HIV latency

Cold Spring Harbor Perspectives in Medicine

Volumn 1, Issue 1, 2011, Pages

  Siliciano, Robert F ^a   Greene, Warner C ^b  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b GLADSTONE INSTITUTE OF VIROLOGY AND IMMUNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTI HUMAN IMMUNODEFICIENCY VIRUS AGENT; VIRUS DNA; VIRUS RNA;

CD4+ T LYMPHOCYTE; DRUG EFFECT; GENETICS; HIGHLY ACTIVE ANTIRETROVIRAL THERAPY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; IMMUNOLOGY; METABOLISM; PHYSIOLOGY; REVIEW; VIROLOGY; VIRUS LATENCY;

ANTI-HIV AGENTS; ANTIRETROVIRAL THERAPY, HIGHLY ACTIVE; CD4-POSITIVE T-LYMPHOCYTES; DNA, VIRAL; HIV INFECTIONS; HIV-1; HUMANS; RNA, VIRAL; VIRUS LATENCY;

EID: 84865200182     PISSN: None     EISSN: 21571422     Source Type: Journal    
DOI: 10.1101/cshperspect.a007096     Document Type: Article

References (132)

1. Archin NM, Espeseth A, Parker D, Cheema M, Hazuda D, Margolis DM. 2009. Expression of latent HIV induced by the potent HDAC inhibitor suberoylanilide hydroxamic acid. AIDS Res Hum Retrov 25: 207-212.
2. + cell infection. PLoS One 5: e9390.
3. Arfi V, Riviere L, Jarrosson-Wuilleme L, Goujon C, Rigal D, Darlix JL, CimarelliA. 2008. Characterization of the early steps of infection of primary blood monocytes by human immunodeficiency virus type 1. J Virol 82: 6557-6565.
4. Bai L, Morozov AV. 2010. Gene regulation by nucleosome positioning. Trends Genet 26: 476-483.
5. Bailey J, Blankson JN, Wind-Rotolo M, Siliciano RF. 2004. Mechanisms of HIV-1 escape from immune responses and antiretroviral drugs. Curr Opin Immunol 16: 470-476.
6. + T cells. J Virol 80: 6441-6457.
7. Barboric M, Peterlin BM. 2005. A new paradigm in eukaryotic biology: HIV Tat and the control of transcriptional elongation. PLoS Biol 3: e76.
8. Barboric M, Nissen RM, Kanazawa S, Jabrane-Ferrat N, Peterlin BM. 2001. NF-κB binds P-TEFb to stimulate transcriptional elongation by RNA polymerase II. Mol Cell 8: 327-337.
9. Blazkova J, Trejbalova K, Gondois-Rey F, Halfon P, Philibert P, Guiguen A, Verdin E, Olive D, Van Lint C, Hejnar J, et al. 2009. CpG methylation controls reactivation of HIV from latency. PLoS Pathog 5: e1000554.
10. Bohnlein E, Lowenthal JW, Siekevitz M, Ballard DW, Franza BR, Greene WC. 1988. The same inducible nuclear proteins regulates mitogen activation of both the interleukin-2 receptor-α gene and type 1 HIV. Cell 53: 827-836.
11. Bourgeois CF, Kim YK, Churcher MJ, West MJ, Karn J. 2002. Spt5 cooperates with human immunodeficiency virus type 1 Tat by preventing premature RNA release at terminator sequences. Mol Cell Biol 22: 1079-1093.
12. Brahic M, Stowring L, Ventura P, Haase AT. 1981. Gene expression in visna virus infection in sheep. Nature 292: 240-242.
13. + T cells reveals a novel source of residual viremia in patients on antiretroviral therapy. J Virol 83: 8470-8481.
14. Brooks DG, Hamer DH, Arlen PA, Gao L, Bristol G, Kitchen CM, Berger EA, ZackJA. 2003. Molecular characterization, reactivation, and depletion of latent HIV. Immunity 19: 413-423.
15. Bukrinsky MI, Stanwick TL, Dempsey MP, Stevenson M. 1991. Quiescent T lymphocytes as an inducible virus reservoir in HIV-1 infection. Science 254: 423-427.
16. Carter CC, Onafuwa-Nuga A, McNamara LA, Riddell J IV, Bixby D, Savona MR, Collins KL. 2010. HIV-1 infects multipotent progenitor cells causing cell death and establishing latent cellular reservoirs. Nat Med 16: 446-451.
17. Chen LF, Greene WC. 2004. Shaping the nuclear action of NF-κB. Nat Rev Mol Cell Biol 5: 392-401.
18. Chen LF, Mu Y, Greene WC. 2002. Acetylation of RelA at discrete sites regulates distinct nuclear functions of NF-κB. EMBO J 21: 6539-6548.
19. Chen L, Fischle W, Verdin E, Greene WC. 2001. Duration of nuclear NF-κB action regulated by reversible acetylation. Science 293: 1653-1657.
20. Chiang CM, Roeder RG. 1995. Cloning of an intrinsic human TFIID subunit that interacts with multiple transcriptional activators. Science 267: 531-536.
21. Chomont N, El-Far M, Ancuta P, Trautmann L, Procopio FA, Yassine-Diab B, Boucher G, Boulassel MR, Ghattas G, Brenchley JM, et al. 2009. HIV reservoir size and persistence are driven by T cell survival and homeostatic proliferation. Nat Med 15: 893-900.
22. Chun TW, Finzi D, Margolick J, Chadwick K, Schwartz D, Siliciano RF. 1995. In vivo fate of HIV-1-infected T cells: Quantitative analysis of the transition to stable latency. Nat Med 1: 1284-1290.
23. Chun TW, Carruth L, Finzi D, Shen X, Digiuseppe JA, Taylor H, Hermankova M, Chadwick K, Margolick J, Quinn TC, et al. 1997a. Quantitation of latent tissue reservoirs and total body load in HIV-1 infection. Nature 387: 183-188.
24. Chun TW, Stuyver L, Mizell SB, Ehler LA, Mican JA, Baseler M, Lloyd AL, NowakMA, Fauci AS. 1997b. Presence of an inducible HIV-1 latent reservoir during highly active antiretroviral therapy. Proc Natl Acad Sci 94: 13193-13197.
25. Chun TW, Nickle DC, Justement JS, Large D, Semerjian A, Curlin ME, O'SheaMA, Hallahan CW, Daucher M, Ward DJ, et al. 2005. HIV-infected individuals receiving effective antiviral therapy for extended periods of time continually replenish their viral reservoir. J Clin Invest 115: 3250-3255.
26. Clements JE, Babas T, Mankowski JL, Suryanarayana K, Piatak M Jr., TarwaterPM, Lifson JD, Zink MC. 2002. The central nervous system as a reservoir for simian immunodeficiency virus (SIV): Steady-state levels of SIV DNA in brain from acute through asymptomatic infection. J Infect Dis 186: 905-913.
27. Colin L, Van Lint C. 2009. Molecular control of HIV-1 postintegration latency: Implications for the development of new therapeutic strategies. Retrovirology 6: 111.
28. Coull JJ, Romerio F, Sun JM, Volker JL, Galvin KM, Davie JR, Shi Y, Hansen U, Margolis DM. 2000. The human factors YY1 and LSF repress the human immunodeficiency virus type 1 long terminal repeat via recruitment of histone deacetylase 1. J Virol 74: 6790-6799.
29. Davey RT Jr., Bhat N, Yoder C, Chun TW, Metcalf JA, Dewar R, Natarajan V, Lempicki RA, Adelsberger JW, Miller KD, et al. 1999. 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 96: 15109-15114.
30. Deeks SG, Wrin T, Liegler T, Hoh R, Hayden M, Barbour JD, Hellmann NS, Petropoulos CJ, McCune JM, Hellerstein MK, et al. 2001. Virologic and immunologic consequences of discontinuing combination antiretroviral-drug therapy in HIV-infected patients with detectable viremia. N Engl J Med 344: 472-480.
31. De Marco A, Biancotto C, Knezevich A, Maiuri P, Vardabasso C, Marcello A. 2008. Intragenic transcriptional cis-activation of the human immunodeficiency virus 1 does not result in allele-specific inhibition of the endogenous gene. Retrovirology 5: 98.
32. Dinoso JB, Kim SY, Wiegand AM, Palmer SE, Gange SJ, Cranmer L, O'Shea A, Callender M, Spivak A, Brennan T, et al. 2009a. Treatment intensification does not reduce residual HIV-1 viremia in patients on highly active antiretroviral therapy. Proc Natl Acad Sci 106: 9403-9408.
33. Dinoso JB, Rabi SA, Blankson JN, Gama L, Mankowski JL, Siliciano RF, Zink MC, Clements JE. 2009b. A simian immunodeficiency virus-infected macaque model to study viral reservoirs that persist during highly active antiretroviral therapy. J Virol 83: 9247-9257.
34. Dornadula G, Zhang H, VanUitert B, Stern J, Livornese L Jr., Ingerman MJ, WitekJ, Kedanis RJ, Natkin J, DeSimone J, et al. 1999. Residual HIV-1 RNA in blood plasma of patients taking suppressive highly active antiretroviral therapy. JAMA282: 1627-1632.
35. Duh EJ, Maury WJ, Folks TM, Fauci AS, Rabson AB. 1989. Tumor necrosis factor α activates human immunodeficiency virus type 1 through induction of nuclear factor binding to the NF-κB sites in the long terminal repeat. Proc Natl Acad Sci 86: 5974-5978.
36. Emili A, Greenblatt J, Ingles CJ. 1994. Species-specific interaction of the glutamine-rich activation domains of Sp1 with the TATA box-binding protein. Mol Cell Biol 14: 1582-1593.
37. Felsenfeld G, Groudine M. 2003. Controlling the double helix. Nature 421: 448-453.
38. Finzi D, Hermankova M, Pierson T, Carruth LM, Buck C, Chaisson RE, QuinnTC, Chadwick K, Margolick J, Brookmeyer R, et al. 1997. Identification of a reservoir for HIV-1 in patients on highly active antiretroviral therapy. Science 278: 1295-1300.
39. + T cells provides a mechanism for lifelong persistence of HIV-1, even in patients on effective combination therapy. Nat Med 5: 512-517.
40. Fischle W, Wang Y, Allis CD. 2003. Binary switches and modification cassettes in histone biology and beyond. Nature 425: 475-479.
41. Folks T, Powell DM, Lightfoote MM, Benn S, Martin MA, Fauci AS. 1986. Induction of HTLV-III/LAV from a nonvirus-producing T-cell line: Implications for latency. Science 231: 600-602.
42. Fujinaga K, Irwin D, Huang Y, Taube R, Kurosu T, Peterlin BM. 2004. Dynamics of human immunodeficiency virus transcription: P-TEFb phosphorylates RD and dissociates negative effectors from the transactivation response element. Mol Cell Biol 24: 787-795.
43. Gandhi RT, Zheng L, Bosch RJ, Chan ES, Margolis DM, Read S, Kallungal B, Palmer S, Medvik K, Lederman MM, et al. 2010a. The effect of raltegravir intensification on low-level residual viremia in HIV-infected patients on antiretroviral therapy: A randomized controlled trial. PLoS Med 7: 1000321.
44. Gandhi RT, Bosch RJ, Aga E, Albrecht M, Demeter LM, Dykes C, Bastow B, ParaM, Lai J, Siliciano RF, et al. 2010b. No evidence for decay of the latent reservoir in HIV-1-infected patients receiving intensive enfuvirtide-containing antiretroviral therapy. J Infect Dis 201: 293-296.
45. Gartner S, Markovits P, Markovitz DM, Kaplan MH, Gallo RC, Popovic M. 1986. The role of mononuclear phagocytes in HTLV-III/LAV infection. Science 233: 215-219.
46. Gerritsen ME, Williams AJ, Neish AS, Moore S, Shi Y, Collins T. 1997. CREB-binding protein/p300 are transcriptional coactivators of 65. Proc Natl Acad Sci 94: 2927-2932.
47. Goldberg AD, Allis CD, Bernstein E. 2007. Epigenetics: A landscape takes shape. Cell 128: 635-638.
48. Gras G, Kaul M. 2010. Molecular mechanisms of neuroinvasion by monocytes-macrophages in HIV-1 infection. Retrovirology 7: 30.
49. Greger IH, Demarchi F, Giacca M, Proudfoot NJ. 1998. Transcriptional interference perturbs the binding of Sp1 to the HIV-1 promoter. Nucl Acids Res 26: 1294-1301.
50. Gulick RM, Mellors JW, Havlir D, Eron JJ, Gonzalez C, McMahon D, Richman DD, Valentine FT, Jonas L, Meibohm A, et al. 1997. Treatment with indinavir, zidovudine, and lamivudine in adults with human immunodeficiency virus infection and prior antiretroviral therapy. N Engl J Med 337: 734-739.
51. Hammer SM, Squires KE, Hughes MD, Grimes JM, Demeter LM, Currier JS, EronJJ Jr., Feinberg JE, Balfour HH Jr., Deyton LR, et al. 1997. A controlled trial of two nucleoside analogues plus indinavir in persons with human immunodeficiency virus infection and CD4 cell counts of 200 per cubic millimeter or less. AIDS Clinical Trials Group 320 Study Team. N Engl J Med 337: 725-733.
52. + T cells from human immunodeficiency virus type 1 (HIV-1)-infected individuals carry integrated HIV-1 genomes within actively transcribed host genes. J Virol 78: 6122-6133.
53. Han Y, Lin YB, An W, Xu J, Yang HC, O'Connell K, Dordai D, Boeke JD, SilicianoJD, Siliciano RF. 2008. Orientation-dependent regulation of integrated HIV-1 expression by host gene transcriptional readthrough. Cell Host Microbe 4: 134-146.
54. He N, Liu M, Hsu J, Xue Y, Chou S, Burlingame A, Krogan NJ, Alber T, Zhou Q. 2010. HIV-1 Tat and host AFF4 recruit two transcription elongation factors into a bifunctional complex for coordinated activation of HIV-1 transcription. Mol Cell 38: 428-438.
55. Hermankova M, Ray SC, Ruff C, Powell-Davis M, Ingersoll R, D'Aquila RT, Quinn TC, Siliciano JD, Siliciano RF, Persaud D. 2001. HIV-1 drug resistance profiles in children and adults with viral load of <50 copies/ml receiving combination therapy. JAMA 286: 196-207.
56. Ho DD, Neumann AU, Perelson AS, Chen W, Leonard JM, Markowitz M. 1995. Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection. Nature 373: 123-126.
57. Hoxie JA, June CH. 2011. Novel cell and gene therapies for HIV. Cold Spring Harb Perspect Med doi: 10. 1101/cshperspect. a007179.
58. Hsia SC, Shi YB. 2002. Chromatin disruption and histone acetylation in regulation of the human immunodeficiency virus type 1 long terminal repeat by thyroid hormone receptor. Mol Cell Biol 22: 4043-4052.
59. + T cells by a highly pathogenic simian immunodeficiency virus/HIV type 1 chimera (SHIV): Implications for HIV-1 infections of humans. Proc Natl Acad Sci 98: 658-663.
60. Jordan A, Defechereux P, Verdin E. 2001. The site of HIV-1 integration in the human genome determines basal transcriptional activity and response to Tat transactivation. EMBO J 20: 1726-1738.
61. Jordan A, Bisgrove D, Verdin E. 2003. HIV reproducibly establishes a latent infection after acute infection of T cells in vitro. EMBO J 22: 1868-1877.
62. Karn J. 2011. The molecular biology of HIV latency: Breaking and restoring the Tat-dependent transcriptional circuit. Curr Opin HIV AIDS 6: 4-11.
63. Kauder SE, Bosque A, Lindqvist A, Planelles V, Verdin E. 2009. Epigenetic regulation of HIV-1 latency by cytosine methylation. PLoS Pathog 5: e1000495.
64. Kieffer TL, Finucane MM, Nettles RE, Quinn TC, Broman KW, Ray SC, Persaud D, Siliciano RF. 2004. Genotypic analysis of HIV-1 drug resistance at the limit of detection: Virus production without evolution in treated adults with undetectable HIV loads. J Infect Dis 189: 1452-1465.
65. Kim YK, Bourgeois CF, Isel C, Churcher MJ, Karn J. 2002. Phosphorylation of the RNA polymerase II carboxyl-terminal domain by CDK9 is directly responsible for human immunodeficiency virus type 1 Tat-activated transcriptional elongation. Mol Cell Biol 22: 4622-4637.
66. Kinoshita S, Chen BK, Kaneshima H, Nolan GP. 1998. Host control of HIV-1 parasitism in T cells by the nuclear factor of activated T cells. Cell 95: 595-604.
67. Korin YD, Brooks DG, Brown S, Korotzer A, Zack JA. 2002. Effects of prostratin on T-cell activation and human immunodeficiency virus latency. J Virol 76: 8118-8123.
68. Kulkosky J, Culnan DM, Roman J, Dornadula G, Schnell M, Boyd MR, PomerantzRJ. 2001. Prostratin: Activation of latent HIV-1 expression suggests a potential inductive adjuvant therapy for HAART. Blood 98: 3006-3015.
69. Kwon HS, Brent MM, Getachew R, Jayakumar P, Chen LF, Schnolzer M, McBurney MW, Marmorstein R, Greene WC, Ott M. 2008. Human immunodeficiency virus type 1 Tat protein inhibits the SIRT1 deacetylase and induces T cell hyperactivation. Cell Host Microbe 3: 158-167.
70. Lassen K, Han Y, Zhou Y, Siliciano J, Siliciano RF. 2004. The multifactorial nature of HIV-1 latency. Trends Mol Med 10: 525-531.
71. + T cells. PLoS Pathog 2: e68.
72. Laughlin MA, Zeichner S, Kolson D, Alwine JC, Seshamma T, Pomerantz RJ, Gonzalez-Scarano F. 1993. Sodium butyrate treatment of cells latently infected with HIV-1 results in the expression of unspliced viral RNA. Virology 196: 496-505.
73. Lehrman G, Hogue IB, Palmer S, Jennings C, Spina CA, Wiegand A, Landay AL, Coombs RW, Richman DD, Mellors JW, et al. 2005. Depletion of latent HIV-1 infection in vivo: A proof-of-concept study. Lancet 366: 549-555.
74. Lenasi T, Contreras X, Peterlin BM. 2008. Transcriptional interference antagonizes proviral gene expression to promote HIV latency. Cell Host Microbe 4: 123-133.
75. Lewinski MK, Bisgrove D, Shinn P, Chen H, Hoffmann C, Hannenhalli S, VerdinE, Berry CC, Ecker JR, Bushman FD. 2005. Genome-wide analysis of chromosomal features repressing human immunodeficiency virus transcription. J Virol 79: 6610-6619.
76. Liou LY, Herrmann CH, Rice AP. 2002. Transient induction of cyclin T1 during human macrophage differentiation regulates human immunodeficiency virus type 1 Tat transactivation function. J Virol 76: 10579-10587.
77. Liu N, Balliano A, Hayes JJ. 2011. Mechanism(s) of SWI/SNF-induced nucleosome mobilization. Chembiochem 12: 196-204.
78. Maldarelli F, Palmer S, King MS, Wiegand A, Polis MA, Mican J, Kovacs JA, Davey RT, Rock-Kress D, Dewar R, et al. 2007. ART suppresses plasma HIV-1 RNA to a stable set point predicted by pretherapy viremia. PLoS Pathog 3: e46.
79. McMahon D, Jones J, Wiegand A, Gange SJ, Kearney M, Palmer S, McNulty S, Metcalf JA, Acosta E, Rehm C, et al. 2010. Short-course raltegravir intensification does not reduce persistent low-level viremia in patients with HIV-1 suppression during receipt of combination antiretroviral therapy. Clin Infect Dis 50: 912-919.
80. Meehan AM, Saenz DT, Morrison JH, Garcia-Rivera JA, Peretz M, Llano M, Poeschla EM. 2009. LEDGF/p75 proteins with alternative chromatin tethers are functional HIV-1 cofactors. PLoS Pathog 5: e1000522.
81. Nabel G, Baltimore D. 1987. An inducible transcription factor activates expression of human immunodeficiency virus in T cells. Nature 326: 711-713.
82. Nettles RE, Kieffer TL, Kwon P, Monie D, Han Y, Parsons T, Cofrancesco J Jr., Gallant JE, Quinn TC, Jackson B, et al. 2005. Intermittent HIV-1 viremia (Blips) and drug resistance in patients receiving HAART. JAMA 293: 817-829.
83. Nickle DC, Jensen MA, Shriner D, Brodie SJ, Frenkel LM, Mittler JE, Mullins JI. 2003. Evolutionary indicators of human immunodeficiency virus type 1 reservoirs and compartments. J Virol 77: 5540-5546.
84. Noe A, Plum J, Verhofstede C. 2005. The latent HIV-1 reservoir in patients undergoing HAART: An archive of pre-HAART drug resistance. J Antimicrob Chemother 55: 410-412.
85. North TW, Higgins J, Deere JD, Hayes TL, Villalobos A, Adamson L, ShacklettBL, Schinazi RF, Luciw PA. 2010. Viral sanctuaries during highly active antiretroviral therapy in a nonhuman primate model for AIDS. J Virol 84: 2913-2922.
86. Palmer S, Maldarelli F, Wiegand A, Bernstein B, Hanna GJ, Brun SC, Kempf DJ, Mellors JW, Coffin JM, King MS. 2008. Low-level viremia persists for at least 7 years in patients on suppressive antiretroviral therapy. Proc Natl Acad Sci 105: 3879-3884.
87. Parada CA, Roeder RG. 1996. Enhanced processivity of RNA polymerase II triggered by Tat-induced phosphorylation of its carboxy-terminal domain. Nature 384: 375-378.
88. Perelson AS, Essunger P, Cao Y, Vesanen M, Hurley A, Saksela K, Markowitz M, Ho DD. 1997. Decay characteristics of HIV-1-infected compartments during combination therapy. Nature 387: 188-191.
89. Perkins ND, Edwards NL, Duckett CS, Agranoff AB, Schmid RM, Nabel GJ. 1993. A cooperative interaction between NF-κ B and Sp1 is required for HIV-1 enhancer activation. EMBO J 12: 3551-3558.
90. Perng GC, Jones C. 2010. Towards an understanding of the herpes simplex virus type 1 latency-reactivation cycle. Interdiscip Perspect Infect Dis 2010: 262415.
91. + T lymphocytes in infected children. J Clin Invest 105: 995-1003.
92. Persaud D, Siberry GK, Ahonkhai A, Kajdas J, Monie D, Hutton N, Watson DC, Quinn TC, Ray SC, Siliciano RF. 2004. Continued production of drug-sensitive human immunodeficiency virus type 1 in children on combination antiretroviral therapy who have undetectable viral loads. J Virol 78: 968-979.
93. Piatak M Jr., Saag MS, Yang LC, Clark SJ, Kappes JC, Luk KC, Hahn BH, ShawGM, Lifson JD. 1993. High levels of HIV-1 in plasma during all stages of infection determined by competitive PCR. Science 259: 1749-1754.
94. Richman DD, Margolis DM, Delaney M, Greene WC, Hazuda D, Pomerantz RJ. 2009. The challenge of finding a cure for HIV infection. Science 323: 1304-1307.
95. Rohr O, Marban C, Aunis D, Schaeffer E. 2003. Regulation of HIV-1 gene transcription: From lymphocytes to microglial cells. J Leukocyte Biol 74: 736-749.
96. Ross EK, Buckler-White AJ, Rabson AB, Englund G, Martin MA. 1991. Contribution of NF-κB and Sp1 binding motifs to the replicative capacity of human immunodeficiency virus type 1: Distinct patterns of viral growth are determined by T-cell types. J Virol 65: 4350-4358.
97. Ruff CT, Ray SC, Kwon P, Zinn R, Pendleton A, Hutton N, Ashworth R, Gange S, Quinn TC, Siliciano RF, et al. 2002. Persistence of wild-type virus and lack of temporal structure in the latent reservoir for human immunodeficiency virus type 1 in pediatric patients with extensive antiretroviral exposure. J Virol 76: 9481-9492.
98. Sahu GK, Paar D, Frost SD, Smith MM, Weaver S, Cloyd MW. 2009. Low-level plasma HIVs in patients on prolonged suppressive highly active antiretroviral therapy are produced mostly by cells other than CD4 T-cells. J Med Virol 81: 9-15.
99. Schnell G, Spudich S, Harrington P, Price RW, Swanstrom R. 2009. Compartmentalized human immunodeficiency virus type 1 originates from long-lived cells in some subjects with HIV-1-associated dementia. PLoS Pathog 5: e1000395.
100. Schroder AR, Shinn P, Chen H, Berry C, Ecker JR, Bushman F. 2002. HIV-1 integration in the human genome favors active genes and local hotspots. Cell 110: 521-529.
101. Shan L, Yang HC, Rabi SA, Bravo HC, Irizarry RA, Zhang H, Margolick JB, Siliciano JD, Siliciano RF. 2011. Influence of host gene transcription level and orientation on HIV-1 latency in a primary cell model. J Virol doi: 101128/JVI02536-10.
102. Shao Z, Ruppert S, Robbins PD. 1995. The retinoblastoma-susceptibility gene product binds directly to the human TATA-binding protein-associated factor TAFII250. Proc Natl Acad Sci 92: 3115-3119.
103. + T lymphocytes but not thymocytes provide a latent viral reservoir in a simian immunodeficiency virus-Macaca nemestrina model of human immunodeficiency virus type 1-infected patients on highly active antiretroviral therapy. J Virol 77: 4938-4949.
104. Shen L, Peterson S, Sedaghat AR, McMahon MA, Callender M, Zhang H, Zhou Y, Pitt E, Anderson KS, Acosta EP, et al. 2008. Dose-response curve slope sets class-specific limits on inhibitory potential of anti-HIV drugs. Nat Med 14: 762-766.
105. Siekevitz M, Josephs SF, Dukovich M, Peffer N, Wong-Staal F, Greene WC. 1987. Activation of the HIV-1 LTR by T cell mitogens and the trans-activator protein of HTLV-I. Science 238: 1575-1578.
106. + T cells. Nat Med 9: 727-728.
107. Siliciano JD, Lai J, Callender M, Pitt E, Zhang H, Margolick JB, Gallant JE, Cofrancesco J Jr., Moore RD, Gange SJ, et al. 2007. Stability of the latent reservoir for HIV-1 in patients receiving valproic acid. J Infect Dis 195: 833-836.
108. Sobhian B, Laguette N, Yatim A, Nakamura M, Levy Y, Kiernan R, Benkirane M. 2010. HIV-1 Tat assembles a multifunctional transcription elongation complex and stably associates with the 7SK snRNP. Mol Cell 38: 439-451.
109. Spivak AM, Rabi SA, McMahon MA, Shan L, Sedaghat AR, Wilke CO, SilicianoRF. 2011. Dynamic constraints on the second phase compartment of HIV-infected cells. AIDS Res Hum Retrov doi: 10. 1089/aid. 2010. 0199.
110. Strain MC, Gunthard HF, Havlir DV, Ignacio CC, Smith DM, Leigh-Brown AJ, Macaranas TR, Lam RY, Daly OA, Fischer M, et al. 2003. Heterogeneous clearance rates of long-lived lymphocytes infected with HIV: Intrinsic stability predicts lifelong persistence. Proc Natl Acad Sci 100: 4819-4824.
111. Sun SC, Ganchi PA, Ballard DW, Greene WC. 1993. NF-κB controls expression of inhibitor I κ B α: Evidence for an inducible autoregulatory pathway. Science 259: 1912-1915.
112. Sune C, Garcia-Blanco MA. 1995. Sp1 transcription factor is required for in vitro basal and Tat-activated transcription from the human immunodeficiency virus type 1 long terminal repeat. J Virol 69: 6572-6576.
113. Swanstorm R, Coffin J. 2011. HIV-1 pathogenesis: The virus. Cold Spring Harb Perspect Med doi: 10. 1101/cshperspect. a007443.
114. Tahirov TH, Babayeva ND, Varzavand K, Cooper JJ, Sedore SC, Price DH. 2010. Crystal structure of HIV-1 Tat complexed with human P-TEFb. Nature 465: 747-751.
115. Tamaru H. 2010. Confining euchromatin/heterochromatin territory: Jumonji crosses the line. Genes Dev 24: 1465-1478.
116. Tobin NH, Learn GH, Holte SE, Wang Y, Melvin AJ, McKernan JL, Pawluk DM, Mohan KM, Lewis PF, Mullins JI, et al. 2005. Evidence that low-level viremias during effective highly active antiretroviral therapy result from two processes: Expression of archival virus and replication of virus. J Virol 79: 9625-9634.
117. Van Lint C, Emiliani S, Ott M, Verdin E. 1996. Transcriptional activation and chromatin remodeling of the HIV-1 promoter in response to histone acetylation. EMBO J 15: 1112-1120.
118. Verdin E, Paras P Jr., Van Lint C. 1993. Chromatin disruption in the promoter of human immunodeficiency virus type 1 during transcriptional activation. EMBO J 12: 3249-3259.
119. Wei X, Ghosh SK, Taylor ME, Johnson VA, Emini EA, Deutsch P, Lifson JD, Bonhoeffer S, Nowak MA, Hahn BH, et al. 1995. Viral dynamics in human immunodeficiency virus type 1 infection. Nature 373: 117-122.
120. Wei P, Garber ME, Fang SM, Fischer WH, Jones KA. 1998. A novel CDK9-associated C-type cyclin interacts directly with HIV-1 Tat and mediates its high-affinity, loop-specific binding to TAR RNA. Cell 92: 451-462.
121. Weinberger LS, Burnett JC, Toettcher JE, Arkin AP, Schaffer DV. 2005. Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity. Cell 122: 169-182.
122. Williams SA, Chen LF, Kwon H, Fenard D, Bisgrove D, Verdin E, Greene WC. 2004. Prostratin antagonizes HIV latency by activating NF-κB. J Biol Chem 279: 42008-42017.
123. Williams SA, Chen LF, Kwon H, Ruiz-Jarabo CM, Verdin E, Greene WC. 2006. NF-κB pp50 promotes HIV latency through HDAC recruitment and repression of transcriptional initiation. EMBO J 25: 139-149.
124. Wong JK, Hezareh M, Gunthard HF, Havlir DV, Ignacio CC, Spina CA, RichmanDD. 1997. Recovery of replication-competent HIV despite prolonged suppression of plasma viremia. Science 278: 1291-1295.
125. Yang HC. 2011. Primary cell models of HIV latency. Curr Opin HIV AIDS 6: 62-67.
126. Yang Z, Zhu Q, Luo K, Zhou Q. 2001. The 7SK small nuclear RNA inhibits the CDK9/cyclin T1 kinase to control transcription. Nature 414: 317-322.
127. Yang Z, Yik JH, Chen R, He N, Jang MK, Ozato K, Zhou Q. 2005. Recruitment of P-TEFb for stimulation of transcriptional elongation by the bromodomain protein Brd4. Mol Cell 19: 535-545.
128. Yeung F, Hoberg JE, Ramsey CS, Keller MD, Jones DR, Frye RA, Mayo MW. 2004. Modulation of NF-κB-dependent transcription and cell survival by the SIRT1 deacetylase. EMBO J 23: 2369-2380.
129. Ylisastigui L, Archin NM, Lehrman G, Bosch RJ, Margolis DM. 2004. Coaxing HIV-1 from resting CD4 T cells: Histone deacetylase inhibition allows latent viral expression. AIDS 18: 1101-1108.
130. Zack JA, Arrigo SJ, Weitsman SR, Go AS, Haislip A, Chen IS. 1990. HIV-1 entry into quiescent primary lymphocytes: Molecular analysis reveals a labile, latent viral structure. Cell 61: 213-222.
131. + T cells. J Virol 79: 2199-2210.
132. + monocytes and its potential role as a source of virus in patients on highly active antiretroviral therapy. J Virol 76: 707-716.