Site-directed genome modification: Derivatives of DNA-modifying enzymes as targeting tools

Trends in Biotechnology

Volumn 23, Issue 8, 2005, Pages 407-419

  Coates, Craig J ^a   Kaminski, Joseph M ^b   Summers, James B ^c   Segal, David J ^d   Miller, Andrew D ^e   Kolb, Andreas F ^f  

^a TEXAS A AND M UNIVERSITY   (United States)

^b Transpovec Corporation   (United States)

^c UNIVERSITY OF SOUTH ALABAMA COLLEGE OF MEDICINE   (United States)

^d UNIVERSITY OF ARIZONA COLLEGE OF MEDICINE   (United States)

^e IMPERIAL COLLEGE LONDON   (United Kingdom)

^f HANNAH RESEARCH INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; ENZYMES; GENES; METABOLISM;

ANIMAL TRANSGENESIS; CELLULAR METABOLISMS; DNA MODIFYING ENZYMES; GENOME MODIFICATION;

GENETIC ENGINEERING;

ADENOVIRUS VECTOR; BLOOD CLOTTING FACTOR 9; C 31 RECOMBINASE; CRE RECOMBINASE; INTEGRASE; LENTIVIRUS VECTOR; MILK PROTEIN; PLASMID DNA; POLYDEOXYRIBONUCLEOTIDE SYNTHASE; RECOMBINASE; RESOLVASE; RETROVIRUS VECTOR; SCLEROPROTEIN; TRANSPOSASE; UNCLASSIFIED DRUG; VIRUS DNA;

BACTERIOPHAGE; DNA BINDING; DNA BINDING MOTIF; DNA INTEGRATION; DNA MODIFICATION; DNA REPAIR; DNA SEQUENCE; ENZYME ACTIVITY; GENE ACTIVITY; GENE EXPRESSION; GENE INACTIVATION; GENE SILENCING; GENE THERAPY; GENETIC ENGINEERING; HUMAN; LIFESPAN; MILK; NONHUMAN; NONVIRAL GENE DELIVERY SYSTEM; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN DOMAIN; PROTEIN ENGINEERING; PROTEIN EXPRESSION; PROTEIN TARGETING; REVIEW; SITE DIRECTED MUTAGENESIS; TRANSGENE; TRANSPOSON; VIRAL GENE DELIVERY SYSTEM; VIRUS DNA CELL DNA INTERACTION; VIRUS GENE;

ANIMALS; DNA REPAIR; EXODEOXYRIBONUCLEASES; GENE TARGETING; GENE THERAPY; GENETIC ENHANCEMENT; GENOMICS; HUMANS; MUTAGENESIS, SITE-DIRECTED; PROTEIN ENGINEERING;

ANIMALIA; MAMMALIA;

EID: 22744443611     PISSN: 01677799     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tibtech.2005.06.009     Document Type: Review

References (110)

1. A.F. Kolb Site-directed genome modification: nucleic acid and protein modules for targeted integration and gene correction Trends Biotechnol 2005 10.1016/j.tibtech.2005.06.005
2. W.S. Reznikoff Tn5 as a model for understanding DNA transposition Mol. Microbiol. 47 2003 1199 1206
3. N.L. Craig Target site selection in transposition Annu. Rev. Biochem. 66 1997 437 474
4. A. Akopian Chimeric recombinases with designed DNA sequence recognition Proc. Natl. Acad. Sci. U.S.A. 100 2003 8688 8691
5. N. Christ, and P. Droge Genetic manipulation of mouse embryonic stem cells by mutant lambda integrase Genesis 32 2002 203 208
6. D.R. Davies Three-dimensional structure of the Tn5 synaptic complex transposition intermediate Science 289 2000 77 85
7. S. McTaggart, and M. Al-Rubeai Retroviral vectors for human gene delivery Biotechnol. Adv. 20 2002 1 31
8. W.Y. Chen Reactivation of silenced, virally transduced genes by inhibitors of histone deacetylase Proc. Natl. Acad. Sci. U. S. A. 94 1997 5798 5803
9. T. Kafri Gene delivery by lentivirus vectors an overview Methods Mol. Biol. 246 2004 367 390
10. A. Hofmann Efficient transgenesis in farm animals by lentiviral vectors EMBO Rep. 4 2003 1054 1060
11. V. Sandrin Targeting retroviral and lentiviral vectors Curr. Top. Microbiol. Immunol. 281 2003 137 178
12. M. Sadelain Insertional oncogenesis in gene therapy: how much of a risk? Gene Ther. 11 2004 569 573
13. M.L. Holmes-Son, and S.A. Chow Correct integration mediated by integrase-LexA fusion proteins incorporated into HIV-1 Mol. Ther. 5 2002 360 370
14. R. Daniel Evidence that stable retroviral transduction and cell survival following DNA integration depend on components of the nonhomologous end joining repair pathway J. Virol. 78 2004 8573 8581
15. J.Y. Wang Structure of a two-domain fragment of HIV-1 integrase: implications for domain organization in the intact protein EMBO J. 20 2001 7333 7343
16. R.S. Appa Role of the nonspecific DNA-binding region and alpha helices within the core domain of retroviral integrase in selecting target DNA sites for integration J. Biol. Chem. 276 2001 45848 45855
17. X. Wu, and S.M. Burgess Integration target site selection for retroviruses and transposable elements Cell. Mol. Life Sci. 61 2004 2588 2596
18. L.F. Maxfield Relationship between retroviral DNA-integration-site selection and host cell transcription Proc. Natl. Acad. Sci. U. S. A. 102 2005 1436 1441
19. F. Bushman Tethering human immunodeficiency virus 1 integrase to a DNA site directs integration to nearby sequences Proc. Natl. Acad. Sci. U. S. A. 91 1994 9233 9237
20. F. Bushman, and M. Miller Tethering human immunodeficiency virus type 1 preintegration complexes to target DNA promotes integration at nearby sites J. Virol. 71 1997 458 464
21. R.A. Katz Targeting of retroviral integrase by fusion to a heterologous DNA binding domain: in vitro activities and incorporation of a fusion protein into viral particles Virology 217 1996 178 190
22. M.L. Holmes-Son, and S.A. Chow Integrase-LexA fusion proteins incorporated into human immunodeficiency virus type 1 that contains a catalytically inactive integrase gene are functional to mediate integration J. Virol. 74 2000 11548 11556
23. W. Tan Fusion proteins consisting of human immunodeficiency virus type 1 integrase and the designed polydactyl zinc finger protein E2C direct integration of viral DNA into specific sites J. Virol. 78 2004 1301 1313
24. R.M. Linden The recombination signals for adeno-associated virus site-specific integration Proc. Natl. Acad. Sci. U. S. A. 93 1996 7966 7972
25. N. Dutheil Adeno-associated virus site-specifically integrates into a muscle-specific DNA region Proc. Natl. Acad. Sci. U. S. A. 97 2000 4862 4866
26. S. Lamartina Characteristics of the adeno-associated virus preintegration site in human chromosome 19: open chromatin conformation and transcription-competent environment J. Virol. 74 2000 7671 7677
27. J.C. Bakowska Targeted transgene integration into transgenic mouse fibroblasts carrying the full-length human AAVS1 locus mediated by HSV/AAV rep(+) hybrid amplicon vector Gene Ther. 10 2003 1691 1702
28. M. Yoon Amino-terminal domain exchange redirects origin-specific interactions of adeno-associated virus Rep78 in vitro J. Virol. 75 2001 3230 3239
29. M.Y. Jang Stable secondary structure near the nicking site for adeno-associated virus type 2 Rep proteins on human chromosome 19 J. Virol. 79 2005 3544 3556
30. A.B. Hickman The nuclease domain of adeno-associated virus rep coordinates replication initiation using two distinct DNA recognition interfaces Mol. Cell 13 2004 403 414
31. R.H. Smith, and R.M. Kotin An adeno-associated virus (AAV) initiator protein, Rep78, catalyzes the cleavage and ligation of single-stranded AAV ori DNA J. Virol. 74 2000 3122 3129
32. S. Weger Topors, a p53 and topoisomerase I binding protein, interacts with the adeno-associated virus (AAV-2) Rep78/68 proteins and enhances AAV-2 gene expression J. Gen. Virol. 83 2002 511 516
33. L. Tenenbaum Evaluation of risks related to the use of adeno-associated virus-based vectors Curr. Gene Ther. 3 2003 545 565
34. H. Nakai Large-scale molecular characterization of adeno-associated virus vector integration in mouse liver J. Virol. 79 2005 3606 3614
35. D.G. Miller Adeno-associated virus vectors integrate at chromosome breakage sites Nat. Genet. 36 2004 767 773
36. M.H. Porteus Efficient gene targeting mediated by adeno-associated virus and DNA double-strand breaks Mol. Cell. Biol. 23 2003 3558 3565
37. K. Kogure Targeted integration of foreign DNA into a defined locus on chromosome 19 in K562 cells using AAV-derived components Int. J. Hematol. 73 2001 469 475
38. T. Ueno Site-specific integration of a transgene mediated by a hybrid adenovirus/adeno-associated virus vector using the Cre/loxP-expression-switching system Biochem. Biophys. Res. Commun. 273 2000 473 478
39. E. Ryder, and S. Russell Transposable elements as tools for genomics and genetics in Drosophila Brief Funct. Genomic Proteomic 2 2003 57 71
40. M. Szabo Transposition and targeting of the prokaryotic mobile element IS30 in zebrafish FEBS Lett. 550 2003 46 50
41. Z. Izsvak, and Z. Ivics Sleeping beauty transposition: biology and applications for molecular therapy Mol. Ther. 9 2004 147 156
42. G. Luo Chromosomal transposition of a Tc1/mariner-like element in mouse embryonic stem cells Proc. Natl. Acad. Sci. U. S. A. 95 1998 10769 10773
43. S.R. Yant Somatic integration and long-term transgene expression in normal and haemophilic mice using a DNA transposon system Nat. Genet. 25 2000 35 41
44. P.A. Rice, and T.A. Baker Comparative architecture of transposase and integrase complexes Nat. Struct. Biol. 8 2001 302 307
45. T.A. Naumann, and W.S. Reznikoff Tn5 transposase with an altered specificity for transposon ends J. Bacteriol. 184 2002 233 240
46. R. Rezsohazy The IS4 family of insertion sequences: evidence for a conserved transposase motif Mol. Microbiol. 9 1993 1283 1295
47. L.A. Braam, and W.S. Reznikoff Functional characterization of the Tn5 transposase by limited proteolysis J. Biol. Chem. 273 1998 10908 10913
48. S.R. Yant Mutational analysis of the N-terminal DNA-binding domain of sleeping beauty transposase: critical residues for DNA binding and hyperactivity in mammalian cells Mol. Cell. Biol. 24 2004 9239 9247
49. Z. Izsvak Involvement of a bifunctional, paired-like DNA-binding domain and a transpositional enhancer in sleeping beauty transposition J. Biol. Chem. 277 2002 34581 34588
50. A.E. Stellwagen, and N.L. Craig Mobile DNA elements: controlling transposition with ATP-dependent molecular switches Trends Biochem. Sci. 23 1998 486 490
51. C.C. Lee DNA binding by the KP repressor protein inhibits P element transposase activity in vitro EMBO J. 17 1998 4166 4174
52. Y. Zhu Controlling integration specificity of a yeast retrotransposon Proc. Natl. Acad. Sci. U. S. A. 100 2003 5891 5895
53. R.H. Plasterk Resident aliens: the Tc1/mariner superfamily of transposable elements Trends Genet. 15 1999 326 332
54. A.M. Handler Use of the piggyBac transposon for germ-line transformation of insects Insect Biochem. Mol. Biol. 32 2002 1211 1220
55. N. Guimond Patterns of Hermes transposition in Drosophila melanogaster Mol. Genet. Genomics 268 2003 779 790
56. G. Liu Target-site preferences of Sleeping Beauty transposons J. Mol. Biol. 346 2005 161 173
57. S.R. Yant High-resolution genome-wide mapping of transposon integration in mammals Mol. Cell. Biol. 25 2005 2085 2094
58. T.J. Vigdal Common physical properties of DNA affecting target site selection of sleeping beauty and other Tc1/mariner transposable elements J. Mol. Biol. 323 2002 441 452
59. K. Yusa Enhancement of Sleeping Beauty transposition by CpG methylation: possible role of heterochromatin formation Mol. Cell. Biol. 24 2004 4004 4018
60. H. Zayed The DNA-bending protein HMGB1 is a cellular cofactor of Sleeping Beauty transposition Nucleic Acids Res. 31 2003 2313 2322
61. P.N. Kuduvalli Target DNA structure plays a critical role in Tn7 transposition EMBO J. 20 2001 924 932
62. P.L. Sharpe, and N.L. Craig Host proteins can stimulate Tn7 transposition: a novel role for the ribosomal protein L29 and the acyl carrier protein EMBO J. 17 1998 5822 5831
63. P.N. Kuduvalli Site-specific Tn7 transposition into the human genome Nucleic Acids Res. 33 2005 857 863
64. J.M. Kaminski Design of a nonviral vector for site-selective, efficient integration into the human genome FASEB J. 16 2002 1242 1247
65. Z. Nagy Analysis of the N-terminal DNA binding domain of the IS30 transposase Mol. Microbiol. 54 2004 478 488
66. A.C. Groth, and M.P. Calos Phage integrases: biology and applications J. Mol. Biol. 335 2004 667 678
67. A.F. Kolb Genome engineering using site-specific recombinases Cloning Stem Cells 4 2002 65 80
68. T. Schlake, and J. Bode Use of mutated FLP recognition target (FRT) sites for the exchange of expression cassettes at defined chromosomal loci Biochemistry 33 1994 12746 12751
69. M. Kolot Site-specific recombination in mammalian cells expressing the Int recombinase of bacteriophage HK022 Mol. Biol. Rep. 26 1999 207 213
70. E.C. Olivares Phage R4 integrase mediates site-specific integration in human cells Gene 278 2001 167 176
71. S.M. Stoll Phage TP901-1 site-specific integrase functions in human cells J. Bacteriol. 184 2002 3657 3663
72. H.J. Kwon Flexibility in DNA recombination: structure of the lambda integrase catalytic core Science 276 1997 126 131
73. F. Guo Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse Nature 389 1997 40 46
74. Y. Chen Crystal structure of a Flp recombinase-Holliday junction complex: assembly of an active oligomer by helix swapping Mol. Cell 6 2000 885 897
75. H.S. Subramanya Crystal structure of the site-specific recombinase, XerD EMBO J. 16 1997 5178 5187
76. K. Abremski Studies on the properties of P1 site-specific recombination: evidence for topologically unlinked products following recombination Cell 32 1983 1301 1311
77. R.H. Hoess, and K. Abremski Interaction of the bacteriophage P1 recombinase Cre with the recombining site loxP Proc. Natl. Acad. Sci. U. S. A. 81 1984 1026 1029
78. P. Waterhouse Combinatorial infection and in vivo recombination: a strategy for making large phage antibody repertoires Nucleic Acids Res. 21 1993 2265 2266
79. V. Srivastava, and D.W. Ow Marker-free site-specific gene integration in plants Trends Biotechnol. 22 2004 627 629
80. B. Thyagarajan Mammalian. genomes contain active recombinase recognition sites Gene 244 2000 47 54
81. E.E. Schmidt Illegitimate Cre-dependent chromosome rearrangements in transgenic mouse spermatids Proc. Natl. Acad. Sci. U. S. A. 97 2000 13702 13707
82. S.W. Santoro, and P.G. Schultz Directed evolution of the site specificity of Cre recombinase Proc. Natl. Acad. Sci. U. S. A. 99 2002 4185 4190
83. F. Buchholz, and A.F. Stewart Alteration of Cre recombinase site specificity by substrate-linked protein evolution Nat. Biotechnol. 19 2001 1047 1052
84. Y. Voziyanov Stepwise manipulation of DNA specificity in Flp recombinase: progressively adapting Flp to individual and combinatorial mutations in its target site J. Mol. Biol. 326 2003 65 76
85. H.M. Thorpe, and M.C. Smith In vitro site-specific integration of bacteriophage DNA catalyzed by a recombinase of the resolvase/invertase family Proc. Natl. Acad. Sci. U. S. A. 95 1998 5505 5510
86. A.C. Groth A phage integrase directs efficient site-specific integration in human cells Proc. Natl. Acad. Sci. U. S. A. 97 2000 5995 6000
87. B. Thyagarajan Site-specific genomic integration in mammalian cells mediated by phage phiC31 integrase Mol. Cell. Biol. 21 2001 3926 3934
88. E.C. Olivares Site-specific genomic integration produces therapeutic Factor IX levels in mice Nat. Biotechnol. 20 2002 1124 1128
89. S. Ortiz-Urda Stable nonviral genetic correction of inherited human skin disease Nat. Med. 8 2002 1166 1170
90. C.R. Sclimenti Directed evolution of a recombinase for improved genomic integration at a native human sequence Nucleic Acids Res. 29 2001 5044 5051
91. M. Hartung, and B. Kisters-Woike Cre mutants with altered DNA binding properties J. Biol. Chem. 273 1998 22884 22891
92. W. Yang, and T.A. Steitz Crystal structure of the site-specific recombinase gamma delta resolvase complexed with a 34 bp cleavage site Cell 82 1995 193 207
93. H.A. Greisman, and C.O. Pabo A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites Science 275 1997 657 661
94. I. Wilmut Production of pharmaceutical proteins in milk Experientia 47 1991 905 912
95. A.F. Kolb Engineering immunity in the mammary gland J. Mammary Gland Biol. Neoplasia 7 2002 123 134
96. S. Kumar Milk composition and lactation of beta-casein-deficient mice Proc. Natl. Acad. Sci. U. S. A. 91 1994 6138 6142
97. M. McClenaghan Secretory proteins compete for production in the mammary gland of transgenic mice Biochem. J. 310 1995 637 641
98. K.J. McCreath Production of gene-targeted sheep by nuclear transfer from cultured somatic cells Nature 405 2000 1066 1069
99. K.H. Rowan Tn5 as an insect gene vector Insect Biochem. Mol. Biol. 34 2004 695 705
100. A.J. Dupuy Mammalian germ-line transgenesis by transposition Proc. Natl. Acad. Sci. U. S. A. 99 2002 4495 4499
101. M.A. Riehle Towards genetic manipulation of wild mosquito populations to combat malaria: advances and challenges J. Exp. Biol. 206 2003 3809 3816
102. C.J. Coates Promoter-directed expression of recombinant fire-fly luciferase in the salivary glands of Hermes-transformed Aedes aegypti Gene 226 1999 317 325
103. V. Kokoza Engineering blood meal-activated systemic immunity in the yellow fever mosquito, Aedes aegypti Proc. Natl. Acad. Sci. U. S. A. 97 2000 9144 9149
104. A.A. James Blocking malaria parasite invasion of mosquito salivary glands J. Exp. Biol. 206 2003 3817 3821
105. C.S. Swindle, and C.A. Klug Mechanisms that regulate silencing of gene expression from retroviral vectors J. Hematother. Stem Cell Res. 11 2002 449 456
106. S. Kochanek A new adenoviral vector: replacement of all viral coding sequences with 28 kb of DNA independently expressing both full-length dystrophin and beta-galactosidase Proc. Natl. Acad. Sci. U. S. A. 93 1996 5731 5736
107. S. Ortiz-Urda Sustainable correction of junctional epidermolysis bullosa via transposon-mediated nonviral gene transfer Gene Ther. 10 2003 1099 1104
108. S.R. Yant Transposition from a gutless adeno-transposon vector stabilizes transgene expression in vivo Nat. Biotechnol. 20 2002 999 1005
109. X. Lu Safe two-plasmid production for the first clinical lentivirus vector that achieves >99% transduction in primary cells using a one-step protocol J. Gene Med. 6 2004 963 973
110. B. Rost Protein fold recognition by prediction-based threading J. Mol. Biol. 270 1997 471 480