Position effects influence HIV latency reversal

Nature Structural and Molecular Biology

Volumn 24, Issue 1, 2017, Pages 47-54

  Chen, Heng Chang ^a,b   Martinez, Javier P ^b   Zorita, Eduard ^a,b   Meyerhans, Andreas ^b,c   Filion, Guillaume J ^a,b  

^a BARCELONA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Spain)

^b UNIVERSITAT POMPEU FABRA   (Spain)

^c INSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS ICREA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

PHYTOHEMAGGLUTININ; VORINOSTAT;

ARTICLE; CELL POPULATION; CONTROLLED STUDY; HUMAN; HUMAN CELL; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; JURKAT CELL LINE; NONHUMAN; POSITION EFFECT; PRIORITY JOURNAL; PROVIRUS; VIRUS GENOME; VIRUS LATENCY; VIRUS REACTIVATION; HUMAN IMMUNODEFICIENCY VIRUS 1; PHYSIOLOGY; VIROLOGY; VIRUS DNA CELL DNA INTERACTION; VIRUS GENE;

GENES, VIRAL; HIV INFECTIONS; HIV-1; HUMANS; JURKAT CELLS; VIRUS INTEGRATION; VIRUS LATENCY;

EID: 84996835488     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb.3328     Document Type: Article

References (39)

1. Chun, T.W. et al. Relationship between pre-existing viral reservoirs and the re-emergence of plasma viremia after discontinuation of highly active anti-retroviral therapy. Nat. Med. 6, 757-761 (2000).
2. Davey, R.T. Jr. et al. HIV-1 and T cell dynamics after interruption of highly active antiretroviral therapy (HAART) in patients with a history of sustained viral suppression. Proc. Natl. Acad. Sci. USA 96, 15109-15114 (1999).
3. Durand, C.M., Blankson, J.N. & Siliciano, R.F. Developing strategies for HIV-1 eradication. Trends Immunol. 33, 554-562 (2012).
4. Rosenberg, E.S. et al. Immune control of HIV-1 after early treatment of acute infection. Nature 407, 523-526 (2000).
5. Deeks, S.G. HIV: shock and kill. Nature 487, 439-440 (2012).
6. Eriksson, S. et al. Comparative analysis of measures of viral reservoirs in HIV-1 eradication studies. PLoS Pathog. 9, e1003174 (2013).
7. Chun, T.W. et al. Quantification of latent tissue reservoirs and total body viral load in HIV-1 infection. Nature 387, 183-188 (1997).
8. Ho, Y.-C. et al. Replication-competent noninduced proviruses in the latent reservoir increase barrier to HIV-1 cure. Cell 155, 540-551 (2013).
9. Muller, H.J. Types of visible variations induced by X-rays in Drosophila. J. Genet. 22, 299-334 (1930).
10. Rea, S. et al. Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature 406, 593-599 (2000).
11. Kellum, R. & Schedl, P. A position-effect assay for boundaries of higher order chromosomal domains. Cell 64, 941-950 (1991).
12. Akhtar, W. et al. Chromatin position effects assayed by thousands of reporters integrated in parallel. Cell 154, 914-927 (2013).
13. Jordan, A., Defechereux, P. & Verdin, E. The site of HIV-1 integration in the human genome determines basal transcriptional activity and response to Tat transactivation. EMBO J. 20, 1726-1738 (2001).
14. Jordan, A., Bisgrove, D. & Verdin, E. HIV reproducibly establishes a latent infection after acute infection of T cells in vitro. EMBO J. 22, 1868-1877 (2003).
15. Schröder, A.R.W. et al. HIV-1 integration in the human genome favors active genes and local hotspots. Cell 110, 521-529 (2002).
16. Lewinski, M.K. et al. Genome-wide analysis of chromosomal features repressing human immunodeficiency virus transcription. J. Virol. 79, 6610-6619 (2005).
17. Marini, B. et al. Nuclear architecture dictates HIV-1 integration site selection. Nature 521, 227-231 (2015).
18. Archin, N.M. et al. Administration of vorinostat disrupts HIV-1 latency in patients on antiretroviral therapy. Nature 487, 482-485 (2012).
19. Wang, Z. et al. Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell 138, 1019-1031 (2009).
20. Sarzotti-Kelsoe, M. et al. Optimization and validation of the TZM-bl assay for standardized assessments of neutralizing antibodies against HIV-1. J. Immunol. Methods 409, 131-146 (2014).
21. Ochman, H., Gerber, A.S. & Hartl, D.L. Genetic applications of an inverse polymerase chain reaction. Genetics 120, 621-623 (1988).
22. Triglia, T., Peterson, M.G. & Kemp, D.J. A procedure for in vitro amplification of DNA segments that lie outside the boundaries of known sequences. Nucleic Acids Res. 16, 8186 (1988).
23. Wang, G.P., Ciuffi, A., Leipzig, J., Berry, C.C. & Bushman, F.D. HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications. Genome Res. 17, 1186-1194 (2007).
24. Spitz, F. & Furlong, E.E.M. Transcription factors: from enhancer binding to developmental control. Nat. Rev. Genet. 13, 613-626 (2012).
25. Meyerhans, A., Breinig, T., Vartanian, J.-P. & Wain-Hobson, S. in HIV Sequence Compendium 2003 (eds. Leitner, T et al.) 14-21 (Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, 2003).
26. Matsuda, Y. et al. Epigenetic heterogeneity in HIV-1 latency establishment. Sci. Rep. 5, 7701 (2015).
27. Spina, C.A. et al. An in-depth comparison of latent HIV-1 reactivation in multiple cell model systems and resting CD4+ T cells from aviremic patients. PLoS Pathog. 9, e1003834 (2013).
28. Bullen, C.K., Laird, G.M., Durand, C.M., Siliciano, J.D. & Siliciano, R.F. New ex vivo approaches distinguish effective and ineffective single agents for reversing HIV-1 latency in vivo. Nat. Med. 20, 425-429 (2014).
29. Hnisz, D. et al. Activation of proto-oncogenes by disruption of chromosome neighborhoods. Science 351, 1454-1458 (2016).
30. Mansour, M.R. et al. Oncogene regulation: an oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element. Science 346, 1373-1377 (2014).
31. Reeder, J.E., Kwak, Y.-T., McNamara, R.P., Forst, C.V. & D'Orso, I. HIV Tat controls RNA Polymerase II and the epigenetic landscape to transcriptionally reprogram target immune cells. eLife 4, e08955 (2015).
32. Dieudonné, M. et al. Transcriptional competence of the integrated HIV-1 provirus at the nuclear periphery. EMBO J. 28, 2231-2243 (2009).
33. Esteller, M. Epigenetic gene silencing in cancer: the DNA hypermethylome. Hum. Mol. Genet. 16, R50-R59 (2007).
34. Rouzine, I.M., Weinberger, A.D. & Weinberger, L.S. An evolutionary role for HIV latency in enhancing viral transmission. Cell 160, 1002-1012 (2015).
35. Dahabieh, M.S., Battivelli, E. & Verdin, E. Understanding HIV latency: the road to an HIV cure. Annu. Rev. Med. 66, 407-421 (2015).
36. Ruelas, D.S. & Greene, W.C. An integrated overview of HIV-1 latency. Cell 155, 519-529 (2013).
37. Razooky, B.S., Pai, A., Aull, K., Rouzine, I.M. & Weinberger, L.S. A hardwired HIV latency program. Cell 160, 990-1001 (2015).
38. Weinberger, L.S., Burnett, J.C., Toettcher, J.E., Arkin, A.P. & Schaffer, D.V. Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity. Cell 122, 169-182 (2005).
39. Laird, G.M. et al. Ex vivo analysis identifies effective HIV-1 latency-reversing drug combinations. J. Clin. Invest. 125, 1901-1912 (2015).