z., Lin, S. & Zhang, B. 2013a. EENdb: a database and knowledge base of ZFNs and TALENs for endonuclease engineering. Nucleic Acids Res. 41, D415D422.
  • Xiao, A., Wang, Z., Hu, Y., Wu, Y., Luo, Z., Yang, Z., Zu, Y., Li, W., Huang, P., Tong, X., Zhu, Z., Lin, S. & Zhang, B. 2013b. Chromosomal deletions and inversions mediated by TALENs and CRISPR/Cas in zebrafish. Nucleic Acids Res. 41, e141.
  • Yaghmai, R. & Cutting, G. R. 2002. Optimized regulation of gene expression using artificial transcription factors. Mol. Ther. 5, 685694.
  • Yang, H., Wang, H., Shivalila, C. S., Cheng, A. W., Shi, L. & Jaenisch, R. 2013. One-step generation of mice carrying reporter and conditional alleles by CRISPR/Cas-mediated genome engineering. Cell 154, 13701379.
  • Young, J. J., Cherone, J. M., Doyon, Y., Ankoudinova, I., Faraji, F. M., Lee, A. H., Ngo, C., Guschin, D. Y., Paschon, D. E., Miller, J. C., Zhang, L., Rebar, E. J., Gregory, P. D., Urnov, F. D., Harland, R. M. & Zeitler, B. 2011. Efficient targeted gene disruption in the soma and germ line of the frog Xenopus tropicalis using engineered zinc-finger nucleases. Proc. Natl Acad. Sci. USA 108, 70527057.
  • Yusa, K., Rad, R., Takeda, J. & Bradley, A. 2009. Generation of transgene-free induced pluripotent mouse stem cells by the piggyBac transposon. Nat. Methods 6, 363369.
  • Zu, Y., Tong, X., Wang, Z., Liu, D., Pan, R., Li, Z., Hu, Y., Luo, Z., Huang, P., Wu, Q., Zhu, Z., Zhang, B. & Lin, S. 2013. TALEN-mediated precise genome modification by homologous recombination in zebrafish. Nat. Methods 10, 329331.