Latent infection of the host cell by aav and its disruption by helper viruses

Parvoviruses

Volumn , Issue , 2005, Pages 237-252

  Owens, Roland A ^a  

^a National Institutes of Health US Department of Health and Human Services   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 35948983805     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (204)

1. Afione, S. A., Conrad, C. K., Kearns, W. G. et al. 1996. In vivo model of adeno-associated virus vector persistence and rescue. Journal of Virology 70: 3235-41.
2. Alexander, I. E., Russell, D. W. and Miller, A. D. 1994. DNA-damaging agents greatly increase the transduction of nondividing cells by adeno-associated virus vectors. Journal of Virology 68: 8282-7.
3. Ali, R. R., Reichel, M. B., De Alwis, M. et al. 1998. Adeno-associated virus gene transfer to mouse retina. Human Gene Therapy 9: 81-6.
4. Amiss, T. J., McCarty, D. M., Skulimowski, A. and Samulski, R. J. 2003. Identification and characterization of an adeno-associated virus integration site in CV-1 cells from the African green monkey. Journal ofVirology 77: 1904-15.
5. Atchison, R. W. 1970. The role of herpesviruses in adenovirus- associated virus replication in vitro. Virology 42: 155-62.
6. Atchison, R. W., Casto, B. C. and Hammon, W. M. 1965. Adenovirus- associated defective virus particles. Science 149: 754-6.
7. Babiss, L. E. and Ginsberg, H. S. 1984. Adenovirus type 5 early region 1b gene product is required for efficient shutoff of host protein synthesis. Journal ofVirology 50: 202-12.
8. Babiss, L. E., Ginsberg, H. S. and Darnell, J. E. 1985. Adenovirus E1B proteins are required for accumulation of late viral mRNA and for effects on cellular mRNA translation and transport. Molecular and Cellular Biology 5: 2552-8.
9. Balagué, C., Kalla, M. and Zhang, W. W. 1997. Adeno-associated virus Rep78 protein and terminal repeats enhance integration of DNA sequences into the cellular genome. Journal ofVirology 71: 3299-306.
10. Bantel-Schaal, U. and zur Hausen, H. 1984. Characterization of the DNA of a defective human parvovirus isolated from a genital site. Virology 134: 52-63.
11. Bartlett, R. J., Secore, S. L., Singer, J. T. et al. 1996. Long-term expression of a fluorescent reporter gene via direct injection of plasmid vector into mouse skeletal muscle: comparison of human creatine kinase and CMV promoter expression levels in vivo. Cell Transplantation 5: 411-19.
12. Batchu, R. B., Kotin, R. M. and Hermonat, P. L. 1994. The regulatory Rep protein of adeno-associated virus binds to sequences within the c-H-ras promoter. Cancer Letters 86: 23-31.
13. Beaton, A., Palumbo, P. and Berns, K. I. 1989. Expression from the adeno-associated virus p5 and p19 promoters is negatively regulated in trans by the Rep protein. Journal ofVirology 63: 4450-4.
14. Becerra, S. P., Rose, J. A., Hardy, M. et al. 1985. Direct mapping of adeno-associated virus capsid proteins B and C: a possible ACG initiation codon. Proceedings of National Academy of Sciences USA 82:7919-7923.
15. Becerra, S. P., Koczot, F., Fabisch, P. and Rose, J. A. 1988. Synthesis of adeno-associated virus structural proteins requires both alternative mRNA splicing and alternative initiations from a single transcript. Journal ofVirology 62: 2745-54.
16. Berns, K. I., Pinkerton, T. C., Thomas, G. F. and Hoggan, M. D. 1975. Detection of adeno-associated virus (AAV)-specific nucleotide sequences in DNA isolated from latently infected Detroit 6 cells. Virology 68: 556-60.
17. Blacklow, N. R., Hoggan, M. D. and Rowe, W. P. 1967. Isolation of adenovirus-associated viruses from man. Proceedings of National Academy of Sciences USA 58: 1410-15.
18. Bossis, I. and Chiorini, J. A. 2003. Cloning of an avian adeno- associated virus (AAAV) and generation of recombinant AAAV particles. Journal ofVirology 77: 6799-810.
19. Brister, J. R. and Muzyczka, N. 1999. Rep-mediated nicking of the adeno-associated virus origin requires two biochemical activities, DNA helicase activity and transesterification. Journal ofVirology 73: 9325-36.
20. Buller, R. M., Straus, S. E. and Rose, J. A. 1979. Mechanism of host restriction of adenovirus-associated virus replication in African green monkey kidney cells. Journal of General Virology 43: 663-72.
21. Burguete, T., Rabreau, M., Fontanges-Darriet, M. et al. 1999. Evidence for infection of the human embryo with adeno-associated virus in pregnancy. Human Reproduction 14: 2396-2401.
22. Carter, B. J. 1990. Adeno-associated virus helper functions. In: P. Tijssen (ed.), HandbookofParvoviruses, Vol. 1. Boca Raton, Fl.: CRC Press, Inc., pp. 255-82.
23. Carter, B. J., Marcus-Sekura, C. J., Laughlin, C. A. and Ketner, G. 1983. Properties of an adenovirus type 2 mutant, Ad2dl807: having a deletion near the right-hand genome terminus: failure to help AAV replication. Virology 126: 505-16.
24. Carter, B. J., Mendelson, E. and Trempe, J. P. 1990a. AAV DNA replication, integration and genetics. In P. Tijssen (ed.), Handbook ofParvoviruses, Vol. 1. Boca Raton, Fl.: CRC Press, Inc., pp. 169-226.
25. Carter, B. J., Trempe, J. P. and Mendelson, E. 1990b. Adeno-associated virus gene expression and regulation. In P. Tijssen (ed.), Handbook ofParvoviruses, Vol. 1. Boca Raton, Fl.: CRC Press, Inc., pp. 227-54.
26. Casto, B. C., Atchison, R. W. and Hammon, W. M. 1967. Studies on the relationship between adeno-associated virus type I (AAV1) and adenoviruses. I. Replication of AAV1 in certain cell cultures and its effect on helper adenovirus. Virology 32: 52-9.
27. Cathomen, T., Stracker, T. H., Gilbert, L. B. and Weitzman, M. D. 2001. A genetic screen identifies a cellular regulator of adeno- associated virus. Proceedings of NationalAcademy of Sciences USA 98: 14991-6.
28. Challberg, M. D. 1986. A method for identifying the viral genes required for herpesvirus DNA replication. Proceedings of National Academy of Sciences USA 83: 9094-8.
29. Champoux, J. J. 2001. DNA topoisomerases: structure, function and mechanism. Annual Review ofBiochemistry 70: 369-413.
30. Chang, L. S., Shi, Y. and Shenk, T. 1989. Adeno-associated virus P5 promoter contains an adenovirus E1A-inducible element and a binding site for the major late transcription factor. Journal of Virology 63: 3479-88.
31. Chejanovsky, N. and Carter, B. J. 1989. Mutagenesis of an AUG codon in the adeno-associated virus rep gene: effects on viral DNA replication. Virology 173: 120-8.
32. Cheung, A. K., Hoggan, M. D., Hauswirth, W. W. and Berns, K. I. 1980. Integration of the adeno-associated virus genome into cellular DNA in latently infected human Detroit 6 cells. Journal of Virology 33: 739-48.
33. Chiorini, J. A., Weitzman, M. D., Owens, R. A. et al. 1994. Biologically active Rep proteins of adeno-associated virus type 2 produced as fusion proteins in Escherichia coli. Journal of Virology 68: 797-804.
34. Chiorini, J. A., Yang, L., Liu, Y. et al. 1997. Cloning of adeno-associated virus type 4 (AAV4) and generation of recombinant AAV4 particles. Journal of Virology 71: 6823-33.
35. Chiorini, J. A., Afione, S. and Kotin, R. M. 1999a. Adeno-associated virus (AAV) type 5 Rep protein cleaves a unique terminal resolution site compared with other AAV serotypes. Journal of Virology 73: 4293-8.
36. Chiorini, J. A., Kim, F., Yang, L. and Kotin, R. M. 1999b. Cloning and characterization of adeno-associated virus type 5. Journal of Virology 73: 1309-19.
37. Corsini, J., Tal, J. and Winocour, E. 1997. Directed integration of minute virus of mice DNA into episomes. Journal of Virology 71: 9008-15.
38. Davis, M. D., Wu, J. and Owens, R. A. 2000. Mutational analysis of adeno-associated virus type 2 Rep68 protein endonuclease activity on partially single-stranded substrates. Journal of Virology 74: 2936-42.
39. Debbas, M. and White, E. 1993. Wild-type p53 mediates apoptosis by E1A, which is inhibited by E1B. Genes and Development 7: 546-54.
40. Duan, D., Sharma, P., Yang, J. et al. 1998. Circular intermediates of recombinant adeno-associated virus have defined structural characteristics responsible for long-term episomal persistence in muscle tissue. Journal of Virology 72: 8568-77.
41. Duan, D., Yan, Z., Yue, Y. and Engelhardt, J. F. 1999. Structural analysis of adeno-associated virus transduction circular intermediates. Virology 261: 8-14.
42. Duan, D., Yue, Y. and Engelhardt, J. F. 2003. Consequences of DNA- dependent protein kinase catalytic subunit deficiency on recombinant adeno-associated virus genome circularization and heterodimerization in muscle tissue. Journal of Virology 77: 4751-9.
43. Dutheil, N., Malhomme, O., Provost, N. et al. 1997. Presence of integrated DNA sequences of adeno-associated virus type 2 in four cell lines of human embryonic origin. Journal of General Virology 78: 3039-43.
44. Dutheil, N., Shi, F., Dupressoir, T. and Linden, R. M. 2000. Adeno- associated virus site-specifically integrates into a muscle- specific DNA region. Proceedings of National Academy of Sciences USA 97: 4862-6.
45. Dyall, J. and Berns, K. I. 1998. Site-specific integration of adeno- associated virus into an episome with the target locus via a deletion-substitution mechanism. Journal of Virology 72: 6195-8.
46. Ferrari, F. K., Samulski, T., Shenk, T. and Samulski, R. J., 1996. Second- strand synthesis is a rate-limiting step for efficient transduction by recombinant adeno-associated virus vectors. Journal of Virology 70: 3227-34.
47. Fisher, K. J., Gao, G. P., Weitzman, M. D. et al. 1996. Transduction with recombinant adeno-associated virus for gene therapy is limited by leading-strand synthesis. Journal ofVirology 70: 520-32.
48. Flotte, T. R., Solow, R., Owens, R. A. et al. 1992. Gene expression from adeno-associated virus vectors in airway epithelial cells. American Journal of Respiratory Cell Molecular Biology 7: 349-56.
49. Flotte, T. R., Afione, S. A., Conrad, C. et al. 1993. Stable in vivo expression of the cystic fibrosis transmembrane conductance regulator with an adeno-associated virus vector. Proceedings of National Academy of Sciences USA 90: 10613-17.
50. Friedman-Einat, M., Grossman, Z., Mileguir, F. et al. 1997. Detection of adeno-associated virus type 2 sequences in the human genital tract. Journal of Clinical Microbiology 35: 71-8.
51. Gao, G. P., Alvira, M. R., Wang, L. et al. 2002. Novel adeno-associated viruses from rhesus monkeys as vectors for human gene therapy. Proceedings of National Academy of Sciences USA 99: 11854-9.
52. Gao, G., Alvira, M. R., Somanathan, S. et al. 2003. Adeno-associated viruses undergo substantial evolution in primates during natural infections. Proceedings of National Academy of Sciences USA 100: 6081-6.
53. Giraud, C., Winocour, E. and Berns, K. I. 1994. Site-specific integration by adeno-associated virus is directed by a cellular DNA sequence. Proceedings of National Academy of Sciences USA 91: 10039-43.
54. Giraud, C., Winocour, E. and Berns, K. I. 1995. Recombinant junctions formed by site-specific integration of adeno-associated virus into an episome. Journal ofVirology 69: 6917-24.
55. Gottlieb, J. and Muzyczka, N. 1988. In vitro excision of adeno- associated virus DNA from recombinant plasmids: isolation of an enzyme fraction from HeLa cells that cleaves DNA at poly(G) sequences. Molecular and Cellular Biology 8: 2513-22.
56. Gottlieb, J. and Muzyczka, N. 1990. Substrate specificity of HeLa endonuclease R. A G-specific mammalian endonuclease. Journal of Biological Chemistry 265: 10842-50.
57. Graham, F. L., Smiley, J., Russell, W. C. and Nairn, R. 1977. Characteristics of a human cell line transformed by DNA from human adenovirus type 5. Journal of General Virology 36: 59-72.
58. Grossman, Z., Mendelson, E., Brok-Simoni, F. et al. 1992. Detection of adeno-associated virus type 2 in human peripheral blood cells. Journal of General Virology 73: 961-6.
59. Handa, H. and Carter, B. J. 1979. Adeno-associated virus DNA replication complexes in herpes simplex virus or adenovirus- infected cells. Journal ofBiological Chemistry 254: 6603-10.
60. Heilbronn, R., Engstler, M., Weger, S. et al. 2003. ssDNA-dependent colocalization of adeno-associated virus Rep and herpes simplex virus ICP8 in nuclear replication domains. NucleicAcids Research 31: 6206-13.
61. Hermonat, P. L., Labow, M. A., Wright, R. et al. 1984. Genetics of adeno-associated virus: isolation and preliminary characterization of adeno-associated virus type 2 mutants. Journal of Virology 51: 329-39.
62. Herzog, R. W., Hagstrom, J. N., Kung, S. H. et al. 1997. Stable gene transfer and expression of human blood coagulation factor IX after intramuscular injection of recombinant adeno-associated virus. Proceedings of National Academy of Sciences USA 94: 5804-9.
63. Hoggan, M. D., Blacklow, N. R. and Rowe, W. P. 1966. Studies of small DNA viruses found in various adenovirus preparations: physical, biological and immunological characteristics. Proceedings of National Academy of Sciences USA 55: 1467-74.
64. Horer, M., Weger, S., Butz, K. et al. 1995. Mutational analysis of adeno-associated virus Rep protein-mediated inhibition of heterologous and homologous promoters. Journal of Virology 69: 5485-96.
65. Horwitz, M. S. 1985. Adenoviruses and their replication. In: B. N. Fields (ed.), Fields Virology. New York: Raven Press, pp. 433-76.
66. Hüser, D., Weger, S. and Heilbronn, R. 2002. Kinetics and freque ncy of adeno-associated virus site-specific integration into human chromosome 19 monitored by quantitative real-time PCR.Journal ofVirology 76: 7554-9.
67. Hüser, D., Weger, S. and Heilbronn, R. 2003. Packaging of human chromosome 19-specific adeno-associated virus (AAV) integration sites in AAV virions during AAV wild-type and recombinant AAV vector production. Journal ofVirology 77: 4881-7.
68. Im, D. S. and Muzyczka, N. 1990. The AAV origin binding protein Rep68 is an ATP-dependent site-specific endonuclease with DNA helicase activity. Cell 61: 447-57.
69. Im, D. S. and Muzyczka, N. 1992. Partial purification of adeno- associated virus Rep78: Rep52: and Rep40 and their biochemical characterization. Journal ofVirology 66: 1119-28.
70. Ishibashi, M. and Ito, M. 1971. The potentiation of type 1 adeno- associated virus by temperature-sensitive conditional-lethal mutants of CELO virus at the restrictive temperature. Virology 45: 317-20.
71. Ito, M. and Suzuki, E. 1970. Adeno-associated satellite virus growth supported by a temperature-sensitive mutant of human adenovirus. Journal of General Virology 9: 243-5.
72. Janik, J. E., Huston, M. M., Cho, K. and Rose, J. A. 1989. Efficient synthesis of adeno-associated virus structural proteins requires both adenovirus DNA binding protein and VA I RNA. Virology 168: 320-9.
73. Janik, J. E., Huston, M. M. and Rose, J. A. 1981. Locations of adenovirus genes required for the replication of adenovirus-associated virus. Proceedings of National Academy of Sciences USA 78: 1925-9.
74. Jay, F. T., Laughlin, C. A. and Carter, B. J. 1981. Eukaryotic translational control: adeno-associated virus protein synthesis is affected by a mutation in the adenovirus DNA-binding protein. Proceedings of National Academy of Sciences USA 78: 2927-31.
75. Kaplitt, M. G., Leone, P., Samulski, R. J. et al. 1994. Long-term gene expression and phenotypic correction using adeno-associated virus vectors in the mammalian brain. Nature Genetics 8: 148-54.
76. Kearns, W. G., Afione, S. A., Fulmer, S. B. et al. 1996. Recombinant adeno-associated virus (AAV-CFTR) vectors do not integrate in a site-specific fashion in an immortalized epithelial cell line. Gene Therapy 3: 748-55.
77. King, J. A., Dubielzig, R., Grimm, D. and Kleinschmidt, J. A. 2001. DNA helicase-mediated packaging of adeno-associated virus type 2 genomes into preformed capsids. EMBO Journal 20: 3282-91.
78. Koeberl, D. D., Alexander, I. E., Halbert, C. L. et al. 1997. Persistent expression of human clotting factor IX from mouse liver after intravenous injection of adeno-associated virus vectors. Proceedings of National Academy of Sciences USA 94: 1426-31.
79. Kotin, R. M. and Berns, K. I. 1989. Organization of adeno-associated virus DNA in latently infected Detroit 6 cells. Virology 170: 460-7.
80. Kotin, R. M., Siniscalco, M., Samulski, R. J. et al. 1990. Site-specific integration by adeno-associated virus. Proceedings of National Academy of Sciences USA 87: 2211-15.
81. Kotin, R. M., Menninger, J. C., Ward, D. C. and Berns, K. I. 1991. Mapping and direct visualization of a region-specific viral DNA integration site on chromosome 19q13-qter. Genomics 10: 831-4.
82. Kotin, R. M., Linden, R. M. and Berns, K. I. 1992. Characterization of a preferred site on human chromosome 19q for integration of adeno-associated virus DNA by non-homologous recombination. EMBO Journal 11: 5071-8.
83. Kyostio, S. R. M., Owens, R. A., Weitzman, M. D. et al. 1994. Analysis of adeno-associated virus (AAV) wild-type and mutant Rep proteins for their abilities to negatively regulate AAV p5 and p19 mRNA levels. Journal ofVirology 68: 2947-57.
84. Kyostio, S. R. M., Wonderling, R. S. and Owens, R. A. 1995. Negative regulation of the adeno-associated virus (AAV) P5 promoter involves both the P5 Rep binding site and the consensus ATP- binding motif of the AAV Rep68 protein. Journal ofVirology 69: 6787-96.
85. Labow, M. A., Hermonat, P. L. and Berns, K. I. 1986. Positive and negative autoregulation of the adeno-associated virus type 2 genome. Journal ofVirology 60: 251-8.
86. Lalwani, A. K., Walsh, B. J., Reilly, P. G. et al. 1998. Long-term in vivo cochlear transgene expression mediated by recombinant adeno- associated virus. Gene Therapy 5: 277-81.
87. Lamartina, S., Sporeno, E., Fattori, E. and Toniatti, C. 2000. Characteristics of the adeno-associated virus pre-integration site in human chromosome 19: open chromatin conformation and transcription-competent environment. Journal ofVirology 74: 7671-7.
88. Laughlin, C. A., Jones, N. and Carter, B. J. 1982. Effect of deletions in adenovirus early region 1 genes upon replication of adeno- associated virus. Journal ofVirology 41: 868-76.
89. Laughlin, C. A., Tratschin, J. D., Coon, H. and Carter, B. J. 1983. Cloning of infectious adeno-associated virus genomes in bacterial plasmids. Gene 23: 65-73.
90. Laughlin, C. A., Cardellichio, C. B. and Coon, H. C. 1986. Latent infection of KB cells with adeno-associated virus type 2. Journal of Virology 60: 515-24.
91. Lehman, I. R. and Boehmer, P. E. 1999. Replication of herpes simplex virus DNA. Journal of Biological Chemistry 274: 28059-62.
92. Leppard, K. N. 1997. E4 gene function in adenovirus, adenovirus vector and adeno-associated virus infections. Journal of General Virology 78: 2131-8.
93. Lewis, B. A., Tullis, G., Seto, E. et al. 1995. Adenovirus E1A proteins interact with the cellular YY1 transcription factor. Journal of Virology 69: 1628-36.
94. Linden, R. M., Winocour, E. and Berns, K. I. 1996. The recombination signals for adeno-associated virus site-specific integration. Proceedings of National Academy of Sciences USA 93: 7966-72.
95. Lipps, B. V. and Mayor, H. D. 1980. Transplacental infection with adeno-associated virus type 1 in mice. Intervirology 14: 118-23.
96. McCarty, D. M., Christensen, M. and Muzyczka, N. 1991. Sequences required for coordinate induction of adeno-associated virus p19 and p40 promoters by Rep protein. Journal ofVirology 65: 2936-45.
97. McCarty, D. M., Ni, T. H. and Muzyczka, N. 1992. Analysis of mutations in adeno-associated virus Rep protein in vivo and in vitro. Journal ofVirology 66: 4050-7.
98. McCarty, D. M., Pereira, D. J., Zolotukhin, I. et al. 1994a. Identification of linear DNA sequences that specifically bind the adeno- associated virus Rep protein. Journal ofVirology 68: 4988-97.
99. McCarty, D. M., Ryan, J. H., Zolotukhin, S. et al. 1994b. Interaction of the adeno-associated virus Rep protein with a sequence within the A palindrome of the viral terminal repeat. Journal ofVirology 68: 4998-5006.
100. McCown, T. J., Xiao, X., Li, J. et al. 1996. Differential and persistent expression patterns of CNS gene transfer by an adeno-associated virus (AAV) vector. Brain Research 713: 99-107.
101. Mendelson, E., Trempe, J. P. and Carter, B. J. 1986. Identification of the trans-acting Rep proteins of adeno-associated virus by antibodies to a synthetic oligopeptide. Journal ofVirology 60: 823-32.
102. Mendelson, E., Smith, M. G. and Carter, B. J. 1988a. Expression and rescue of a nonselected marker from an integrated AAV vector. Virology 166: 154-65.
103. Mendelson, E., Smith, M. G., Miller, I. L. and Carter, B. J. 1988b. Effect of a viral rep gene on transformation of cells by an adeno- associated virus vector. Virology 166: 612-15.
104. Miller, D. G., Rutledge, E. A. and Russell, D. W. 2002. Chromosomal effects of adeno-associated virus vector integration. Nature Genetics 30: 147-8.
105. Monahan, P. E., Samulski, R. J., Tazelaar, J. et al. 1998. Direct intramuscular injection with recombinant AAV vectors results in sustained expression in a dog model of hemophilia. Gene Therapy 5: 40-9.
106. Muramatsu, S., Mizukami, H., Young, N. S. and Brown, K. E. 1996. Nucleotide sequencing and generation of an infectious clone of adeno-associated virus 3. Virology 221: 208-17.
107. Muramatsu, S., Handa, A., Kajigaya, S. and Brown, K. E. 1998. Transcription-positive cofactor 4 enhances rescue of adeno- associated virus genome from an infectious clone. Journal of General Virology 79: 2157-61.
108. Murphy, J. E., Zhou, S., Giese, K. et al. 1997. Long-term correction of obesity and diabetes in genetically obese mice by a single intramuscular injection of recombinant adeno-associated virus encoding mouse leptin. Proceedings of National Academy of Sciences USA 94: 13921-6.
109. Myers, M. W. and Carter, B. J. 1980. Assembly of adeno-associated virus. Virology 102: 71-82.
110. Myers, M. W. and Carter, B. J. 1981. Adeno-associated virus replication. The effect of L-canavanine or a helper virus mutation on accumulation of viral capsids and progeny single-stranded DNA. Journal of Biological Chemistry 256: 567-70.
111. Myers, M. W., Laughlin, C. A., Jay, F. T. and Carter, B. J. 1980. Adenovirus helper function for growth of adeno-associated virus: effect of temperature-sensitive mutations in adenovirus early gene region 2. Journal ofVirology 35: 65-75.
112. Nakai, H., Yant, S. R., Storm, T. A. et al. 2001. Extrachromosomal recombinant adeno-associated virus vector genomes are primarily responsible for stable liver transduction in vivo. Journal ofVirology 75: 6969-76.
113. Nakai, H., Fuess, S., Storm, T. A. et al. 2003a. Free DNA ends are essential for concatemerization of synthetic double-stranded adeno-associated virus vector genomes transfected into mouse hepatocytes in vivo. Molecular Therapy 7: 112-21.
114. Nakai, H., Montini, E., Fuess, S. et al. 2003b. AAV serotype 2 vectors preferentially integrate into active genes in mice. Nature Genetics 34: 297-302.
115. Nakai, H., Storm, T. A., Fuess, S. and Kay, M. A. 2003c. Pathways of removal of free DNA vector ends in normal and DNA-PKcs- deficient SCID mouse hepatocytes transduced with rAAV vectors. Human Gene Therapy 14: 871-81.
116. Ni, T. H., McDonald, W. F., Zolotukhin, I. et al. 1998. Cellular proteins required for adeno-associated virus DNA replication in the absence of adenovirus coinfection. Journal ofVirology 72: 2777-87.
117. Ogata, T., Kozuka, T. and Kanda, T. 2003. Identification of an insulator in AAVS1: a preferred region for integration of adeno-associated virus DNA. Journal ofVirology 77: 9000-7.
118. Omori, F., Messner, H. A., Ye, C. et al. 1999. Nontargeted stable integration of recombinant adeno-associated virus into human leukemia and lymphoma cell lines as evaluated by fluorescence in situ hybridization. Human Gene Therapy 10: 537-43.
119. Ostrove, J. M. and Berns, K. I. 1980. Adenovirus early region 1b gene function required for rescue of latent adeno-associated virus. Virology 104: 502-5.
120. Owens, R. A., Weitzman, M. D., Kyostio, S. R. M. and Carter, B. J. 1993. Identification of a DNA-binding domain in the amino terminus of adeno-associated virus Rep proteins. Journal ofVirology 67: 997-1005.
121. Palombo, F., Monciotti, A., Recchia, A. et al. 1998. Site-specific integration in mammalian cells mediated by a new hybrid baculovirus-adeno-associated virus vector. Journal ofVirology 72: 5025-34.
122. Pereira, D. J. and Muzyczka, N. 1997a. The adeno-associated virus type 2 p40 promoter requires a proximal Sp1 interaction and a p19 CArG-like element to facilitate Rep transactivation. Journal ofVirology 71: 4300-9.
123. Pereira, D. J. and Muzyczka, N. 1997b. The cellular transcription factor SP1 and an unknown cellular protein are required to mediate Rep protein activation of the adeno-associated virus p19 promoter. Journal ofVirology 71: 1747-56.
124. Pereira, D. J., McCarty, D. M. and Muzyczka, N. 1997. The adeno- associated virus (AAV) Rep protein acts as both a repressor and an activator to regulate AAV transcription during a productive infection. Journal ofVirology 71: 1079-88.
125. Philip, R., Brunette, E., Kilinski, L. et al. 1994. Efficient and sustained gene expression in primary T lymphocytes and primary and cultured tumor cells mediated by adeno-associated virus plasmid DNA complexed to cationic liposomes. Molecular and Cellular Biology 14: 2411-18.
126. Philpott, N. J., Giraud-Wali, C., Dupuis, C. etal. 2002. Efficient integration of recombinant adeno-associated virus DNA vectors requires a p5-rep sequence in cis. Journal of Virology 76: 5411-21.
127. Pilder, S., Moore, M., Logan, J. and Shenk, T. 1986. The adenovirus E1B-55K transforming polypeptide modulates transport or cytoplasmic stabilization of viral and host cell mRNAs. Molecular and Cellular Biology 6: 470-6.
128. Qing, K., Khuntirat, B., Mah, C. et al. 1998. Adeno-associated virus type 2-mediated gene transfer: correlation of tyrosine phosphorylation of the cellular single-stranded D sequence- binding protein with transgene expression in human cells in vitro and murine tissues in vivo. Journal of Virology 72: 1593-9.
129. Rabinowitz, J. E., Rolling, F., Li, C. et al. 2002. Cross-packaging of a single adeno-associated virus (AAV) type 2 vector genome into multiple AAV serotypes enables transduction with broad specificity. Journal of Virology 76: 791-801.
130. Russell, D. W., Alexander, I. E. and Miller, A. D. 1995. DNA synthesis and topoisomerase inhibitors increase transduction by adeno- associated virus vectors. Proceedings of NationalAcademy of Sciences USA 92: 5719-23.
131. Rutledge, E. A., Halbert, C. L. and Russell, D. W. 1998. Infectious clones and vectors derived from adeno-associated virus (AAV) serotypes other than AAV type 2. Journal of Virology 72: 309-19.
132. Samulski, R. J., Berns, K. I., Tan, M. and Muzyczka, N. 1982. Cloning of adeno-associated virus into pBR322: rescue of intact virus from the recombinant plasmid in human cells. Proceedings of National Academy of Sciences USA 79: 2077-81.
133. Samulski, R. J., Srivastava, A., Berns, K. I. and Muzyczka, N. 1983. Rescue of adeno-associated virus from recombinant plasmids: gene correction within the terminal repeats of AAV. Cell 33: 135-43.
134. Samulski, R. J., Zhu, X., Xiao, X. et al. 1991. Targeted integration of adeno-associated virus (AAV) into human chromosome 19. EMBO Journal 10: 3941-50.
135. Sarnow, P., Hearing, P. Anderson, C. W. et al. 1984. Adenovirus early region 1B 58 000-dalton tumor antigen is physically associated with an early region 4 25 000-dalton protein in productively infected cells. Journal ofVirology 49: 692-700.
136. Sarnow, P., Ho, Y. S., Williams, J. and Levine, A. J. 1982. Adenovirus E1b-58kd tumor antigen and SV40 large tumor antigen are physically associated with the same 54 kd cellular protein in transformed cells. Cell 28: 387-94.
137. Schlehofer, J. R., Ehrbar, M. and zur Hausen, H. 1986. Vaccinia virus, herpes simplex virus and carcinogens induce DNA amplification in a human cell line and support replication of a helpervirus- dependent parvovirus. Virology 152: 110-17.
138. Schmidt, M., Afione, S. and Kotin, R. M. 2000. Adeno-associated virus type 2 Rep78 induces apoptosis through caspase activation independently of p53. Journal ofVirology 74: 9441-50.
139. Seto, E., Shi, Y. and Shenk, T. 1991. YY1 is an initiator sequence- binding protein that directs and activates transcription in vitro. Nature 354: 241-5.
140. Seto, E., Lewis, B. and Shenk, T. 1993. Interaction between transcription factors Sp1 and YY1. Nature 365: 462-4.
141. Shelling, A. N. and Smith, M. G. 1994. Targeted integration of transfected and infected adeno-associated virus vectors containing the neomycin resistance gene. Gene Therapy 1: 165-9.
142. Shi, Y., Seto, E., Chang, L. S. and Shenk, T. 1991. Transcriptional repression by YY1: a human GLI-Kruppel-related protein and relief of repression by adenovirus E1A protein. Cell 67: 377-88.
143. Siegl, G., Bates, R. C., Berns, K. I. et al. 1985. Characteristics and taxonomy of Parvoviridae. Intervirology 23: 61-73.
144. Smith, R. H. and Kotin, R. M. 2000. An adeno-associated virus (AAV) initiator protein, Rep78, catalyzes the cleavage and ligation of single-stranded AAV ori DNA. Journal ofVirology 74: 3122-9.
145. Snyder, R. O., Im, D. S. and Muzyczka, N. 1990a. Evidence for covalent attachment of the adeno-associated virus (AAV) Rep protein to the ends of the AAV genome. Journal ofVirology 64: 6204-13.
146. Snyder, R. O., Samulski, R. J. and Muzyczka, N. 1990b. In vitro resolution of covalently joined AAV chromosome ends. Cell 60: 105-13.
147. Snyder, R. O., Im, D. S., Ni, T. et al. 1993. Features of the adeno- associated virus origin involved in substrate recognition by the viral Rep protein. Journal ofVirology 67: 6096-104.
148. Snyder, R. O., Spratt, S. K., Lagarde, C. et al. 1997. Efficient and stable adeno-associated virus-mediated transduction in the skeletal muscle of adult immunocompetent mice. Human Gene Therapy 8: 1891-900.
149. Snyder, R. O., Miao, C., Meuse, L. et al. 1999. Correction of hemophilia B in canine and murine models using recombinant adeno- associated viral vectors. Nature Medicine 5: 64-70.
150. Song, S., Laipis, P. J., Berns, K. I. and Flotte, T. R. 2001. Effect of DNA- dependent protein kinase on the molecular fate of the rAAV2 genome in skeletal muscle. Proceedings of National Academy of Sciences USA 98: 4084-8.
151. Southern, E. M. 1975. Detection of specific sequences among DNA fragments separated by gel electrophoresis. Journal of Molecular Biology 98: 503-17.
152. Srivastava, A., Lusby, E. W. and Berns, K. I. 1983. Nucleotide sequence and organization of the adeno-associated virus 2 genome. Journal ofVirology 45: 555-64.
153. Steigerwald, R., Rabe, C., Schmitz, V. et al. 2003. Requirements for adeno-associated virus-derived non-viral vectors to achieve stable and site-specific integration of plasmid DNA in liver carcinoma cells. Digestion 68: 13-23.
154. Straus, S. E., Sebring, E. D. and Rose, J. A. 1976. Concatemers of alternating plus and minus strands are intermediates in adenovirus-associated virus DNA synthesis. Proceedings of National Academy ofSciences USA 73: 742-6.
155. Thimmappaya, B., Weinberger, C., Schneider, R. J. and Shenk, T. 1982. Adenovirus VAI RNA is required for efficient translation of viral mRNAs at late times after infection. Cell 31: 543-51.
156. Thomson, B. J., Efstathiou, S. and Honess, R. W. 1991. Acquisition of the human adeno-associated virus type-2 rep gene by human herpesvirus type-6. Nature 351: 78-80.
157. Thomson, B. J., Weindler, F. W., Gray, D. et al. 1994. Human herpesvirus 6 (HHV-6) is a helper virus for adeno-associated virus type 2 (AAV2) and the AAV2 rep gene homologue in HHV-6 can mediate AAV2 DNA replication and regulate gene expression. Virology 204: 304-11.
158. Tratschin, J. D., Miller, I. L. and Carter, B. J. 1984. Genetic analysis of adeno-associated virus: properties of deletion mutants constructed in vitro and evidence for an adeno-associated virus replication function. Journal ofVirology 51: 611-19.
159. Tratschin, J. D., Tal, J. and Carter, B. J. 1986. Negative and positive regulation in trans of gene expression from adeno-associated virus vectors in mammalian cells by a viral rep gene product. Molecular and Cellular Biology 6: 2884-94.
160. Trempe, J. P. and Carter, B. J. 1988. Alternate mRNA splicing is required for synthesis of adeno-associated virus VP1 capsid protein. Journal ofVirology 62: 3356-63.
161. Urabe, M., Hasumi, Y., Kume, A. et al. 1999. Charged-to-alanine scanning mutagenesis of the N-terminal half of adeno-associated virus type 2 Rep78 protein. Journal ofVirology 73: 2682-93.
162. Urabe, M., Kogure, K., Kume, A. et al. 2003. Positive and negative effects of adeno-associated virus Rep on AAVSMargeted integration. Journal of General Virology 84: 2127-32.
163. Urcelay, E., Ward, P., Wiener, S. M. et al. 1995. Asymmetric replication in vitro from a human sequence element is dependent on adeno- associated virus Rep protein. Journal ofVirology 69: 2038-46.
164. van Dyck, E., Stasiak, A. Z., Stasiak, A. and West, S. C. 1999. Binding of double-strand breaks in DNA by human Rad52 protein. Nature 398: 728-31.
165. Walz, C. and Schlehofer, J. R. 1992. Modification of some biological properties of HeLa cells containing adeno-associated virus DNA integrated into chromosome 17. Journal ofVirology 66: 2990-3002.
166. Walz, C., Deprez, A., Dupressoir, T. et al. 1997. Interaction of human papillomavirus type 16 and adeno-associated virus type 2 co- infecting human cervical epithelium. Journal of General Virology 78: 1441-52.
167. Wang, L., Takabe, K., Bidlingmaier, S. M. et al. 1999. Sustained correction of bleeding disorder in hemophilia B mice by gene therapy. Proceedings of National Academy of Sciences USA 96: 3906-10.
168. Ward, P. and Berns, K. I. 1991. In vitro rescue of an integrated hybrid adeno-associated virus/simian virus 40 genome. Journal of Moleclar Biology 218: 791-804.
169. Ward, P., Urcelay, E., Kotin, R. et al. 1994. Adeno-associated virus DNA replication in vitro: activation by a maltose binding protein/Rep68 fusion protein. Journal ofVirology 68: 6029-37.
170. Ward, P., Dean, F. B., O'Donnell, M. E. and Berns, K. I. 1998. Role of the adenovirus DNA-binding protein in in vitro adeno-associated virus DNA replication. Journal ofVirology 72: 420-7.
171. Ward, P., Falkenberg, M., Elias, P. et al. 2001. Rep-dependent initiation of adeno-associated virus type 2 DNA replication by a herpes simplex virus type 1 replication complex in a reconstituted system. Journal ofVirology 75: 10250-8.
172. Weber, M., Rabinowitz, J., Provost, N. et al. 2003. Recombinant adeno-associated virus serotype 4 mediates unique and exclusive long-term transduction of retinal pigmented epithelium in rat, dog and nonhuman primate after subretinal delivery. Molecular Therapy 7: 774-81.
173. Weger, S., Wendland, M., Kleinschmidt, J. A. and Heilbronn, R. 1999. The adeno-associated virus type 2 regulatory proteins rep78 and rep68 interact with the transcriptional coactivator PC4. Journal ofVirology 73: 260-9.
174. Weger, S., Hammer, E. and Heilbronn, R. 2002. Topors, a p53 and topoisomerase I binding protein, interacts with the adeno- associated virus (AAV2) Rep78/68 proteins and enhances AAV2 gene expression. Journal of General Virology 83: 511-16.
175. Weindler, F. W. and Heilbronn, R. 1991. A subset of herpes simplex virus replication genes provides helper functions for productive adeno- associated virus replication. Journal ofVirology 65: 2476-83.
176. Weitzman, M. D., Kyostio, S. R. M., Kotin, R. M. and Owens, R. A. 1994. Adeno-associated virus (AAV) Rep proteins mediate complex formation between AAV DNA and its integration site in human DNA. Proceedings of National Academy of Sciences USA 91: 5808-12.
177. Weitzman, M. D., Fisher, K. J. and Wilson, J. M. 1996. Recruitment of wild-type and recombinant adeno-associated virus into adenovirus replication centers. Journal ofVirology 70: 1845-54.
178. West, M. H., Trempe, J. P., Tratschin, J. D. and Carter, B. J. 1987. Gene expression in adeno-associated virus vectors: the effects of chimeric mRNA structure, helper virus and adenovirus VA| RNA. Virology 160: 38-47.
179. Winocour, E., Puzis, L., Etkin, S. et al. 1992. Modulation of the cellular phenotype by integrated adeno-associated virus. Virology 190: 316-29.
180. Wonderling, R. S. and Owens, R. A. 1996. The Rep68 protein of adeno- associated virus type 2 stimulates expression of the platelet- derived growth factor B c-sis proto-oncogene. Journal of Virology 70: 4783-6.
181. Wonderling, R. S. and Owens, R. A. 1997. Binding sites for adeno- associated virus Rep proteins within the human genome. Journal ofVirology 71: 2528-34.
182. Wu, C. A., Nelson, N. J., McGeoch, D. J. and Challberg, M. D. 1988. Identification of herpes simplex virus type 1 genes required for origin-dependent DNA synthesis. Journal ofVirology 62: 435-43.
183. Wu, P., Phillips, M. I., Bui, J. and Terwilliger, E. F. 1998. Adeno-associated virus vector-mediated transgene integration into neurons and other nondividing cell targets. Journal ofVirology 72: 5919-26.
184. Wu, J., Davis, M. D. and Owens, R. A. 1999. Factors affecting the terminal resolution site endonuclease, helicase and ATPase activities of adeno-associated virus type 2 Rep proteins. Journal ofVirology 73: 8235-44.
185. Xiao, X., deVlaminck, W. and Monahan, J. 1993. Adeno-associated virus (AAV) vectors for gene transfer. Advanced Drug Delivery Reviews 12: 201-15.
186. Xiao, X., Li, J. and Samulski, R. J. 1996. Efficient long-term gene transfer into muscle tissue of immunocompetent mice by adeno- associated virus vector. Journal ofVirology 70: 8098-108.
187. Xiao, X., Xiao, W., Li, J. and Samulski, R. J. 1997. A novel 165-base- pair terminal repeat sequence is the sole cis requirement for the adeno-associated virus life cycle. Journal ofVirology 71: 941-8.
188. Xiao, X., Li, J. and Samulski, R. J. 1998. Production of high-titer recombinant adeno-associated virus vectors in the absence of helper adenovirus. Journal ofVirology 72: 2224-32.
189. Xiao, W., Chirmule, N., Berta, S. C. et al. 1999. Gene therapy vectors based on adeno-associated virus type 1. Journal ofVirology 73: 3994-4003.
190. Xiao, W., Warrington, K. H., Hearing, P. et al. 2002. Adenovirus- facilitated nuclear translocation of adeno-associated virus type 2. Journal ofVirology 76: 11505-17.
191. Yakobson, B., Koch, T. and Winocour, E. 1987. Replication of adeno- associated virus in synchronized cells without the addition of a helper virus. Journal ofVirology 61: 972-81.
192. Yakobson, B., Hrynko, T. A., Peak, M. J. and Winocour, E. 1989. Replication of adeno-associated virus in cells irradiated with UV light at 254nm. Journal ofVirology 63: 1023-30.
193. Yalkinoglu, A. O., Heilbronn, R., Bürkle, A. et al. 1988. DNA amplification of adeno-associated virus as a response to cellular genotoxic stress. Cancer Res. 48: 3123-9.
194. Yalkinoglu, A. O., Zentgraf, H. and Hübscher, U. 1991. Origin of adeno- associated virus DNA replication is a target of carcinogen- inducible DNA amplification. Journal ofVirology 65: 3175-84.
195. Yang, Q., Chen, F. and Trempe, J. P. 1994. Characterization of cell lines that inducibly express the adeno-associated virus Rep proteins. Journal ofVirology 68: 4847-56.
196. Yang, C. C., Xiao, X., Zhu, X. et al. 1997. Cellular recombination pathways and viral terminal repeat hairpin structures are sufficient for adeno-associated virus integration in vivo and in vitro. Journal ofVirology 71: 9231-47.
197. Yates, V. J., el-Mishad, A. M., McCormick, K. J. and Trentin, J. J. 1973. Isolation and characterization of an avian adenovirus-associated virus. Infection and Immunity 7: 973-80.
198. Young, S. M., McCarty, D. M., Degtyareva, N. and Samulski, R. J. 2000. Roles of adeno-associated virus Rep protein and human chromosome 19 in site-specific recombination. Journal of Virology 74: 3953-66.
199. Young, S. M. and Samulski, R. J. 2001. Adeno-associated virus (AAV) site-specific recombination does not require a Rep-dependent origin of replication within the AAV terminal repeat. Proceedings of National Academy of Sciences USA 98: 13525-30.
200. Zentilin, L., Marcello, A. and Giacca, M. 2001. Involvement of cellular double-stranded DNA break binding proteins in processing of the recombinant adeno-associated virus genome. Journal of Virology 75: 12279-87.
201. Zhou, X. and Muzyczka, N. 1998. In vitro packaging of adeno- associated virus DNA. Journal ofVirology 72: 3241-3247.
202. Zhou, C., Yang, Q. and Trempe, J. P. 1999a. Enhancement of UV- induced cytotoxicity by the adeno-associated virus replication proteins. Biochimica Biophysica Acta 1444: 371-83.
203. Zhou, X., Zolotukhin, I., Im, D. S. and Muzyczka, N. 1999b. Biochemical characterization of adeno-associated virus Rep68 DNA helicase and ATPase activities. Journal ofVirology 73: 1580-90.
204. Zhu, J. and Schiestl, R. H. 1996. Topoisomerase I involvement in illegitimate recombination in Saccharomyces cerevisiae. Molecular and Cellular Biology 16: 1805-12.