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Review Article

Molecular scissors for in situ cellular repair

, &
Pages 207-221 | Received 15 Sep 2011, Accepted 19 Dec 2011, Published online: 28 Jan 2012

References

  • Alwin S, Gere MB, Guhl E, Effertz K, Barbas CF 3rd, Segal DJ, Weitzman MD, Cathomen T. 2005. Custom zinc-finger nucleases for use in human cells. Mol Ther 12:610–617.
  • Arnaudeau-Bégard C, Brellier F, Chevallier-Lagente O, Hoeijmakers J, Bernerd F, Sarasin A, Magnaldo T. 2003. Genetic correction of DNA repair-deficient/cancer-prone xeroderma pigmentosum group C keratinocytes. Hum Gene Ther 14:983–996.
  • Arnould S, Chames P, Perez C, Lacroix E, Duclert A, Epinat JC, Stricher F, Petit AS, Patin A, Guillier S, Rolland S, Prieto J, Blanco FJ, Bravo J, Montoya G, Serrano L, Duchateau P, Pâques F. 2006. Engineering of large numbers of highly specific homing endonucleases that induce recombination on novel DNA targets. J Mol Biol 355:443–458.
  • Arnould S, Delenda C, Grizot S, Desseaux C, Pâques F, Silva GH, Smith J. 2011. The I-CreI meganuclease and its engineered derivatives: applications from cell modification to gene therapy. Protein Eng Des Sel 24:27–31.
  • Arnould S, Perez C, Cabaniols JP, Smith J, Gouble A, Grizot S, Epinat JC, Duclert A, Duchateau P, Pâques F. 2007. Engineered I-CreI derivatives cleaving sequences from the human XPC gene can induce highly efficient gene correction in mammalian cells. J Mol Biol 371:49–65.
  • Ashworth J, Havranek JJ, Duarte CM, Sussman D, Monnat RJ Jr, Stoddard BL, Baker D. 2006. Computational redesign of endonuclease DNA binding and cleavage specificity. Nature 441:656–659.
  • Ashworth J, Taylor GK, Havranek JJ, Quadri SA, Stoddard BL, Baker D. 2010. Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs. Nucleic Acids Res 38:5601–5608.
  • Barzel A, Privman E, Peeri M, Naor A, Shachar E, Burstein D, Lazary R, Gophna U, Pupko T, Kupiec M. 2011. Native homing endonucleases can target conserved genes in humans and in animal models. Nucleic Acids Res 39:6646–6659.
  • Beerli RR, Dreier B, Barbas CF 3rd. 2000. Positive and negative regulation of endogenous genes by designed transcription factors. Proc Natl Acad Sci USA 97:1495–1500.
  • Beerli RR, Segal DJ, Dreier B, Barbas CF 3rd. 1998. Toward controlling gene expression at will: specific regulation of the erbB-2/HER-2 promoter by using polydactyl zinc finger proteins constructed from modular building blocks. Proc Natl Acad Sci USA 95:14628–14633.
  • Bitinaite J, Wah DA, Aggarwal AK, Schildkraut I. 1998. FokI dimerization is required for DNA cleavage. Proc Natl Acad Sci USA 95:10570–10575.
  • 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 326:1509–1512.
  • Boulton SJ, Jackson SP. 1996. Saccharomyces cerevisiae Ku70 potentiates illegitimate DNA double-strand break repair and serves as a barrier to error-prone DNA repair pathways. EMBO J 15:5093–5103.
  • Cabaniols JP, Ouvry C, Lamamy V, Fery I, Craplet ML, Moulharat N, Guenin SP, Bedut S, Nosjean O, Ferry G, Devavry S, Jacqmarcq C, Lebuhotel C, Mathis L, Delenda C, Boutin JA, Duchâteau P, Cogé F, Pâques F. 2010. Meganuclease-driven targeted integration in CHO-K1 cells for the fast generation of HTS-compatible cell-based assays. J Biomol Screen 15:956–967.
  • Carroll D. 2008. Progress and prospects: zinc-finger nucleases as gene therapy agents. Gene Ther 15:1463–1468.
  • Carroll D. 2011a. Genome engineering with zinc-finger nucleases. Genetics 188:773–782.
  • Carroll D. 2011b. Zinc-finger nucleases: a panoramic view. Curr Gene Ther 11:2–10.
  • Certo MT, Ryu BY, Annis JE, Garibov M, Jarjour J, Rawlings DJ, Scharenberg AM. 2011. Tracking genome engineering outcome at individual DNA breakpoints. Nat Methods 8:671–676.
  • Chapdelaine P, Pichavant C, Rousseau J, Pâques F, Tremblay JP. 2010. Meganucleases can restore the reading frame of a mutated dystrophin. Gene Ther 17:846–858.
  • Chen Z, Wen F, Sun N, Zhao H. 2009. Directed evolution of homing endonuclease I-SceI with altered sequence specificity. Protein Eng Des Sel 22:249–256.
  • Chevalier B, Sussman D, Otis C, Noël AJ, Turmel M, Lemieux C, Stephens K, Monnat RJ Jr, Stoddard BL. 2004. Metal-dependent DNA cleavage mechanism of the I-CreI LAGLIDADG homing endonuclease. Biochemistry 43:14015–14026.
  • Chevalier BS, Kortemme T, Chadsey MS, Baker D, Monnat RJ, Stoddard BL. 2002. Design, activity, and structure of a highly specific artificial endonuclease. Mol Cell 10:895–905.
  • Chevalier BS, Stoddard BL. 2001. Homing endonucleases: structural and functional insight into the catalysts of intron/intein mobility. Nucleic Acids Res 29:3757–3774.
  • Choulika A, Perrin A, Dujon B, Nicolas JF. 1995. Induction of homologous recombination in mammalian chromosomes by using the I-SceI system of Saccharomyces cerevisiae. Mol Cell Biol 15:1968–1973.
  • Christian M, Cermak T, Doyle EL, Schmidt C, Zhang F, Hummel A, Bogdanove AJ, Voytas DF. 2010. Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186:757–761.
  • Cleaver JE, Thompson LH, Richardson AS, States JC. 1999. A summary of mutations in the UV-sensitive disorders: xeroderma pigmentosum, Cockayne syndrome, and trichothiodystrophy. Hum Mutat 14:9–22.
  • Cohen-Tannoudji M, Robine S, Choulika A, Pinto D, El Marjou F, Babinet C, Louvard D, Jaisser F. 1998. I-SceI-induced gene replacement at a natural locus in embryonic stem cells. Mol Cell Biol 18:1444–1448.
  • Copelan EA. 2006. Hematopoietic stem-cell transplantation. N Engl J Med 354:1813–1826.
  • Cutler C, Antin JH. 2001. Peripheral blood stem cells for allogeneic transplantation: a review. Stem Cells 19:108–117.
  • Delacôte F, Lopez BS. 2008. Importance of the cell cycle phase for the choice of the appropriate DSB repair pathway, for genome stability maintenance: the trans-S double-strand break repair model. Cell Cycle 7:33–38.
  • Donoho G, Jasin M, Berg P. 1998. Analysis of gene targeting and intrachromosomal homologous recombination stimulated by genomic double-strand breaks in mouse embryonic stem cells. Mol Cell Biol 18:4070–4078.
  • Doyon JB, Pattanayak V, Meyer CB, Liu DR. 2006. Directed evolution and substrate specificity profile of homing endonuclease I-SceI. J Am Chem Soc 128:2477–2484.
  • Elliott B, Richardson C, Winderbaum J, Nickoloff JA, Jasin M. 1998. Gene conversion tracts from double-strand break repair in mammalian cells. Mol Cell Biol 18:93–101.
  • Epinat JC, Arnould S, Chames P, Rochaix P, Desfontaines D, Puzin C, Patin A, Zanghellini A, Pâques F, Lacroix E. 2003. A novel engineered meganuclease induces homologous recombination in yeast and mammalian cells. Nucleic Acids Res 31:2952–2962.
  • Fajardo-Sanchez E, Stricher F, Pâques F, Isalan M, Serrano L. 2008. Computer design of obligate heterodimer meganucleases allows efficient cutting of custom DNA sequences. Nucleic Acids Res 36:2163–2173.
  • Gabriel R, Lombardo A, Arens A, Miller JC, Genovese P, Kaeppel C, Nowrouzi A, Bartholomae CC, Wang J, Friedman G, Holmes MC, Gregory PD, Glimm H, Schmidt M, Naldini L, von Kalle C. 2011. An unbiased genome-wide analysis of zinc-finger nuclease specificity. Nat Biotechnol 29:816–823.
  • Gao H, Smith J, Yang M, Jones S, Djukanovic V, Nicholson MG, West A, Bidney D, Falco SC, Jantz D, Lyznik LA. 2010. Heritable targeted mutagenesis in maize using a designed endonuclease. Plant J 61:176–187.
  • Gaspar HB, Cooray S, Gilmour KC, Parsley KL, Adams S, Howe SJ, Al Ghonaium A, Bayford J, Brown L, Davies EG, Kinnon C, Thrasher AJ. 2011. Long-term persistence of a polyclonal T cell repertoire after gene therapy for X-linked severe combined immunodeficiency. Sci Transl Med 3:97ra79.
  • Glover L, McCulloch R, Horn D. 2008. Sequence homology and microhomology dominate chromosomal double-strand break repair in African trypanosomes. Nucleic Acids Res 36:2608–2618.
  • Gouble A, Smith J, Bruneau S, Perez C, Guyot V, Cabaniols JP, Leduc S, Fiette L, Avé P, Micheau B, Duchateau P, Pâques F. 2006. Efficient in toto targeted recombination in mouse liver by meganuclease-induced double-strand break. J Gene Med 8:616–622.
  • Grizot S, Duclert A, Thomas S, Duchateau P, Pâques F. 2011. Context dependence between subdomains in the DNA binding interface of the I-CreI homing endonuclease. Nucleic Acids Res 39:6124–6136.
  • Grizot S, Epinat JC, Thomas S, Duclert A, Rolland S, Pâques F, Duchateau P. 2010. Generation of redesigned homing endonucleases comprising DNA-binding domains derived from two different scaffolds. Nucleic Acids Res 38:2006–2018.
  • Grizot S, Smith J, Prieto J, Daboussi F, Redondo P, Merino N, Villate M, Thomas S, Lemaire L, Montoya G, Blanco FJ, Paques F, Duchateau P. 2009. Efficient targeting of a SCID gene by an engineered single chain homing endonuclease. Nucleic Acids Research.
  • Grosse S, Huot N, Mahiet C, Arnould S, Barradeau S, Clerre DL, Chion-Sotinel I, Jacqmarcq C, Chapellier B, Ergani A, Desseaux C, Cedrone F, Conseiller E, Paques F, Labetoulle M, Smith J. 2011. Meganuclease-mediated inhibition of HSV1 infection in cultured cells. Mol Ther 19:694–702.
  • Gupta A, Meng X, Zhu LJ, Lawson ND, Wolfe SA. 2011. Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleases. Nucleic Acids Res 39:381–392.
  • Hacein-Bey-Abina S, Garrigue A, Wang GP, Soulier J, Lim A, Morillon E, Clappier E, Caccavelli L, Delabesse E, Beldjord K, Asnafi V, Macintyre E, Dal Cortivo L, Radford I, Brousse N, Sigaux F, Moshous D, Hauer J, Borkhardt A, Belohradsky BH, Wintergerst U, Velez MC, Leiva L, Sorensen R, Wulffraat N, Blanche S, Bushman FD, Fischer A, Cavazzana-Calvo M. 2008. Insertional oncogenesis in 4 patients after retrovirus-mediated gene therapy of SCID-X1. J Clin Invest 118:3132–3142.
  • Hacein-Bey-Abina S, von Kalle C, Schmidt M, Le Deist F, Wulffraat N, McIntyre E, Radford I, Villeval JL, Fraser CC, Cavazzana-Calvo M, Fischer A. 2003a. A serious adverse event after successful gene therapy for X-linked severe combined immunodeficiency. N Engl J Med 348:255–256.
  • Hacein-Bey-Abina S, Von Kalle C, Schmidt M, McCormack MP, Wulffraat N, Leboulch P, Lim A, Osborne CS, Pawliuk R, Morillon E, Sorensen R, Forster A, Fraser P, Cohen JI, de Saint Basile G, Alexander I, Wintergerst U, Frebourg T, Aurias A, Stoppa-Lyonnet D, Romana S, Radford-Weiss I, Gross F, Valensi F, Delabesse E, Macintyre E, Sigaux F, Soulier J, Leiva LE, Wissler M, Prinz C, Rabbitts TH, Le Deist F, Fischer A, Cavazzana-Calvo M. 2003b. LMO2-associated clonal T cell proliferation in two patients after gene therapy for SCID-X1. Science 302:415–419.
  • Handel EM, Alwin S, Cathomen T. 2009. Expanding or restricting the target site repertoire of zinc-finger nucleases: the inter-domain linker as a major determinant of target site selectivity. Mol Ther: the journal of the American Society of Gene Therapy 17:104–111.
  • Hockemeyer D, Wang H, Kiani S, Lai CS, Gao Q, Cassady JP, Cost GJ, Zhang L, Santiago Y, Miller JC, Zeitler B, Cherone JM, Meng X, Hinkley SJ, Rebar EJ, Gregory PD, Urnov FD, Jaenisch R. 2011. Genetic engineering of human pluripotent cells using TALE nucleases. Nat Biotechnol 29:731–734.
  • Howe SJ, Mansour MR, Schwarzwaelder K, Bartholomae C, Hubank M, Kempski H, Brugman MH, Pike-Overzet K, Chatters SJ, de Ridder D, Gilmour KC, Adams S, Thornhill SI, Parsley KL, Staal FJ, Gale RE, Linch DC, Bayford J, Brown L, Quaye M, Kinnon C, Ancliff P, Webb DK, Schmidt M, von Kalle C, Gaspar HB, Thrasher AJ. 2008. Insertional mutagenesis combined with acquired somatic mutations causes leukemogenesis following gene therapy of SCID-X1 patients. J Clin Invest 118:3143–3150.
  • Inoue M, Tomizawa K, Matsushita M, Lu YF, Yokoyama T, Yanai H, Takashima A, Kumon H, Matsui H. 2006. p53 protein transduction therapy: successful targeting and inhibition of the growth of the bladder cancer cells. Eur Urol 49:161–168.
  • Johnson RD, Jasin M. 2001. Double-strand-break-induced homologous recombination in mammalian cells. Biochem Soc Trans 29:196–201.
  • Jurica MS, Monnat RJ Jr, Stoddard BL. 1998. DNA recognition and cleavage by the LAGLIDADG homing endonuclease I-CreI. Mol Cell 2:469–476.
  • Kern S, Eichler H, Stoeve J, Klüter H, Bieback K. 2006. Comparative analysis of mesenchymal stem cells from bone marrow, umbilical cord blood, or adipose tissue. Stem Cells 24:1294–1301.
  • Lee GS, Neiditch MB, Salus SS, Roth DB. 2004. RAG proteins shepherd double-strand breaks to a specific pathway, suppressing error-prone repair, but RAG nicking initiates homologous recombination. Cell 117:171–184.
  • Li H, Pellenz S, Ulge U, Stoddard BL, Monnat RJ Jr. 2009. Generation of single-chain LAGLIDADG homing endonucleases from native homodimeric precursor proteins. Nucleic Acids Res 37:1650–1662.
  • Li T, Huang S, Jiang WZ, Wright D, Spalding MH, Weeks DP, Yang B. 2011. TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain. Nucleic Acids Res 39:359–372.
  • Lieber MR. 2010. The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Annu Rev Biochem 79:181–211.
  • Macnab S, Whitehouse A. 2009. Progress and prospects: human artificial chromosomes. Gene Ther 16:1180–1188.
  • Maggert KA, Gong WJ, Golic KG. 2008. Methods for homologous recombination in Drosophila. Methods Mol Biol 420:155–174.
  • Marcaida MJ, Muñoz IG, Blanco FJ, Prieto J, Montoya G. 2010. Homing endonucleases: from basics to therapeutic applications. Cell Mol Life Sci 67:727–748.
  • Marcaida MJ, Prieto J, Redondo P, Nadra AD, Alibés A, Serrano L, Grizot S, Duchateau P, Pâques F, Blanco FJ, Montoya G. 2008. Crystal structure of I-DmoI in complex with its target DNA provides new insights into meganuclease engineering. Proc Natl Acad Sci USA 105:16888–16893.
  • Martins CP, Brown-Swigart L, Evan GI. 2006. Modeling the therapeutic efficacy of p53 restoration in tumors. Cell 127:1323–1334.
  • McConnell Smith A, Takeuchi R, Pellenz S, Davis L, Maizels N, Monnat RJ Jr, Stoddard BL. 2009. Generation of a nicking enzyme that stimulates site-specific gene conversion from the I-AniI LAGLIDADG homing endonuclease. Proc Natl Acad Sci USA 106:5099–5104.
  • Metzger MJ, McConnell-Smith A, Stoddard BL, Miller AD. 2011. Single-strand nicks induce homologous recombination with less toxicity than double-strand breaks using an AAV vector template. Nucleic Acids Res 39:926–935.
  • Michiue H, Tomizawa K, Wei FY, Matsushita M, Lu YF, Ichikawa T, Tamiya T, Date I, Matsui H. 2005. The NH2 terminus of influenza virus hemagglutinin-2 subunit peptides enhances the antitumor potency of polyarginine-mediated p53 protein transduction. J Biol Chem 280:8285–8289.
  • Miller DG, Petek LM, Russell DW. 2003. Human gene targeting by adeno-associated virus vectors is enhanced by DNA double-strand breaks. Mol Cell Biol 23:3550–3557.
  • Miller JC, Tan S, Qiao G, Barlow KA, Wang J, Xia DF, Meng X, Paschon DE, Leung E, Hinkley SJ, Dulay GP, Hua KL, Ankoudinova I, Cost GJ, Urnov FD, Zhang HS, Holmes MC, Zhang L, Gregory PD, Rebar EJ. 2011. A TALE nuclease architecture for efficient genome editing. Nat Biotechnol 29:143–148.
  • Mimitou EP, Symington LS. 2009. Nucleases and helicases take center stage in homologous recombination. Trends Biochem Sci 34:264–272.
  • Moore JK, Haber JE. 1996. Cell cycle and genetic requirements of two pathways of nonhomologous end-joining repair of double-strand breaks in Saccharomyces cerevisiae. Mol Cell Biol 16:2164–2173.
  • Moure CM, Gimble FS, Quiocho FA. 2003. The crystal structure of the gene targeting homing endonuclease I-SceI reveals the origins of its target site specificity. J Mol Biol 334:685–695.
  • Moynahan ME, Jasin M. 1997. Loss of heterozygosity induced by a chromosomal double-strand break. Proc Natl Acad Sci USA 94:8988–8993.
  • Müller-Sieburg CE, Cho RH, Thoman M, Adkins B, Sieburg HB. 2002. Deterministic regulation of hematopoietic stem cell self-renewal and differentiation. Blood 100:1302–1309.
  • Muñoz IG, Prieto J, Subramanian S, Coloma J, Redondo P, Villate M, Merino N, Marenchino M, D’Abramo M, Gervasio FL, Grizot S, Daboussi F, Smith J, Chion-Sotinel I, Pâques F, Duchateau P, Alibés A, Stricher F, Serrano L, Blanco FJ, Montoya G. 2011. Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus. Nucleic Acids Res 39:729–743.
  • Mussolino C, Morbitzer R, Lütge F, Dannemann N, Lahaye T, Cathomen T. 2011. A novel TALE nuclease scaffold enables high genome editing activity in combination with low toxicity. Nucleic Acids Res 39:9283–9293.
  • Niu Y, Tenney K, Li H, Gimble FS. 2008. Engineering variants of the I-SceI homing endonuclease with strand-specific and site-specific DNA-nicking activity. J Mol Biol 382:188–202.
  • Papworth M, Kolasinska P, Minczuk M. 2006. Designer zinc-finger proteins and their applications. Gene 366:27–38.
  • Pâques F, Duchateau P. 2007. Meganucleases and DNA double-strand break-induced recombination: perspectives for gene therapy. Curr Gene Ther 7:49–66.
  • Pattanayak V, Ramirez CL, Joung JK, Liu DR. 2011. Revealing off-target cleavage specificities of zinc-finger nucleases by in vitro selection. Nat Methods 8:765–770.
  • Petek LM, Russell DW, Miller DG. 2010. Frequent endonuclease cleavage at off-target locations in vivo. Mol Ther: the journal of the American Society of Gene Therapy 18:983–986.
  • Porteus MH. 2006. Mammalian gene targeting with designed zinc finger nucleases. Mol Ther 13:438–446.
  • Porteus MH, Baltimore D. 2003. Chimeric nucleases stimulate gene targeting in human cells. Science 300:763.
  • Puchta H, Dujon B, 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.
  • Redondo P, Prieto J, Muñoz IG, Alibés A, Stricher F, Serrano L, Cabaniols JP, Daboussi F, Arnould S, Perez C, Duchateau P, Pâques F, Blanco FJ, Montoya G. 2008. Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases. Nature 456:107–111.
  • Rémy S, Tesson L, Ménoret S, Usal C, Scharenberg AM, Anegon I. 2010. Zinc-finger nucleases: a powerful tool for genetic engineering of animals. Transgenic Res 19:363–371.
  • Richardson C, Moynahan ME, Jasin M. 1998. Double-strand break repair by interchromosomal recombination: suppression of chromosomal translocations. Genes Dev 12:3831–3842.
  • Rong YS, Titen SW, Xie HB, Golic MM, Bastiani M, Bandyopadhyay P, Olivera BM, Brodsky M, Rubin GM, Golic KG. 2002. Targeted mutagenesis by homologous recombination in D. melanogaster. Genes Dev 16:1568–1581.
  • Rosen LE, Morrison HA, Masri S, Brown MJ, Springstubb B, Sussman D, Stoddard BL, Seligman LM. 2006. Homing endonuclease I-CreI derivatives with novel DNA target specificities. Nucleic Acids Res 34:4791–4800.
  • Rouet P, Smih F, Jasin M. 1994. Introduction of double-strand breaks into the genome of mouse cells by expression of a rare-cutting endonuclease. Mol Cell Biol 14:8096–8106.
  • Seligman LM, Chisholm KM, Chevalier BS, Chadsey MS, Edwards ST, Savage JH, Veill et al. 2002. Mutations altering the cleavage specificity of a homing endonuclease. Nucleic Acids Res 30:3870–3879.
  • Slabicki M, Theis M, Krastev DB, Samsonov S, Mundwiller E, Junqueira M, Paszkowski-Rogacz M, Teyra J, Heninger AK, Poser I, Prieur F, Truchetto J, Confavreux C, Marelli C, Durr A, Camdessanche JP, Brice A, Shevchenko A, Pisabarro MT, Stevanin G, Buchholz F. 2010. A genome-scale DNA repair RNAi screen identifies SPG48 as a novel gene associated with hereditary spastic paraplegia. PLoS Biol 8:e1000408.
  • Smih F, Rouet P, Romanienko PJ, Jasin M. 1995. Double-strand breaks at the target locus stimulate gene targeting in embryonic stem cells. Nucleic Acids Res 23:5012–5019.
  • Smith J, Bibikova M, Whitby FG, Reddy AR, Chandrasegaran S, Carroll D. 2000. Requirements for double-strand cleavage by chimeric restriction enzymes with zinc finger DNA-recognition domains. Nucleic Acids Res 28:3361–3369.
  • Smith J, Grizot S, Arnould S, Duclert A, Epinat JC, Chames P, Prieto J, Redondo P, Blanco FJ, Bravo J, Montoya G, Pâques F, Duchateau P. 2006. A combinatorial approach to create artificial homing endonucleases cleaving chosen sequences. Nucleic Acids Res 34:e149.
  • Smith JA, Bannister LA, Bhattacharjee V, Wang Y, Waldman BC, Waldman AS. 2007. Accurate homologous recombination is a prominent double-strand break repair pathway in mammalian chromosomes and is modulated by mismatch repair protein Msh2. Mol Cell Biol 27:7816–7827.
  • Sussman D, Chadsey M, Fauce S, Engel A, Bruett A, Monnat R Jr, Stoddard BL, Seligman LM. 2004. Isolation and characterization of new homing endonuclease specificities at individual target site positions. J Mol Biol 342:31–41.
  • Takeuchi R, Lambert AR, Mak AN, Jacoby K, Dickson RJ, Gloor GB, Scharenberg AM, Edgell DR, Stoddard BL. 2011. Tapping natural reservoirs of homing endonucleases for targeted gene modification. Proc Natl Acad Sci USA 108:13077–13082.
  • Tedesco FS, Hoshiya H, D’Antona G, Gerli MF, Messina G, Antonini S, Tonlorenzi R, Benedetti S, Berghella L, Torrente Y, Kazuki Y, Bottinelli R, Oshimura M, Cossu G. 2011. Stem cell-mediated transfer of a human artificial chromosome ameliorates muscular dystrophy. Sci Transl Med 3:96ra78.
  • Thermes V, Grabher C, Ristoratore F, Bourrat F, Choulika A, Wittbrodt J, Joly JS. 2002. I-SceI meganuclease mediates highly efficient transgenesis in fish. Mech Dev 118:91–98.
  • Ulge UY, Baker DA, Monnat RJ Jr. 2011. Comprehensive computational design of mCreI homing endonuclease cleavage specificity for genome engineering. Nucleic Acids Res 39:4330–4339.
  • Urnov FD, Miller JC, Lee YL, Beausejour CM, Rock JM, Augustus S, Jamieson AC, Porteus MH, Gregory PD, Holmes MC. 2005. Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature 435:646–651.
  • Urnov FD, Rebar EJ, Holmes MC, Zhang HS, Gregory PD. 2010. Genome editing with engineered zinc finger nucleases. Nat Rev Genet 11:636–646.
  • Ventura A, Kirsch DG, McLaughlin ME, Tuveson DA, Grimm J, Lintault L, Newman J, Reczek EE, Weissleder R, Jacks T. 2007. Restoration of p53 function leads to tumour regression in vivo. Nature 445:661–665.
  • Wadia JS, Dowdy SF. 2002. Protein transduction technology. Curr Opin Biotechnol 13:52–56.
  • Windbichler N, Papathanos PA, Catteruccia F, Ranson H, Burt A, Crisanti A. 2007. Homing endonuclease mediated gene targeting in Anopheles gambiae cells and embryos. Nucleic Acids Res 35:5922–5933.
  • Xu GL, Bestor TH. 1997. Cytosine methylation targetted to pre-determined sequences. Nat Genet 17:376–378.
  • Zhang F, Cong L, Lodato S, Kosuri S, Church GM, Arlotta P. 2011. Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. Nat Biotechnol 29:149–153.
  • Zhao X, Liu Q, Cai Q, Li Y, Xu C, Li Y, Li Z, Zhang X. 2011. Dr.VIS: a database of human disease-related viral integration sites. Nucleic Acid Res 40:1041–1046.
  • Zhou H, Wu S, Joo JY, Zhu S, Han DW, Lin T, Trauger S, Bien G, Yao S, Zhu Y, Siuzdak G, Schöler HR, Duan L, Ding S. 2009. Generation of induced pluripotent stem cells using recombinant proteins. Cell Stem Cell 4:381–384.

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