Zinc-Finger nucleases: A panoramic view

Current Gene Therapy

Volumn 11, Issue 1, 2011, Pages 2-10

  Carroll, Dana ^a  

^a UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

Author keywords

DNA repair; Gene targeting; Homologous recombination; Nonhomologous end joining (NHEJ); Zinc fingers; Zinc finger nuclease (ZFN)

Indexed keywords

HYBRID PROTEIN; UNCLASSIFIED DRUG; ZINC FINGER NUCLEASE;

ARTICLE; DNA BINDING; DNA CLEAVAGE; DNA REPAIR; DOUBLE STRANDED DNA BREAK; DRUG DESIGN; GENE SEQUENCE; GENE TARGETING; GENE THERAPY; GENETIC ENGINEERING; GENOME; HUMAN; NONHUMAN; X LINKED SEVERE COMBINED IMMUNODEFICIENCY;

ANIMALS; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; ENDODEOXYRIBONUCLEASES; GENE TARGETING; HUMANS; MODELS, MOLECULAR; PROTEIN ENGINEERING; RECOMBINANT FUSION PROTEINS; ZINC FINGERS;

EID: 79951711771     PISSN: 15665232     EISSN: None     Source Type: Journal    
DOI: 10.2174/156652311794520076     Document Type: Article

References (95)

1. Porteus MH, Carroll D. Gene targeting using zinc finger nucleases. Nat Biotechnol 2005; 23: 967-73.
2. Dion S, Demattei MV, Renault S. Zinc finger proteins: tools forsite-specific correction or modification of the genome. Med Sci (Paris) 2007; 23: 834-9.
3. Carroll D. Progress and prospects: zinc-finger nucleases as genetherapy agents. Gene Ther 2008; 15: 1463-8.
4. Cathomen T, Joung JK. Zinc-finger nucleases: the next generationemerges. Mol Ther 2008; 16: 1200-7.
5. Kandavelou K, Ramalingam S, London V, et al. Targeted manipulationof mammalian genomes using designed zinc finger nucleases. Biochem Biophys Res Commun 2009; 388: 56-61.
6. Le Prevost F, Lillico S, Passet B, Young R, Whitelaw B, Vilotte JL. Zinc finger nuclease techology heralds a new era in mammaliantransgenesis. Trends Biotechnol 2009; 28: 134-41.
7. Remy S, Tesson L, Menoret S, Usal C, Scharenberg AM, Anegon I. Zinc-finger nucleases: a powerful tool for genetic engineering of animals. Transgenic Res 2010; 19: 363-71.
8. Kim Y-G, Cha J, Chandrasegaran S. Hybrid restriction enzymes:zinc finger fusions to Fok I cleavage domain. Proc Natl Acad Sci USA 1996; 93: 1156-60.
9. Bateman A, Birney E, Cerruti L, et al. The Pfam protein familiesdatabase. Nucleic Acids Res 2002; 30: 276-80.
10. Miller J, McLachlan AD, Klug A. Repetitive zinc-binding domainsin the protein transcription factor IIIA from Xenopus oocytes. EMBO J 1985; 4: 1609-14.
11. Klug A. The discovery of zinc fingers and their applications ingene regulation and genome manipulation. Annu Rev Biochem 2010; 79: 213-31.
12. Berg JM. Proposed structure for the zinc-binding domains fromtranscription factor IIIA and related proteins. Proc Natl Acad Sci USA 1988; 85: 99-102.
13. Pavletich NP, Pabo CO. Zinc finger-DNA recognition: crystalstructure of a Zif268-DNA complex at 2.1 A resolution. Science 1991; 252: 809-17.
14. Jantz D, Amann BT, Gatto JGJ, Berg JM. The design of functional DNA-binding proteins based on zinc finger domains. Chem Rev 2004; 104: 789-99.
15. Rebar EJ, Pabo CO. Zinc finger phage: affinity selection of fingerswith new DNA-binding specificities. Science 1994; 263: 671-3.
16. Choo Y, Klug A. Toward a code for the interactions of zinc fingerswith DNA: selection of randomized fingers displayed on phage. Proc Natl Acad Sci USA 1994; 91: 11163-7.
17. Jamieson AC, Kim S-H, Wells JA. In vitro selection of zinc fingerswith altered DNA-binding specificity. Biochemistry 1994; 33: 5689-95.
18. Greisman HA, Pabo CO. A general strategy for selecting highaffinityzinc finger proteins for diverse DNA target sites. Science 1997; 275: 657-61.
19. Segal DJ, Dreier B, Beerli RR, Barbas III CF. Toward controllinggene expression at will: selection and design of zinc finger domainsrecognizing each of the 5'-GNN-3' DNA target sequences. Proc Natl Acad Sci USA 1999; 96: 2758-63.
20. Dreier B, Beerli RR, Segal DJ, Flippin JD, Barbas III CF. Developmentof zinc finger domains for recognition of the 5'-ANN-3'family of DNA sequences and their use in the construction of artificialtranscription factors. J Biol Chem 2001; 276: 29466-78.
21. Dreier B, Fuller RP, Segal DJ, et al. Development of zinc fingerdomains for recognition of the 5'-CNN-3' family DNA sequencesand their use in construction of artificial transcription factors. JBiol Chem 2005; 280: 35588-97.
22. Isalan M, Klug A, Choo Y. A rapid, generally applicable method toengineer zinc fingers illustrated by targeting the HIV-1 promoter. Nature Biotech 2001; 19: 656-60.
23. Moore M, Choo Y, Klug A. Design of polyzinc finger peptideswith structured linkers. Proc Natl Acad Sci USA 2001; 98: 1432-6.
24. Moore M, Klug A, Choo Y. Improved DNA binding specificityfrom polyzinc finger peptides by using strings of two-finger units. Proc Natl Acad Sci USA 2001; 98: 1437-41.
25. Meng X, Thibodeau-Beganny S, Jiang T, Joung JK, Wolfe SA. Profiling the DNA-binding specificities of engineered Cys2His2zinc finger domains using a rapid cell-based method. Nucleic Acids Res 2007; 35: e81.
26. Maeder ML, Thibodeau-Beganny S, Osiak A, et al. Rapid "Open-Source" engineering of customized zinc-finger nucleases for highlyefficient gene modification. Mol Cell 2008; 31: 294-301.
27. Li L, Wu LP, Chandrasegaran S. Functional domains in Fok I restrictionendonuclease. Proc Natl Acad Sci USA 1992; 89: 4275-9.
28. Kim Y-G, Chandrasegaran S. Chimeric restriction endonuclease. Proc Natl Acad Sci USA 1994; 91: 883-7.
29. Kim Y-G, Smith J, Durgesha M, Chandrasegaran S. Chimericrestriction enzyme: Gal4 fusion to Fok I cleavage domain. Biol Chem 1998; 379: 489-95.
30. Bitinaite J, Wah DA, Aggarwal AK, Schildkraut I. Fok I dimerizationis required for DNA cleavage. Proc Natl Acad Sci USA 1998; 95: 10570-5.
31. Vanamee ES, Santagata S, Aggarwal AK. Fok I requires two specific DNA sites for cleavage. J Mol Biol 2001; 309: 69-78.
32. Catto LE, Ganguly S, Milsom SE, Welsh AJ, Halford SE. Proteinassembly and DNA looping by the Fok I restriction endonuclease. Nucleic Acids Res 2006; 34: 1711-20.
33. Keeney S. Mechanism and control of meiotic recombination initiation. Curr Top Dev Biol 2001; 52: 1-53.
34. Jeggo P, Lavin MF. Cellular radiosensitivity: how much better dowe understand it? Int J Radiat Biol 2009; 85: 1061-81.
35. Rudin N, Haber JE. Efficient repair of HO-induced chromosomalbreaks in Saccharomyces cerevisiae by recombination betweenflanking homologous sequences. Mol Cell Biol 1988; 8: 3918-28.
36. Rudin N, Sugarman E, Haber JE. Genetic and physical analysis of double-strand break repair and recombination in Saccharomycescerevisiae. Genetics 1989; 122: 519-34.
37. Plessis A, Perrin A, Haber JE, Dujon B. Site-specific recombinationdetermined by I-Sce I, a mitochondrial group I intron-encodedendonuclease expressed in the yeast nucleus. Genetics 1992; 130: 451-60.
38. Rouet P, Smih F, Jasin M. Introduction of double-strand breaksinto the genome of mouse cells by expression of a rare-cutting endonuclease. Mol Cell Biol 1994; 14: 8096-106.
39. Smih F, Rouet P, Romanienko PJ, Jasin M. Double-strand breaks atthe target locus stimulate gene targeting in embryonic stem cells. Nucleic Acids Res 1995; 23: 5012-9.
40. Segal DJ, Carroll D. Endonuclease-induced, targeted homologousextrachromosomal recombination in Xenopus oocytes. Proc Natl Acad Sci USA 1995; 92: 806-10.
41. Jasin M. Genetic manipulation of genomes with rare-cutting endonucleases. Trends Genet 1996; 12: 224-8.
42. Carroll D, Segal DJ. Induced recombination in model systems. Curr Res Mol Therap 1998; 1: 593-8.
43. Faruqi AF, Seidman MM, Segal DJ, Carroll D, Glazer PM. Recombinationinduced by triple helix-targeted DNA damage inmammalian cells. Mol Cell Biol 1996; 16: 6820-8.
44. Segal DJ, Faruqi AF, Glazer PM, Carroll D. Repair and mutagenesisof targeted psoralen crosslinks in Xenopus oocytes. Mol Cell Biol 1997; 17: 6645-52.
45. Smith J, Bibikova M, Whitby FG, Reddy AR, Chandrasegaran S, Carroll D. Requirements for double-strand cleavage by chimericrestriction enzymes with zinc finger DNA-recognition domains. Nucleic Acids Res 2000; 28: 3361-9.
46. Bibikova M, Golic M, Golic KG, Carroll D. Targeted chromosomalcleavage and mutagenesis in Drosophila using zinc-finger nucleases. Genetics 2002; 161: 1169-75.
47. Porteus MH, Baltimore D. Chimeric nucleases stimulate gene targetingin human cells. Science 2003; 300: 763.
48. Beumer K, Bhattacharyya G, Bibikova M, Trautman JK, Carroll D. Efficient gene targeting in Drosophila with zinc finger nucleases. Genetics 2006; 172: 2391-403.
49. Miller JC, Holmes MC, Wang J, et al. An improved zinc-fingernuclease architecture for highly specific genome cleavage. Nat Biotechnol 2007; 25: 778-85.
50. Szczepek M, Brondani V, Buchel J, Serrano L, Segal DJ, Cathomen T. Structure-based redesign of the dimerization interface reducesthe toxicity of zinc-finger nucleases. Nat Biotechnol 2007; 25: 786-93.
51. Handel E-M, Alwin S, Cathomen T. Expanding or restricting thetarget site repertoire of zinc-finger nucleases: the inter-domainlinker as a major determinant of target site selectivity. Mol Therapy 2009; 17: 104-11.
52. Shimizu Y, Bhakta MS, Segal DJ. Restricted spacer tolerance of azinc finger nuclease with a six amino acid linker. Bioorg Med Chem Lett 2009; 19: 3970-2.
53. Bibikova M, Carroll D, Segal DJ, et al. Stimulation of homologousrecombination through targeted cleavage by chimeric nucleases. Mol Cell Biol 2001; 21: 289-97.
54. Bibikova M, Beumer K, Trautman JK, Carroll D. Enhancing genetargeting with designed zinc finger nucleases. Science 2003; 300: 764.
55. Urnov FD, Miller JC, Lee Y-L, et al. Highly efficient endogenousgene correction using designed zinc-finger nucleases. Nature 2005; 435: 646-51.
56. Beumer KJ, Trautman JK, Bozas A, et al. Efficient gene targetingin Drosophila by direct embryo injection with zinc-finger nucleases. Proc Natl Acad Sci USA 2008; 105: 19821-6.
57. Takasu Y, Kobayashi I, Beumer K, et al. Targeted mutagenesis inthe silkworm Bombyx mori using zinc-finger nuclease mRNA injections. Insect Biochem Mol Biol 2010; 40: 759-65.
58. Doyon Y, MaCammon JM, Miller JC, et al. Heritable targeted genedisruption in zebrafish using designed zinc-finger nucleases. Nat Biotechnol 2008; 26: 702-8.
59. Meng X, Noyes MB, Zhu LJ, Lawson ND, Wolfe SA. Targetedgene inactivation in zebrafish using engineered zinc-finger nucleases. Nat Biotechnol 2008; 26: 695-701.
60. Foley JE, Yeh JR, Maeder ML, et al. Rapid mutation of endogenouszebrafish genes using zinc-finger nucleases made by Oligomerized Pool ENgineering (OPEN). PLoS ONE 2009; 4: e4348.
61. Morton J, Davis MW, Jorgensen EM, Carroll D. Induction and repair of zinc-finger nuclease-targeted double-strand breaks in Caenorhabditis elegans somatic cells. Proc Natl Acad Sci USA 2006; 103: 16370-5.
62. Lombardo A, Genovese P, Beausejour CM, et al. Gene editing inhuman stem cells using zinc finger nucleases and integrasedefectivelentiviral vector delivery. Nat Biotechnol 2007; 25: 1298-306.
63. Kim HJ, Lee HJ, Kim H, Cho SW, Kim J-S. Targeted genomeediting in human cells with zinc finger nucleases constructed viamodular assembly. Genome Res 2009; 19: 1279-88.
64. Lee HJ, Kim E, Kim J-S. Targeted chromosomal deletions in humancells using zinc finger nucleases. Genome Res 2010; 20: 81-9.
65. Geurts AM, Cost GJ, Freyvert Y, Zeitler B, Miller JC, Choi VM, et al. Knockout rats via embryo microinjection of zinc-finger nucleases. Science 2009; 325: 433.
66. Mashimo T, Takizawa A, Voigt B, et al. Generation of knockoutrats with X-linked severe combined immunodeficiency (X-SCID)using zinc-finger nucleases. PLoS ONE 2010; 5: e8870.
67. Carbery ID, Ji D, Harrington A, et al. Targeted genome modificationin mice using zinc-finger nucleases. Genetics 2010; 186: 451-9.
68. Meyer M, Hrabe de Angelis M, Wurst W, Kuhn R. Gene targetingby homologous recombination in mouse zygotes mediated by zincfingernucleases. Proc Natl Acad Sci USA 2010; 107: 15022-6.
69. Ochiai H, Fujita K, Suzuki K, et al. Targeted mutagenesis in thesea urchin embryo using zinc-finger nucleases. Genes Cells 2010; 15: 875-85.
70. Shukla VK, Doyon Y, Miller JC, et al. Precise genome modificationin the crop species Zea mays using zinc-finger nucleases. Nature 2009; 459: 437-41.
71. Townsend JA, Wright DA, Winfrey RJ, et al. High-frequencymodification of plant genes using engineered zinc-finger nucleases. Nature 2009; 459: 442-5.
72. Osakabe K, Osakabe Y, Toki S. Site-directed mutagenesis in Arabidopsis using custom-designed zinc finger nucleases. Proc Natl Acad Sci USA 2010; 107: 12034-9.
73. Zhang F, Maeder ML, Unger-Wallace E, et al. High frequencytargeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases. Proc Natl Acad Sci USA 2010; 107: 12028-33.
74. Bozas A, Beumer KJ, Trautman JK, Carroll D. Genetic analysis of zinc-finger nuclease-induced gene targeting in Drosophila. Genetics 2009; 182: 641-51.
75. Nassif NA, Penney J, Pal S, Engels WR, Gloor GB. Efficient copyingof nonhomologous sequences from ectopic sites via P-elementinducedgap repair. Mol Cell Biol 1994; 14: 1613-25.
76. Elliott B, Richardson C, Winderbaum J, Nickoloff JA, Jasin M. Gene conversion tracts from double-strand break repair in mammaliancells. Mol Cell Biol 1998; 18: 93-101.
77. Carroll D, Morton JJ, Beumer KJ, Segal DJ. Design, constructionand in vitro testing of zinc finger nucleases. Nat Protocols 2006; 1: 1329-41.
78. Segal DJ, Beerli RR, Blancafort P, Dreier B, Effertz K, Huber A, etal. Evaluation of a modular strategy for the construction of novelpolydactyl zinc finger DNA-binding proteins. Biochemistry 2003; 42: 2137-48.
79. Kim J-S, Lee HJ, Carroll D. Genome editing with modularly assembledzinc-finger nucleases. Nat Methods 2010; 7: 91.
80. Joung JK, Voytas DF, Cathomen T. Reply to "Genome editing withmodularly assembled zinc-finger nucleases". Nat Methods 2010; 7: 91-2.
81. Liu Q, Xia ZQ, Zhong X, Case CC. Validated zinc finger proteindesigns for all 16 GNN DNA triplet targets. J Biol Chem 2002; 277: 3850-6.
82. Mandell JG, Barbas III CF. Zinc Finger Tools: custom DNAbindingdomains for transcription factors and nucleases. Nucleic Acids Res 2006; 34: W516-W23.
83. Sander JD, Maeder ML, Reyon D, Voytas DF, Joung JK, Dobbs D. ZiFiT (Zinc Finger Targeter): an updated zinc finger engineeringtool. Nucleic Acids Res 2010; 38 Suppl.: W462-8.
84. Pabo CO, Peisach E, Grant RA. Design and selection of novel Cys2His2 zinc finger proteins. Annu Rev Biochem 2001; 70: 313-40.
85. Zou J, Maeder ML, Mali P, et al. Gene targeting of a diseaserelatedgene in human induced pluripotent stem and embryonicstem cells. Cell Stem Cell 2009; 5: 97-110.
86. Orlando S, Santiago Y, DeKelver RC, et al. Zinc-finger nucleasedriventargeted integration into mammalian genomes using donorswith limited chromosomal homology. Nucleic Acids Res 2010; 38: e152.
87. Cai CQ, Doyon Y, Ainley WM, et al. Targeted transgene integrationin plant cells using designed zinc finger nucleases. Plant Mol Biol 2009; 69: 699-709.
88. Perez EE, Wang J, Miller JC, et al. Establishment of HIV-1 resistancein CD4+ T cells by genome editing using zinc-finger nucleases. Nat Biotechnol 2008; 26: 808-16.
89. Hockemeyer D, Soldner F, Beard C, et al. Efficient targeting of expressed and silent genes in human ESCs and iPSCs using zincfingernucleases. Nat Biotechnol 2009; 27: 851-7.
90. DeKelver RC, Choi VM, Moehle EA, et al. Functional genomics, proteomics, and regulatory DNA analysis in isogenic settings usingzinc finger nuclease-driven transgenesis into a safe harbor locus inthe human genome. Genome Res 2010; 20: 1133-42.
91. Mittelman D, Moye C, Morton J, et al. Zinc-finger directed doublestrandbreaks within CAG repeat tracts promote repeat instability inhuman cells. Proc Natl Acad Sci USA 2009; 106: 9607-12.
92. Orr HT, Zoghbi HY. Trinucleotide repeat disorders. Annu Rev Neurosci 2007; 30: 575-621.
93. Stock G, Campbell J, editors. Engineering the Human Germline. Oxford: Oxford University Press; 2000.
94. Hacein-Bey-Abina S, Von Kalle C, Schmidt M, et al. LMO2-associated clonal T cell proliferation in two patients after genetherapy for SCID-X1. Science 2003; 302: 415-9.
95. Pruett-Miller SM, Reading DW, Porter SN, Porteus MH. Attenuationof zinc finger nuclease toxicity by small-molecule regulationof protein levels. PLoS Genet 2009; 5: e1000376.