BACKGROUND: Human immunodeficiency virus type 1 (HIV-1) latency represents the major barrier to virus eradication in infected individuals because cells harboring latent HIV-1 provirus are not affected by current antiretroviral therapy (ART). We previously demonstrated that DNA methylation of HIV-1 long terminal repeat (5' LTR) restricts HIV-1 reactivation and, together with chromatin conformation, represents an important mechanism of HIV-1 latency maintenance. Here, we explored the new issue of temporal development of DNA methylation in latent HIV-1 5' LTR. RESULTS: In the Jurkat CD4(+) T cell model of latency, we showed that the stimulation of host cells contributed to de novo DNA methylation of the latent HIV-1 5' LTR sequences. Consecutive stimulations of model CD4(+) T cell line with TNF-α and PMA or with SAHA contributed to the progressive accumulation of 5' LTR DNA methylation. Further, we showed that once established, the high DNA methylation level of the latent 5' LTR in the cell line model was a stable epigenetic mark. Finally, we explored the development of 5' LTR DNA methylation in the latent reservoir of HIV-1-infected individuals who were treated with ART. We detected low levels of 5' LTR DNA methylation in the resting CD4(+) T cells of the group of patients who were treated for up to 3 years. However, after long-term ART, we observed an accumulation of 5' LTR DNA methylation in the latent reservoir. Importantly, within the latent reservoir of some long-term-treated individuals, we uncovered populations of proviral molecules with a high density of 5' LTR CpG methylation. CONCLUSIONS: Our data showed the presence of 5' LTR DNA methylation in the long-term reservoir of HIV-1-infected individuals and implied that the transient stimulation of cells harboring latent proviruses may contribute, at least in part, to the methylation of the HIV-1 promoter.

Department of Infectious Diseases 3rd Faculty of Medicine Charles University and Hospital Na Bulovce Prague Budínova 67 2 CZ 18081 Prague 8 Czech Republic

Department of Infectious Tropical and Parasitic Diseases 1st Faculty of Medicine Charles University Prague and Hospital Na Bulovce Budínova 67 2 CZ 18081 Prague 8 Czech Republic

Department of Mathematical Analysis and Applications of Mathematics Faculty of Science of the Palacky University in Olomouc Olomouc CZ 77146 Czech Republic

Institute of Molecular Genetics Academy of Sciences of the Czech Republic Vídeňská 1083 CZ 14220 Prague 4 Czech Republic

Institute of Molecular Genetics Academy of Sciences of the Czech Republic Vídeňská 1083 CZ 14220 Prague 4 Czech Republic ; Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic Flemingovo nám 2 CZ 16610 Prague 6 Czech Republic ; Faculty of Science Department of Genetics and Microbiology Charles University Prague Viničná 5 CZ 12844 Prague 2 Czech Republic ; Inserm Centre de Recherche en Cancérologie de Marseille F 13273 Marseille France ; Institut Paoli Calmettes F 13009 Marseille France ; Aix Marseille Univ F 13284 Marseille France ; CNRS UMR7258 CRCM F 13009 Marseille France

Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic Flemingovo nám 2 CZ 16610 Prague 6 Czech Republic

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Chun TW, Engel D, Mizell SB, Hallahan CW, Fischette M, Park S, et al. Effect of interleukin-2 on the pool of latently infected, resting CD4+ T cells in HIV-1-infected patients receiving highly active anti-retroviral therapy. Nat Med. 1999;5:651–5. doi: 10.1038/9498. PubMed DOI

Davey RT, Bhat N, Yoder C, Chun TW, Metcalf JA, Dewar R, 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 U S A. 1999;96:15109–14. doi: 10.1073/pnas.96.26.15109. PubMed DOI PMC

Finzi D, Blankson J, Siliciano JD, Margolick JB, Chadwick K, Pierson T, et al. Latent infection of CD4+ T cells provides a mechanism for lifelong persistence of HIV-1, even in patients on effective combination therapy. Nat Med. 1999;5:512–7. doi: 10.1038/8394. PubMed DOI

Ramratnam B, Mittler JE, Zhang LQ, Boden D, Hurley A, Fang F, et al. The decay of the latent reservoir of replication-competent HIV-1 is inversely correlated with the extent of residual viral replication during prolonged anti-retroviral therapy. Nat Med. 2000;6:82–5. doi: 10.1038/71577. PubMed DOI

VanLint C, Emiliani S, Ott M, Verdin E. Transcriptional activation and chromatin remodeling of the HIV-1 promoter in response to histone acetylation. Embo Journal. 1996;15:1112–20. PubMed PMC

du Chene I, Basyuk E, Lin YL, Triboulet R, Knezevich A, Chable-Bessia C, et al. Suv39H1 and HP1gamma are responsible for chromatin-mediated HIV-1 transcriptional silencing and post-integration latency. Embo J. 2007;26:424–35. doi: 10.1038/sj.emboj.7601517. PubMed DOI PMC

Marban C, Suzanne S, Dequiedt F, de Walque S, Redel L, Van Lint C, et al. Recruitment of chromatin-modifying enzymes by CTIP2 promotes HIV-1 transcriptional silencing. Embo J. 2007;26:412–23. doi: 10.1038/sj.emboj.7601516. PubMed DOI PMC

He GC, Margolis DM. Counterregulation of chromatin deacetylation and histone deacetylase occupancy at the integrated promoter of human immunodeficiency virus type 1 (HIV-1) by the HIV-1 repressor YY1 and HIV-1 activator Tat. Mol Cell Biol. 2002;22:2965–73. doi: 10.1128/MCB.22.9.2965-2973.2002. PubMed DOI PMC

Tyagi M, Karn J. CBF-1 promotes transcriptional silencing during the establishment of HIV-1 latency. Embo J. 2007;26:4985–95. doi: 10.1038/sj.emboj.7601928. PubMed DOI PMC

Williams SA, Chen LF, Kwon H, Ruiz-Jarabo CM, Verdin E, Greene WC. NF-kappaB p50 promotes HIV latency through HDAC recruitment and repression of transcriptional initiation. Embo J. 2006;25:139–49. doi: 10.1038/sj.emboj.7600900. PubMed DOI PMC

Keedy KS, Archin NM, Gates AT, Espeseth A, Hazuda DJ, Margolis DM. A limited group of class I histone deacetylases acts to repress human immunodeficiency virus type 1 expression. J Virol. 2009;83:4749–56. doi: 10.1128/JVI.02585-08. PubMed DOI PMC

Jordan A, Bisgrove D, Verdin E. HIV reproducibly establishes a latent infection after acute infection of T cells in vitro. Embo J. 2003;22:1868–77. PubMed PMC

Lusic M, Marini B, Ali H, Lucic B, Luzzati R, Giacca M. Proximity to PML nuclear bodies regulates HIV-1 latency in CD4+ T cells. Cell Host Microbe. 2013;13:665–77. doi: 10.1016/j.chom.2013.05.006. PubMed DOI

Karn J. The molecular biology of HIV latency: breaking and restoring the Tat-dependent transcriptional circuit. Curr Opin HIV AIDS. 2011;6:4–11. doi: 10.1097/COH.0b013e328340ffbb. PubMed DOI PMC

Choudhary SK, Curing MDM, HIV Pharmacologic approaches to target HIV-1 latency. Annu Rev Pharmacol Toxicol. 2011;51:397–418. doi: 10.1146/annurev-pharmtox-010510-100237. PubMed DOI PMC

Hakre S, Chavez L, Shirakawa K, Verdin E. HIV latency: experimental systems and molecular models. Fems Microbiol Rev. 2012;36:706–16. doi: 10.1111/j.1574-6976.2012.00335.x. PubMed DOI PMC

Siliciano JD, Lai J, Callender M, Pitt E, Zhang H, Margolick JB, et al. Stability of the latent reservoir for HIV-1 in patients receiving valproic acid. J Infect Dis. 2007;195:833–6. doi: 10.1086/511823. PubMed DOI

Sagot-Lerolle N, Lamine A, Chaix ML, Boufassa F, Aboulker JP, Costagliola D, et al. Prolonged valproic acid treatment does not reduce the size of latent HIV reservoir. Aids. 2008;22:1125–9. doi: 10.1097/QAD.0b013e3282fd6ddc. PubMed DOI

Margolis DM. Histone deacetylase inhibitors and HIV latency. Curr Opin HIV AIDS. 2011;6:25–9. doi: 10.1097/COH.0b013e328341242d. PubMed DOI PMC

Routy JP, Tremblay CL, Angel JB, Trottier B, Rouleau D, Baril JG, et al. Valproic acid in association with highly active antiretroviral therapy for reducing systemic HIV-1 reservoirs: results from a multicentre randomized clinical study. HIV Med. 2012;13:291–6. doi: 10.1111/j.1468-1293.2011.00975.x. PubMed DOI

Archin NM, Bateson R, Tripathy MK, Crooks AM, Yang KH, Dahl NP, et al. HIV-1 expression within resting CD4+ T cells after multiple doses of vorinostat. J Infect Dis. 2014;210:728–35. doi: 10.1093/infdis/jiu155. PubMed DOI PMC

Archin NM, Cheema M, Parker D, Wiegand A, Bosch RJ, Coffin JM, et al. Antiretroviral intensification and valproic acid lack sustained effect on residual HIV-1 viremia or resting CD4+ cell infection. PLoS One. 2010;5 doi: 10.1371/journal.pone.0009390. PubMed DOI PMC

Archin NM, Vaidya NK, Kuruc JD, Liberty AL, Wiegand A, Kearney MF, et al. Immediate antiviral therapy appears to restrict resting CD4+ cell HIV-1 infection without accelerating the decay of latent infection. Proc Natl Acad Sci U S A. 2012;109:9523–8. doi: 10.1073/pnas.1120248109. PubMed DOI PMC

Lehrman G, Hogue IB, Palmer S, Jennings C, Spina CA, Wiegand A, et al. Depletion of latent HIV-1 infection in vivo: a proof-of-concept study. Lancet. 2005;366:549–55. doi: 10.1016/S0140-6736(05)67098-5. PubMed DOI PMC

Archin NM, Eron JJ, Palmer S, Hartmann-Duff A, Martinson JA, Wiegand A, et al. Valproic acid without intensified antiviral therapy has limited impact on persistent HIV infection of resting CD4+ T cells. Aids. 2008;22:1131–5. doi: 10.1097/QAD.0b013e3282fd6df4. PubMed DOI PMC

Routy JP, Angel JB, Spaans JN, Trottier B, Rouleau D, Baril JG, et al. Design and implementation of a randomized crossover study of valproic acid and antiretroviral therapy to reduce the HIV reservoir. HIV Clin Trials. 2012;13:301–7. doi: 10.1310/hct1306-301. PubMed DOI PMC

Archin NM, Espeseth A, Parker D, Cheema M, Hazuda D, Margolis DM. Expression of latent HIV induced by the potent HDAC inhibitor suberoylanilide hydroxamic acid. AIDS Res Hum Retroviruses. 2009;25:207–12. doi: 10.1089/aid.2008.0191. PubMed DOI PMC

Reuse S, Calao M, Kabeya K, Guiguen A, Gatot JS, Quivy V, et al. Synergistic activation of HIV-1 expression by deacetylase inhibitors and prostratin: implications for treatment of latent infection. PLoS One. 2009;4 doi: 10.1371/journal.pone.0006093. PubMed DOI PMC

Blazkova J, Trejbalova K, Gondois-Rey F, Halfon P, Philibert P, Guiguen A, et al. CpG methylation controls reactivation of HIV from latency. Plos Pathogens. 2009;5. PubMed PMC

Archin NM, Liberty AL, Kashuba AD, Choudhary SK, Kuruc JD, Crooks AM, et al. Administration of vorinostat disrupts HIV-1 latency in patients on antiretroviral therapy. Nature. 2012;487:482–5. doi: 10.1038/nature11286. PubMed DOI PMC

Elliott JH, Wightman F, Solomon A, Ghneim K, Ahlers J, Cameron MJ, et al. Activation of HIV transcription with short-course vorinostat in HIV-infected patients on suppressive antiretroviral therapy. PLoS Pathog. 2014;10 doi: 10.1371/journal.ppat.1004473. PubMed DOI PMC

Blazkova J, Chun TW, Belay BW, Murray D, Justement JS, Funk EK, et al. Effect of histone deacetylase inhibitors on HIV production in latently infected, resting CD4(+) T cells from infected individuals receiving effective antiretroviral therapy. J Infect Dis. 2012;206:765–9. doi: 10.1093/infdis/jis412. PubMed DOI PMC

Rasmussen TA, Schmeltz Sogaard O, Brinkmann C, Wightman F, Lewin SR, Melchjorsen J, et al. Comparison of HDAC inhibitors in clinical development: effect on HIV production in latently infected cells and T-cell activation. Hum Vaccin Immunother. 2013;9:993–1001. doi: 10.4161/hv.23800. PubMed DOI PMC

Wei DG, Chiang V, Fyne E, Balakrishnan M, Barnes T, Graupe M, et al. Histone deacetylase inhibitor romidepsin induces HIV expression in CD4 T cells from patients on suppressive antiretroviral therapy at concentrations achieved by clinical dosing. Plos Pathogens. 2014;10 doi: 10.1371/journal.ppat.1004071. PubMed DOI PMC

Sogaard OS, Graversen ME, Leth S, Olesen R, Brinkmann CR, Nissen SK, et al. The depsipeptide romidepsin reverses HIV-1 latency in vivo. Plos Pathogens. 2015;11 doi: 10.1371/journal.ppat.1005142. PubMed DOI PMC

Kumar A, Darcis G, Van Lint C, Herbein G. Epigenetic control of HIV-1 post integration latency: implications for therapy. Clinical Epigenetics. 2015;7:103. doi: 10.1186/s13148-015-0137-6. PubMed DOI PMC

Kauder SE, Bosque A, Lindqvist A, Planelles V, Verdin E. Epigenetic regulation of HIV-1 latency by cytosine methylation. Plos Pathogens. 2009;5. PubMed PMC

Pion M, Jordan A, Biancotto A, Dequiedt F, Gondois-Rey F, Rondeau S, et al. Transcriptional suppression of in vitro-integrated human immunodeficiency virus type 1 does not correlate with proviral DNA methylation. J Virol. 2003;77:4025–32. doi: 10.1128/JVI.77.7.4025-4032.2003. PubMed DOI PMC

Blazkova J, Murray D, Justement JS, Funk EK, Nelson AK, Moir S, et al. Paucity of HIV DNA methylation in latently infected, resting CD4+ T cells from infected individuals receiving antiretroviral therapy. J Virol. 2012;86:5390–2. doi: 10.1128/JVI.00040-12. PubMed DOI PMC

Ho Y-C, Shan L, Hosmane Nina N, Wang J, Laskey Sarah B, Rosenbloom Daniel IS, et al. Replication-competent noninduced proviruses in the latent reservoir increase barrier to HIV-1 cure. Cell. 2013;155:540–51. doi: 10.1016/j.cell.2013.09.020. PubMed DOI PMC

Palacios JA, Perez-Pinar T, Toro C, Sanz-Minguela B, Moreno V, Valencia E, et al. Long-term nonprogressor and elite controller patients who control viremia have a higher percentage of methylation in their HIV-1 proviral promoters than aviremic patients receiving highly active antiretroviral therapy. J Virol. 2012;86:13081–4. doi: 10.1128/JVI.01741-12. PubMed DOI PMC

Weber S, Weiser B, Kemal KS, Burger H, Ramirez CM, Korn K, et al. Epigenetic analysis of HIV-1 proviral genomes from infected individuals: predominance of unmethylated CpG's. Virology. 2014;449:181–9. doi: 10.1016/j.virol.2013.11.013. PubMed DOI PMC

Castagna M, Takai Y, Kaibuchi K, Sano K, Kikkawa U, Nishizuka Y. Direct activation of calcium-activated, phospholipid-dependent protein kinase by tumor-promoting phorbol esters. J Biol Chem. 1982;257:7847–51. PubMed

Duh EJ, Maury WJ, Folks TM, Fauci AS, Rabson AB. Tumor necrosis factor alpha activates human immunodeficiency virus type 1 through induction of nuclear factor binding to the NF-kappa B sites in the long terminal repeat. Proc Natl Acad Sci U S A. 1989;86:5974–8. doi: 10.1073/pnas.86.15.5974. PubMed DOI PMC

Osborn L, Kunkel S, Nabel GJ. Tumor necrosis factor alpha and interleukin 1 stimulate the human immunodeficiency virus enhancer by activation of the nuclear factor kappa B. Proc Natl Acad Sci U S A. 1989;86:2336–40. doi: 10.1073/pnas.86.7.2336. PubMed DOI PMC

Hernando-Herraez I, Garcia-Perez R, Sharp AJ, Marques-Bonet T. DNA methylation: insights into human evolution. PLoS Genet. 2015;11 doi: 10.1371/journal.pgen.1005661. PubMed DOI PMC

Pinkevych M, Cromer D, Tolstrup M, Grimm AJ, Cooper DA, Lewin SR, et al. HIV reactivation from latency after treatment interruption occurs on average every 5-8 days—implications for HIV remission. PLoS Pathog. 2015;11 doi: 10.1371/journal.ppat.1005000. PubMed DOI PMC

Shan L, Deng K, Shroff NS, Durand CM, Rabi SA, Yang HC, et al. Stimulation of HIV-1-specific cytolytic T lymphocytes facilitates elimination of latent viral reservoir after virus reactivation. Immunity. 2012;36:491–501. doi: 10.1016/j.immuni.2012.01.014. PubMed DOI PMC

Siliciano RF, Greene WC. HIV latency. Cold Spring Harb Perspect Med. 2011;1:a007096. doi: 10.1101/cshperspect.a007096. PubMed DOI PMC

Lassen K, Han Y, Zhou Y, Siliciano J, Siliciano RF. The multifactorial nature of HIV-1 latency. Trends Mol Med. 2004;10:525–31. doi: 10.1016/j.molmed.2004.09.006. PubMed DOI

Rodriguez RM, Suarez-Alvarez B, Mosen-Ansorena D, Garcia-Peydro M, Fuentes P, Garcia-Leon MJ, et al. Regulation of the transcriptional program by DNA methylation during human alphabeta T-cell development. Nucleic Acids Res. 2015;43:760–74. doi: 10.1093/nar/gku1340. PubMed DOI PMC

Hashimoto S, Ogoshi K, Sasaki A, Abe J, Qu W, Nakatani Y, et al. Coordinated changes in DNA methylation in antigen-specific memory CD4 T cells. J Immunol. 2013;190:4076–91. doi: 10.4049/jimmunol.1202267. PubMed DOI PMC

Komori HK, Hart T, LaMere SA, Chew PV, Salomon DR. Defining CD4 T cell memory by the epigenetic landscape of CpG DNA methylation. J Immunol. 2015;194:1565–79. doi: 10.4049/jimmunol.1401162. PubMed DOI PMC

Li Y, Chen G, Ma L, Ohms SJ, Sun C, Shannon MF, et al. Plasticity of DNA methylation in mouse T cell activation and differentiation. BMC Mol Biol. 2012;13:16. doi: 10.1186/1471-2199-13-16. PubMed DOI PMC

Li Y, Ohms SJ, Shannon FM, Sun C, Fan JY. IL-2 and GM-CSF are regulated by DNA demethylation during activation of T cells, B cells and macrophages. Biochem Biophys Res Commun. 2012;419:748–53. doi: 10.1016/j.bbrc.2012.02.094. PubMed DOI

Bruniquel D, Schwartz RH. Selective, stable demethylation of the interleukin-2 gene enhances transcription by an active process. Nat Immunol. 2003;4:235–40. doi: 10.1038/ni887. PubMed DOI

Dong J, Chang HD, Ivascu C, Qian Y, Rezai S, Okhrimenko A, et al. Loss of methylation at the IFNG promoter and CNS-1 is associated with the development of functional IFN-gamma memory in human CD4(+) T lymphocytes. Eur J Immunol. 2013;43:793–804. doi: 10.1002/eji.201242858. PubMed DOI

Maricato JT, Furtado MN, Takenaka MC, Nunes ER, Fincatti P, Meliso FM, et al. Epigenetic modulations in activated cells early after HIV-1 infection and their possible functional consequences. PLoS One. 2015;10 doi: 10.1371/journal.pone.0119234. PubMed DOI PMC

Klose RJ, Bird AP. Genomic DNA methylation: the mark and its mediators. Trends Biochem Sci. 2006;31:89–97. doi: 10.1016/j.tibs.2005.12.008. PubMed DOI

Baubec T, Ivanek R, Lienert F, Schubeler D. Methylation-dependent and -independent genomic targeting principles of the MBD protein family. Cell. 2013;153:480–92. doi: 10.1016/j.cell.2013.03.011. PubMed DOI

Pandiyan K, You JS, Yang X, Dai C, Zhou XJ, Baylin SB, et al. Functional DNA demethylation is accompanied by chromatin accessibility. Nucleic Acids Res. 2013;41:3973–85. doi: 10.1093/nar/gkt077. PubMed DOI PMC

Marchi E, Zullo KM, Amengual JE, Kalac M, Bongero D, McIntosh CM, et al. The combination of hypomethylating agents and histone deacetylase inhibitors produce marked synergy in preclinical models of T-cell lymphoma. Br J Haematol. 2015;171:215–226. PubMed

Hou L, Ma F, Yang J, Riaz H, Wang Y, Wu W, et al. Effects of histone deacetylase inhibitor oxamflatin on in vitro porcine somatic cell nuclear transfer embryos. Cell Reprogram. 2014;16:253–65. doi: 10.1089/cell.2013.0058. PubMed DOI PMC

Gu S, Tian Y, Chlenski A, Salwen HR, Lu Z, Raj JU, et al. Valproic acid shows a potent antitumor effect with alteration of DNA methylation in neuroblastoma. Anticancer Drugs. 2012;23:1054–66. doi: 10.1097/CAD.0b013e32835739dd. PubMed DOI PMC

Liu Y, Mayo MW, Nagji AS, Smith PW, Ramsey CS, Li D, et al. Phosphorylation of RelA/p65 promotes DNMT-1 recruitment to chromatin and represses transcription of the tumor metastasis suppressor gene BRMS1. Oncogene. 2012;31:1143–54. doi: 10.1038/onc.2011.308. PubMed DOI PMC

Acharyya S, Sharma SM, Cheng AS, Ladner KJ, He W, Kline W, et al. TNF inhibits Notch-1 in skeletal muscle cells by Ezh2 and DNA methylation mediated repression: implications in duchenne muscular dystrophy. PLoS One. 2010;5 doi: 10.1371/journal.pone.0012479. PubMed DOI PMC

Pacaud R, Sery Q, Oliver L, Vallette FM, Tost J, Cartron PF. DNMT3L interacts with transcription factors to target DNMT3L/DNMT3B to specific DNA sequences: role of the DNMT3L/DNMT3B/p65-NFkappaB complex in the (de-)methylation of TRAF1. Biochimie. 2014;104:36–49. doi: 10.1016/j.biochi.2014.05.005. PubMed DOI

Dunican DS, Cruickshanks HA, Suzuki M, Semple CA, Davey T, Arceci RJ, et al. Lsh regulates LTR retrotransposon repression independently of Dnmt3b function. Genome Biol. 2013;14:R146. doi: 10.1186/gb-2013-14-12-r146. PubMed DOI PMC

Li Z, Dai H, Martos SN, Xu B, Gao Y, Li T, et al. Distinct roles of DNMT1-dependent and DNMT1-independent methylation patterns in the genome of mouse embryonic stem cells. Genome Biol. 2015;16:115. doi: 10.1186/s13059-015-0685-2. PubMed DOI PMC

Senigl F, Auxt M, Hejnar J. Transcriptional provirus silencing as a crosstalk of de novo DNA methylation and epigenomic features at the integration site. Nucleic Acids Res. 2012;40:5298–312. doi: 10.1093/nar/gks197. PubMed DOI PMC

Dhayalan A, Rajavelu A, Rathert P, Tamas R, Jurkowska RZ, Ragozin S, et al. The Dnmt3a PWWP domain reads histone 3 lysine 36 trimethylation and guides DNA methylation. J Biol Chem. 2010;285:26114–20. doi: 10.1074/jbc.M109.089433. PubMed DOI PMC

Kolasinska-Zwierz P, Down T, Latorre I, Liu T, Liu XS, Ahringer J. Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet. 2009;41:376–81. doi: 10.1038/ng.322. PubMed DOI PMC

Chomont N, El-Far M, Ancuta P, Trautmann L, Procopio FA, Yassine-Diab B, et al. HIV reservoir size and persistence are driven by T cell survival and homeostatic proliferation. Nat Med. 2009;15:893–900. doi: 10.1038/nm.1972. PubMed DOI PMC

Bosque A, Famiglietti M, Weyrich AS, Goulston C, Planelles V. Homeostatic proliferation fails to efficiently reactivate HIV-1 latently infected central memory CD4+ T cells. Plos Pathogens. 2011;7 doi: 10.1371/journal.ppat.1002288. PubMed DOI PMC

von Stockenstrom S, Odevall L, Lee E, Sinclair E, Bacchetti P, Killian M, et al. Longitudinal genetic characterization reveals that cell proliferation maintains a persistent HIV type 1 DNA pool during effective HIV therapy. J Infect Dis. 2015;212:596–607. doi: 10.1093/infdis/jiv092. PubMed DOI PMC

Maldarelli F, Wu X, Su L, Simonetti FR, Shao W, Hill S, et al. HIV latency. Specific HIV integration sites are linked to clonal expansion and persistence of infected cells. Science. 2014;345:179–83. doi: 10.1126/science.1254194. PubMed DOI PMC

Wagner TA, McLaughlin S, Garg K, Cheung CY, Larsen BB, Styrchak S, et al. HIV latency. Proliferation of cells with HIV integrated into cancer genes contributes to persistent infection. Science. 2014;345:570–3. doi: 10.1126/science.1256304. PubMed DOI PMC

Cohn LB, Silva IT, Oliveira TY, Rosales RA, Parrish EH, Learn GH, et al. HIV-1 integration landscape during latent and active infection. Cell. 2015;160:420–32. doi: 10.1016/j.cell.2015.01.020. PubMed DOI PMC

Weinberger Ariel D, Weinberger LS. Stochastic fate selection in HIV-infected patients. Cell. 2013;155:497–9. doi: 10.1016/j.cell.2013.09.039. PubMed DOI

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. 2001;20:1726–38. doi: 10.1093/emboj/20.7.1726. PubMed DOI PMC

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