Gammaretroviral integration into nucleosomal target DNA in vivo

Journal of Virology

Volumn 85, Issue 14, 2011, Pages 7393-7401

  Roth, Shoshannah L ^a   Malani, Nirav ^a   Bushman, Frederic D ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE I; DNA; GENOMIC DNA; HISTONE; RETROVIRUS VECTOR;

ARTICLE; CD4+ T LYMPHOCYTE; CHROMATIN; CONTROLLED STUDY; GENE ACTIVITY; GENE MAPPING; GENETIC TRANSDUCTION; HISTONE ACETYLATION; HISTONE METHYLATION; HUMAN; HUMAN CELL; HUMAN IMMUNODEFICIENCY VIRUS; IN VIVO STUDY; MURINE LEUKEMIA VIRUS; NONHUMAN; NUCLEOSOME; POLYMERASE CHAIN REACTION; PREDICTION; PRIORITY JOURNAL; PYROSEQUENCING; RETROVIRUS; VIRUS CELL INTERACTION; VIRUS DNA CELL DNA INTERACTION; XENOTROPIC MULV RELATED VIRUS;

ACETYLATION; CD4-POSITIVE T-LYMPHOCYTES; DNA, VIRAL; GAMMARETROVIRUS; HISTONES; HUMANS; NUCLEOSOMES; TRANSDUCTION, GENETIC; VIRUS INTEGRATION;

MURINE LEUKEMIA VIRUS; XENOTROPIC MURINE LEUKEMIA VIRUS;

EID: 79960404187     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.00635-11     Document Type: Article

References (61)

1. Angelov, D., et al. 2004. The histone octamer is invisible when NF-kappa B binds to the nucleosome. J. Biol. Chem. 279:42374-42382.
2. Bannister, A. J., et al. 2001. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410:120-124.
3. Barski, A., et al. 2007. High-resolution profiling of histone methylations in the human genome. Cell 129:823-837.
4. Berry, C., S. Hannenhalli, J. Leipzig, and F. D. Bushman. 2006. Selection of target sites for mobile DNA integration in the human genome. PLoS Comp. Biol. 2:e157.
5. Biasco, L. A., et al. 2011. Integration profile of retroviral vector in gene therapy treated patients is cell-specific according to gene expression and chromatin conformation of target cell. EMBO Mol. Med. 3:89-101.
6. Brady, T., et al. 2009. Integration target site selection by a resurrected human endogenous retrovirus. Genes Dev. 23:633-642.
7. Brady, T., et al. 16 March 2011, posting date. A method to sequence and quantify DNA integration for monitoring outcome in gene therapy. Nucleic Acids Res. doi:10.1093/nar/gkr140.
8. Cattoglio, C., et al. 2007. Hot spots of retroviral integration in human CD34+ hematopoietic cells. Blood 110:1770-1778.
9. Cattoglio, C., et al. 2010. High-definition mapping of retroviral integration sites identifies active regulatory elements in human multipotent hematopoietic progenitors. Blood 116:5507-5517.
10. Cherepanov, P., A. L. Ambrosio, S. Rahman, T. Ellenberger, and A. Engelman. 2005. Structural basis for the recognition between HIV-1 integrase and transcriptional coactivator p75. Proc. Natl. Acad. Sci. U. S. A. 102:17308-17313.
11. Cherepanov, P., et al. 2003. HIV-1 integrase forms stable tetramers and associates with LEDGF/p75 protein in human cells. J. Biol. Chem. 278:372-381.
12. Ciuffi, A., et al. 2005. A role for LEDGF/p75 in targeting HIV DNA integration. Nat. Med. 11:1287-1289.
13. Ciuffi, A., et al. 2009. Methods for integration site distribution analyses in animal cell genomes. Methods 47:261-268.
14. Deichmann, A., et al. 2007. Vector integration is nonrandom and clustered and influences the fate of lymphopoiesis in SCID-X1 gene therapy. J. Clin. Invest. 117:2225-2232.
15. De Rijck, J., K. Bartholomeeusen, H. Ceulemans, Z. Debyser, and R. Gijsbers. 2010. High-resolution profiling of the LEDGF/p75 chromatin interaction in the ENCODE region. Nucleic Acids Res. 38:6135-6147.
16. Emiliani, S., et al. 2005. Integrase mutants defective for interaction with LEDGF/p75 are impaired in chromosome tethering and HIV-1 replication. J. Biol. Chem. 280:25517-25523.
17. Felice, B., et al. 2009. Transcription factor binding sites are genetic determinants of retroviral integration in the human genome. PLoS One 4:e4571.
18. Ferris, A. L., et al. 2010. Lens epithelium-derived growth factor fusion proteins redirect HIV-1 DNA integration. Proc. Natl. Acad. Sci. U. S. A. 107:3135-3140.
19. Garson, J. A., P. Kellam, and G. J. Towers. 2011. Analysis of XMRV integration sites from human prostate cancer tissues suggests PCR contamination rather than genuine human infection. Retrovirology 8:13.
20. Gijsbers, R., et al. 2010. LEDGF hybrids efficiently retarget lentiviral integration into heterochromatin. Mol. Ther. 18:552-560.
21. Hacein-Bey-Abina, S., et al. 2008. Insertional oncogenesis in 4 patients after retrovirus-mediated gene therapy of SCID-X1. J. Clin. Invest. 118:3132-3142.
22. Hue, S., et al. 2010. Disease-associated XMRV sequences are consistent with laboratory contamination. Retrovirology 7:111.
23. Jiang, C., and B. F. Pugh. 2009. Nucleosome positioning and gene regulation: advances through genomics. Nat. Rev. Genet. 10:161-172.
24. Kaplan, N., et al. 2010. Nucleosome sequence preferences influence in vivo nucleosome organization. Nat. Struct. Mol. Biol. 17:918-920.
25. Kaplan, N., et al. 2009. The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 458:362-366.
26. Kim, S., et al. 2008. Integration site preference of xenotropic murine leukemia virus-related virus, a new human retrovirus associated with prostate cancer. J. Virol. 82:9964-9977.
27. Kim, S., et al. 2010. Fidelity of target site duplication and sequence preference during integration of xenotropic murine leukemia virus-related virus. PLoS One 5:e10255.
28. Lewinski, M. K., et al. 2006. Retroviral DNA integration: viral and cellular determinants of target-site selection. PLoS Pathog. 2:e60.
29. Llano, M., et al. 2006. An essential role for LEDGF/p75 in HIV integration. Science 314:461-464.
30. Lombardi, V. C., et al. 2009. Detection of an infectious retrovirus, XMRV, in blood cells of patients with chronic fatigue syndrome. Science 326:585-589.
31. Maertens, G. N., S. Hare, and P. Cherepanov. 2010. The mechanism of retroviral integration from X-ray structures of its key intermediates. Nature 468:326-329.
32. Marshall, H., et al. 2007. Role of PSIP1/LEDGF/p75 in lentiviral infectivity and integration targeting. PLoS One 2:e1340.
33. Mitchell, R. S., et al. 2004. Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences. PLoS Biol. 2:E234.
34. Muller, H. P., and H. E. Varmus. 1994. DNA bending creates favored sites for retroviral integration: an explanation for preferred insertion sites in nucleosomes. EMBO J. 13:4704-4714.
35. Oakes, B., et al. 2010. Contamination of human DNA samples with mouse DNA can lead to false detection of XMRV-like sequences. Retrovirology 7:109.
36. Ocwieja, K. E., et al. 2011. HIV integration targeting: a pathway involving Transportin-3 and the nuclear pore protein RanBP2. PLoS Pathog. 7:e1001313.
37. Ooi, L., and I. C. Wood. 2007. Chromatin crosstalk in development and disease: lessons from REST. Nat. Rev. Genet. 8:544-554.
38. Osipov, S. A., O. V. Preobrazhenskaya, and V. L. Karpov. 2010. Chromatin structure and transcription regulation in Saccharomyces cerevisiae. Mol. Biol. 44:856-869.
39. Panet, A., and H. Cedar. 1977. Selective degradation of integrated murine leukemia proviral DNA by deoxyribonucleases. Cell 11:933-940.
40. Phillips, J. E., and V. G. Corces. 2009. CTCF: master weaver of the genome. Cell 137:1194-1211.
41. Pruss, D., F. D. Bushman, and A. P. Wolffe. 1994. Human immunodeficiency virus integrase directs integration to sites of severe DNA distortion within the nucleosome core. Proc. Natl. Acad. Sci. U. S. A. 91:5913-5917.
42. Pruss, D., R. Reeves, F. D. Bushman, and A. P. Wolffe. 1994. The influence of DNA and nucleosome structure on integration events directed by HIV integrase. J. Biol. Chem. 269:25031-25041.
43. Pryciak, P., H. P. Muller, and H. E. Varmus. 1992. Simian virus 40 minichromosomes as targets for retroviral integration in vivo. Proc. Natl. Acad. Sci. U. S. A. 89:9237-9241.
44. Pryciak, P. M., A. Sil, and H. E. Varmus. 1992. Retroviral integration into minichromosomes in vitro. EMBO J. 11:291-303.
45. Pryciak, P. M., and H. E. Varmus. 1992. Nucleosomes, DNA-binding proteins, and DNA sequence modulate retroviral integration target site selection. Cell 69:769-780.
46. Robinson, M. J., et al. 2010. Mouse DNA contamination in human tissue tested for XMRV. Retrovirology 7:108.
47. Rohdewohld, H., H. Weiher, W. Reik, R. Jaenisch, and M. Breindl. 1987. Retrovirus integration and chromatin structure: Moloney murine leukemia proviral integration sites map near DNase I-hypersensitive sites. J. Virol. 61:336-343.
48. Satchwell, S. C., H. R. Drew, and A. A. Travers. 1986. Sequence periodicities in chicken nucleosome core DNA. J. Mol. Biol. 191:659-675.
49. Schlaberg, R., D. J. Choe, K. R. Brown, H. M. Thaker, and I. R. Singh. 2009. XMRV is present in malignant prostatic epithelium and is associated with prostate cancer, especially high-grade tumors. Proc. Natl. Acad. Sci. U. S. A. 106:16351-16356.
50. Schones, D. E., et al. 2008. Dynamic regulation of nucleosome positioning in the human genome. Cell 132:887-898.
51. Schroder, A. R., et al. 2002. HIV-1 integration in the human genome favors active genes and local hotspots. Cell 110:521-529.
52. Segal, E., et al. 2006. A genomic code for nucleosome positioning. Nature 442:772-778.
53. Shun, M. C., et al. 2007. LEDGF/p75 functions downstream from preintegration complex formation to effect gene-specific HIV-1 integration. Genes Dev. 21:1767-1778.
54. Silvers, R. M., et al. 2010. Modification of integration site preferences of an HIV-1-based vector by expression of a novel synthetic protein. Hum. Gene Ther. 21:337-349.
55. Vijaya, S., D. L. Steffan, and H. L. Robinson. 1986. Acceptor sites for retroviral integrations map near DNase I-hypersensitive sites in chromatin. J. Virol. 60:683-692.
56. Wang, G. P., et al. 2010. Dynamics of gene-modified progenitor cells analyzed by tracking retroviral integration sites in a human SCID-X1 gene therapy trial. Blood 115:4356-4366.
57. Wang, G. P., A. Ciuffi, J. Leipzig, C. C. Berry, and F. D. Bushman. 2007. HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications. Genome Res. 17:1186-1194.
58. Wang, G. P., et al. 2009. Analysis of lentiviral vector integration in HIV plus study subjects receiving autologous infusions of gene modified CD4+ cells. Mol. Ther. 17:844-850.
59. Wang, X., G. O. Bryant, M. Floer, D. Spagna, and M. Ptashne. 2011. An effect of DNA sequence on nucleosome occupancy and removal. Nat. Struct. Mol. Biol. 18:507-509.
60. Wang, Z., et al. 2009. Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell 138:1019-1031.
61. Wu, X., Y. Li, B. Crise, and S. M. Burgess. 2003. Transcription start regions in the human genome are favored targets for MLV integration. Science 300:1749-1751.