Global analysis of cellular transcription following infection with an HIV-based vector

Molecular Therapy

Volumn 8, Issue 4, 2003, Pages 674-687

  Mitchell, Richard ^a   Chiang, Chih Yuan ^a   Berry, Charles ^b   Bushman, Frederic ^a  

^a SALK INSTITUTE FOR BIOLOGICAL STUDIES   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE TRANSFER RNA LIGASE; B7 ANTIGEN; BINDING PROTEIN; CHEMOKINE RECEPTOR CCR4; CLATHRIN; COLLAGEN TYPE 9; CYTOCHROME C OXIDASE; DIMETHYL SULFOXIDE; ELONGATION FACTOR 2; ETOPOSIDE; GALECTIN 1; GAMMA INTERFERON; HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN; HISTONE; IMMUNOGLOBULIN LAMBDA CHAIN; INITIATION FACTOR 3; LECTIN; LENTIVIRUS VECTOR; METALLOTHIONEIN; NUCLEOLIN; ONCOPROTEIN; PHOSPHOPROTEIN PHOSPHATASE 1; POLYPEPTIDE; PROTEASOME; RAS PROTEIN; RETINOBLASTOMA PROTEIN; RIBOSOME PROTEIN; RNA; SMALL NUCLEAR RIBONUCLEOPROTEIN; UNINDEXED DRUG; VIRUS DNA;

APOPTOSIS; ARTICLE; B LYMPHOCYTE; CELL LINE; CONTROLLED STUDY; DATA ANALYSIS; DNA DAMAGE; DNA MICROARRAY; DRUG CYTOTOXICITY; GENE EXPRESSION; GENE THERAPY; HUMAN; HUMAN CELL; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; RNA TRANSCRIPTION; STATISTICAL ANALYSIS; STATISTICAL SIGNIFICANCE; VIRUS GENOME; WILD TYPE;

DNA VIRUSES; EUKARYOTA; HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; LENTIVIRUS;

EID: 0142150948     PISSN: 15250016     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1525-0016(03)00215-6     Document Type: Article

References (35)

1. Coffin, J. M., Hughes, S. H., and Varmus, H. E. (1997). Retroviruses. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
2. Bushman, F. D. (2001). Lateral DNA Transfer: Mechanisms and Consequences. Cold Spring Harbor Laboratory Press, New York.
3. Naldini, L., et al. (1996). In vivo gene delivery and stable transduction of nondividing cells by a lentiviral vector. Science 272: 263-267.
4. Zufferey, R., et al. (1998). Self-inactivating lentivirus vector for safe and efficient in vivo gene delivery. J. Virol. 72: 9873-9880.
5. Brown, P. O., Bowerman, B., Varmus, H. E., and Bishop, J. M. (1987). Correct integration of retroviral DNA in vitro. Cell 49: 347-356.
6. Farnet, C. M., and Haseltine, W. A. (1990). Integration of human immunodeficiency virus type 1 DNA in vitro. Proc. Natl. Acad. Sci. USA 87: 4164-4168.
7. Fassati, A., and Goff, S. P. (1999). Characterization of intracellular reverse transcription complexes of Moloney murine leukemia virus. J. Virol. 73: 8919-8925.
8. Miller, M. D., Farnet, C. M., and Bushman, F. D. (1997). Human immunodeficiency virus type 1 preintegration complexes: studies of organization and composition. J. Virol. 71: 5382-5390.
9. Temin, H. M., Keshet, E., and Weller, S. K. (1980). Correlation of transient accumulation of linear unintegrated viral DNA and transient cell killing by avian leukosis and reticuloendotheliosis viruses. Cold Spring Harbor Symp. Quant. Biol. 44: 773-778.
10. Li, L., et al. (2001). Role of the non-homologous DNA end joining pathway in retroviral infection. EMBO J. 20: 3272-3281.
11. Butler, S., Hansen, M., and Bushman, F. D. (2001). A quantitative assay for HIV cDNA integration in vivo. Nat. Med. 7: 631-634.
12. Zennou, V., et al. (2000). HIV-1 genome nuclear import is mediated by a central DNA flap. Cell 101: 173-185.
13. Bell, P., Montaner, L. J., and Maul, G. G. (2001). Accumulation and intranuclear distribution of unintegrated human immunodeficiency virus type 1 DNA. J. Virol. 75: 7683-7691.
14. Daniel, R., Katz, R. A., and Skalka, A. M. (1999). A role for DNA-PK in retroviral DNA integration. Science 284: 644-647.
15. Daniel, R., et al. (2003). Evidence that the retroviral DNA integration process triggers an ATR-dependent DNA damage response. Proc. Natl. Acad. Sci. USA 100: 4778-4783.
16. Lieber, M. R. (1998). Pathological and physiological double-strand breaks. Am. J. Pathol. 153: 1323-1332.
17. + T cells. Genome Res, 11: 1198-204.
18. Vahey, M. T., et al. (2002). Impact of viral infection on the gene expression profiles of proliferating normal human peripheral blood mononuclear cells infected with HIV type 1 RF. AIDS Res. Hum. Retroviruses 18: 179-192.
19. +-T-cell lines. J. Virol. 77: 1392-1402.
20. Ryo, A., et al. (1999). Serial analysis of gene expression in HIV-1 infected T cell lines. FEBS Lett. 462: 182-186.
21. Follenzi, A., Ailes, L. E., Bakovic, S., Gueuna, M., and Naldini, L. (2000). Gene transfer by lentiviral vectors is limited by nuclear translocation and rescued by HIV-1 pol sequences. Nat. Genet. 25: 217-222.
22. O'Doherty, U., Swiggard, W. J., and Malim, M. H. (2000). Human immunodeficiency virus type 1 spinoculation enhances infection through virus binding. J. Virol. 74: 10074-10080.
23. Affymetrix (2000). Aftymetrix Microarray Suite User Guide ver. 4.
24. Irizarry, R. A., et al. (2003). Exploration, normalization, and summaries of high density oligonucleotide array probe level data. In preparation.
25. Ihaka, R., and Gentleman, R. (1996). A language for data analysis and graphics. J. Comput. Graph. Stat. 5: 299-314.
26. Wang, Y., Rea, T., Bian, J. G. S., and Sun, Y. (1999). Identification of the genes responsive to etoposide-induced apoptosis: application of DNA chip technology. FEBS Lett. 445: 269-273.
27. Tusher, V. G., Tibshirani, R., and Chu, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. USA 98: 5116-5121.
28. Efron, B., Tibshirani, R., Storey, J. D., and Tusher, V. (2001). Empirical Bayes analysis of a microarray experiment. JASA 96: 1151-1160.
29. Efron, B., and Tibshirani, R. (2002). Empirical Bayes methods and false discovery rates for microarrays. Gen. Epidemiol. 23: 70-86.
30. Hartigan, J. A. (1995). Clustering Algorithms. Wiley, New York.
31. Chandra, D., Liu, J. W., and Tang, D. G. (2002). Early mitochondrial activation and cytochrome c up-regulation during apoptosis. J. Biol. Chem. 277: 50842-50854.
32. Lu, H., et al. (2002). Metallothionein protects retinal pigment epithelial cells against apoptosis and oxidative stress. Exp. Eye Res. 74: 83-92.
33. Mi, Y., et al. (2003). Apoptosis in leukemia cells is accompanied by alterations in the levels and localization of nucleolin. J. Biol. Chem. 278: 8572-8579.
34. Arendt, C. W., and Littman, D. R. (2001). HIV: master of the host cell. Genome Biol. 2: 1030.1-1030.4.
35. Schroder, A., et al. (2002). HIV-1 integration in the human genome favors active genes and local hotspots. Cell 110: 521-529.