Epigenetics of HIV infection: Promising research areas and implications for therapy

AIDS Reviews

Volumn 15, Issue 3, 2013, Pages 181-188

  Ay, Eva ^a   Banati, Ferenc ^a   Mezei, Maria ^a   Bakos, Agnes ^a   Helmut Niller, Hans ^b   Buzaś, Krisztina ^a,c   Minarovits, Janos ^a,c  

^a NATIONAL CENTER FOR EPIDEMIOLOGY   (Hungary)

^b UNIVERSITY OF REGENSBURG   (Germany)

^c UNIVERSITY OF SZEGED   (Hungary)

Author keywords

[No Author keywords available]

Indexed keywords

5 HYDROXYMETHYLCYTOSINE; 5 METHYLCYTOSINE; CYTOSINE; DNA METHYLTRANSFERASE 1; DNA METHYLTRANSFERASE 3A; DNA METHYLTRANSFERASE 3B; DOUBLE STRANDED DNA; GAMMA INTERFERON; HISTONE DEACETYLASE 2; HISTONE H3; HISTONE H4; HISTONE LYSINE METHYLTRANSFERASE; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; POLYPYRIMIDINE TRACT BINDING PROTEIN; RNA DIRECTED DNA POLYMERASE; THYMINE DNA GLYCOSYLASE; URIDINE DIPHOSPHATE N ACETYLGLUCOSAMINE; VIRUS RNA;

ACETYLATION; ANTIVIRAL RESISTANCE; CD4+ T LYMPHOCYTE; CHROMATIN IMMUNOPRECIPITATION; CHROMATIN STRUCTURE; DECARBOXYLATION; DNA METHYLATION; DNA MICROARRAY; DOWN REGULATION; EMBRYO DEVELOPMENT; EMBRYONIC STEM CELL; ENZYME ACTIVITY; EPIGENETICS; EXCISION REPAIR; GENE ACTIVATION; GENE SEQUENCE; GENE SILENCING; HIGH THROUGHPUT SCREENING; HISTONE MODIFICATION; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; MACROPHAGE; MONOCYTE; NEXT GENERATION SEQUENCING; NONHUMAN; NUCLEOSOME; PLURIPOTENT STEM CELL; PROMOTER REGION; PROTEIN EXPRESSION; REVIEW; T LYMPHOCYTE ACTIVATION; TRANSCRIPTION REGULATION; VIRUS CELL INTERACTION; VIRUS REPLICATION; VIRUS TRANSMISSION;

ANTIRETROVIRAL THERAPY, HIGHLY ACTIVE; CD4-POSITIVE T-LYMPHOCYTES; EPIGENOMICS; FEMALE; GENE SILENCING; HIV INFECTIONS; HUMANS; MALE; MOLECULAR TARGETED THERAPY; TRANSLATIONAL MEDICAL RESEARCH; VIRUS LATENCY; VIRUS REPLICATION;

EID: 84886676923     PISSN: 11396121     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (80)

1. Minarovits J. Microbe-induced epigenetic alterations in host cells: the coming era of patho-epigenetics of microbial infections. A review. Acta Microbiol Immunol Hung. 2009;56:1-19.
2. Niller H, Banati F, Ay E, Minarovits J. Epigenetic changes in virus-associated neoplasms. In: Patho-Epigenetics of Disease; Minarovits J, Niller H (Eds); Springer: New York, 2012;179-225.
3. Niller H, Banati F, Ay E, Minarovits J. Microbe-induced epigenetic alterations. In: Patho-Epigenetics of Disease; Minarovits J, Niller H, (Eds); Springer: New York, 2012;419-55.
4. Mikovits J, Young H, Vertino P, et al. Infection with human immunodeficiency virus type 1 upregulates DNA methyltransferase, resulting in de novo methylation of the gamma interferon (IFN-gamma) promoter and subsequent downregulation of IFN-gamma production. Mol Cell Biol. 1998;18:5166-77.
5. Robertson K. DNA methylation, methyltransferases, and cancer. Oncogene. 2001;20:3139-55.
6. Nan X, Ng H, Johnson C, et al. Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature. 1998;393:386-9.
7. Ng H, Zhang Y, Hendrich B, et al. MBD2 is a transcriptional repressor belonging to the MeCP1 histone deacetylase complex. Nat Genet. 1999;23:58-61.
8. Blomen V, Boonstra J. Stable transmission of reversible modifications: maintenance of epigenetic information through the cell cycle. Cell Mol Life Sci. 2011;68:27-44.
9. Ringrose L, Paro R. Polycomb/Trithorax response elements and epigenetic memory of cell identity. Development. 2007;134:223-32.
10. Fischle W, Wang Y, Jacobs S, Kim Y, Allis C, Khorasanizadeh S. Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains. Genes Dev. 2003;17:1870-81.
11. Xu J, Pope S, Jazirehi A, et al. Pioneer factor interactions and unmethylated CpG dinucleotides mark silent tissue-specific enhancers in embryonic stem cells. Proc Natl Acad Sci USA. 2007;104:12377-82.
12. Xu J, Watts J, Pope S, et al. Transcriptional competence and the active marking of tissue-specific enhancers by defined transcription factors in embryonic and induced pluripotent stem cells. Genes Dev. 2009;23:2824-38.
13. Ito S, Shen L, Dai Q, et al. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science. 2011;333:1300-3.
14. He Y, Li B, Li Z, et al. Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science. 2011;333:1303-7.
15. Zaret K, Watts J, Xu J, Wandzioch E, Smale S, Sekiya T. Pioneer factors, genetic competence, and inductive signaling: programming liver and pancreas progenitors from the endoderm. Cold Spring Harb Symp Quant Biol. 2008;73:119-26.
16. Burke L, Zhang R, Bartkuhn M, et al. CTCF binding and higher order chromatin structure of the H19 locus are maintained in mitotic chromatin. EMBO J. 2005;24:3291-300.
17. Kelly T, Jones P. Role of nucleosomes in mitotic bookmarking. Cell Cycle. 2011;10:370-1.
18. Hughes T, Webb R, Fei Y, Wren J, Sawalha A. DNA methylome in human CD4+ T cells identifies transcriptionally repressive and non-repressive methylation peaks. Genes Immun. 2010;11:554-60.
19. Schmidl C, Klug M, Boeld T, et al. Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity. Genome Res. 2009;19:1165-74.
20. Tian Y, Jia Z, Wang J, et al. Global mapping of H3K4me1 and H3K4me3 reveals the chromatin state-based cell type-specific gene regulation in human Treg cells. PLoS One. 2011;6:e27770.
21. Wang J, Lunyak V, Jordan I. Genome-wide prediction and analysis of human chromatin boundary elements. Nucleic Acids Res. 2012;40:511-29.
22. Zhang Y, Shin H, Song J, Lei Y, Liu X. Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq. BMC Genomics. 2008;9:537.
23. Bocker M, Hellwig I, Breiling A, Eckstein V, Ho A, Lyko F. Genome-wide promoter DNA methylation dynamics of human hematopoietic progenitor cells during differentiation and aging. Blood. 2011;117:e182-9.
24. Van den Bergh R, Florence E, Vlieghe E, et al. Transcriptome analysis of monocyte-HIV interactions. Retrovirology. 2010;7:53.
25. Karn J. The molecular biology of HIV latency: breaking and restoring the Tat-dependent transcriptional circuit. Curr Opin HIV AIDS. 2011;6:4-11.
26. Richman D, Margolis D, Delaney M, Greene W, Hazuda D, Pomerantz R. The challenge of finding a cure for HIV infection. Science. 2009;323:1304-7.
27. Siliciano R, Greene W. HIV latency. Cold Spring Harb Perspect Med. 2011;1:a007096.
28. Pearson R, Kim Y, Hokello J, et al. Epigenetic silencing of human immunodeficiency virus (HIV) transcription by formation of restrictive chromatin structures at the viral long terminal repeat drives the progressive entry of HIV into latency. J Virol. 2008;82:12291-303.
29. Donahue D, Wainberg M. Cellular and molecular mechanisms involved in the establishment of HIV-1 latency. Retrovirology. 2013;10:11.
30. Taube R, Peterlin M. Lost in transcription: molecular mechanisms that control HIV latency. Viruses. 2013;5:902-27.
31. Van Lint C, Bouchat S, Marcello A. HIV-1 transcription and latency: an update. Retrovirology. 2013;10:67.
32. Archin N, Liberty A, Kashuba A, et al. Administration of vorinostat disrupts HIV-1 latency in patients on antiretroviral therapy. Nature. 2012;487:482-5.
33. Duverger A, Jones J, May J, et al. Determinants of the establishment of human immunodeficiency virus type 1 latency. J Virol. 2009;83:3078-93.
34. Kauder S, Bosque A, Lindqvist A, Planelles V, Verdin E. Epigenetic regulation of HIV-1 latency by cytosine methylation. PLoS Pathog. 2009;5:e1000495.
35. Lin S, Zhang Y, Ying H, Zhu H. HIV-1 reactivation induced by apicidin involves histone modification in latently infected cells. Curr HIV Res. 2011;9:202-8.
36. Margolis D. Histone deacetylase inhibitors and HIV latency. Curr Opin HIV AIDS. 2011;6:25-9.
37. Wolschendorf F, Duverger A, Jones J, et al. Hit-and-run stimulation: a novel concept to reactivate latent HIV-1 infection without cytokine gene induction. J Virol. 2010;84:8712-20.
38. Deeks S. HIV: Shock and kill. Nature. 2012;487:439-40.
39. Margolis D. Eradication therapies for HIV Infection: time to begin again. AIDS Res Hum Retroviruses. 2011;27:347-53.
40. Matalon S, Rasmussen T, Dinarello C. Histone deacetylase inhibitors for purging HIV-1 from the latent reservoir. Mol Med. 2011;17:466-72.
41. Choi B, Lee H, Oh Y, et al. Novel histone deacetylase inhibitors CG05 and CG06 effectively reactivate latently infected HIV-1. AIDS. 2010;24:609-11.
42. Archin N, Espeseth A, Parker D, Cheema M, Hazuda D, Margolis D. Expression of latent HIV induced by the potent HDAC inhibitor suberoylanilide hydroxamic acid. AIDS Res Hum Retroviruses. 2009;25:207-12.
43. Shan L, Deng K, Shroff N, et al. Stimulation of HIV-1-specific cytolytic T lymphocytes facilitates elimination of latent viral reservoir after virus reactivation. Immunity. 2012;36:491-501.
44. Youngblood B, Reich N. The early expressed HIV-1 genes regulate DNMT1 expression. Epigenetics. 2008;3:149-56.
45. Shimura M, Toyoda Y, Iijima K, et al. Epigenetic displacement of HP1 from heterochromatin by HIV-1 Vpr causes premature sister chromatid separation. J Cell Biol. 2011;194:721-35.
46. Shafer R, Rhee S, Pillay D, et al. HIV-1 protease and reverse transcriptase mutations for drug resistance surveillance. AIDS. 2007;21:215-23.
47. Nyce J, Leonard S, Canupp D, Schulz S, Wong S. Epigenetic mechanisms of drug resistance: drug-induced DNA hypermethylation and drug resistance. Proc Natl Acad Sci USA. 1993;90:2960-4.
48. Olivero O. Mechanisms of genotoxicity of nucleoside reverse transcriptase inhibitors. Environ Mol Mutagen. 2007;48:215-23.
49. Wu S, Liu X, Solorzano M, Kwock R, Avramis V. Development of zidovudine (AZT) resistance in Jurkat T cells is associated with decreased expression of the thymidine kinase (TK) gene and hypermethylation of the 5' end of human TK gene. J Acquir Immune Defic Syndr Hum Retrovirol. 1995;8:1-9.
50. Lucarelli M, Palitti F, Carotti D, et al. AZT-induced hypermethylation of human thymidine kinase gene in the absence of total DNA hypermethylation. FEBS Lett. 1996;396:323-6.
51. Senda S, Blanche S, Costagliola D, et al. Altered heterochromatin organization after perinatal exposure to zidovudine. Antivir Ther. 2007;12:179-87.
52. Gyory I, Minarovits J. Epigenetic regulation of lymphoid specific gene sets. Biochem Cell Biol. 2005;83:286-95.
53. Zhu T. HIV-1 in peripheral blood monocytes: an underrated viral source. J Antimicrob Chemother. 2002;50:309-11.
54. Herbein G, Varin A. The macrophage in HIV-1 infection: from activation to deactivation? Retrovirology. 2010;7:33.
55. Chun T, Justement J, Murray D, et al. Rebound of plasma viremia following cessation of antiretroviral therapy despite profoundly low levels of HIV reservoir: implications for eradication. AIDS. 2010;24:2803-8.
56. Finzi D, Hermankova M, Pierson T, et al. Identification of a reservoir for HIV-1 in patients on highly active antiretroviral therapy. Science. 1997;278:1295-300.
57. Margolis D. Mechanisms of HIV latency: an emerging picture of complexity. Curr HIV/AIDS Rep. 2010;7:37-43.
58. Mbonye U, Karn J. Control of HIV latency by epigenetic and non-epigenetic mechanisms. Curr HIV Res. 2011;9:554-67.
59. Siliciano J, Kajdas J, Finzi D, et al. Long-term follow-up studies confirm the stability of the latent reservoir for HIV-1 in resting CD4+ T cells. Nat Med. 2003;9:727-8.
60. Marban C, Suzanne S, Dequiedt F, et al. Recruitment of chromatinmodifying enzymes by CTIP2 promotes HIV-1 transcriptional silencing. EMBO J. 2007;26:412-23.
61. Kim N, Kukkonen S, Gupta S, Aldovini A. Association of Tat with promoters of PTEN and PP2A subunits is key to transcriptional activation of apoptotic pathways in HIV-infected CD4+ T cells. PLoS Pathog. 2010;6:e1001103.
62. Zauli G, Gibellini D. The human immunodeficiency virus type-1 (HIV-1) Tat protein and Bcl-2 gene expression. Leuk Lymphoma. 1996;23:551-60.
63. Zhang M, Li X, Pang X, et al. Bcl-2 upregulation by HIV-1 Tat during infection of primary human macrophages in culture. J Biomed Sci. 2002;9:133-9.
64. Balog K, Minarovits J. Nef: a pleiotropic modulator of primate lentivirus infectivity and pathogenesis. Acta Microbiol Immunol Hung. 2006;53:51-75.
65. Olivetta E, Federico M. HIV-1 Nef protects human-monocyte-derived macrophages from HIV-1-induced apoptosis. Exp Cell Res. 2006;312:890-900.
66. Garaci E, Caroleo M, Aloe L, et al. Nerve growth factor is an autocrine factor essential for the survival of macrophages infected with HIV. Proc Natl Acad Sci USA. 1999;96:14013-18.
67. Busca A, Saxena M, Kumar A. Critical role for antiapoptotic Bcl-xL and Mcl-1 in human macrophage survival and cellular IAP1/2 (cIAP1/2) in resistance to HIV-Vpr-induced apoptosis. J Biol Chem. 2012;287:15118-33.
68. Aquaro S, Bagnarelli P, Guenci T, et al. Long-term survival and virus production in human primary macrophages infected by human immunodeficiency virus. J Med Virol. 2002;68:479-88.
69. Fenyo E, Albert J, Asjo B. Replicative capacity, cytopathic effect and cell tropism of HIV. AIDS. 1989;3(Suppl 1):S5-12.
70. Richman D. Introduction: challenges to finding a cure for HIV infection. Curr Opin HIV AIDS. 2011;6:1-3.
71. Iglesias-Ussel M, Romerio F. HIV reservoirs: the new frontier. AIDS Rev. 2011;13:13-29.
72. Peedicayil J. Pharmacoepigenetics and pharmacoepigenomics. Pharmacogenomics. 2008;9:1785-6.
73. Adler-Wailes D, Guiney E, Koo J, Yanovski J. Effects of ritonavir on adipocyte gene expression: evidence for a stress-related response. Obesity (Silver Spring). 2008;16:2379-87.
74. Fattal E, Barratt G. Nanotechnologies and controlled release systems for the delivery of antisense oligonucleotides and small interfering RNA. Br J Pharmacol. 2009;157:179-94.
75. Weinberg M, Villeneuve L, Ehsani A, et al. The antisense strand of small interfering RNAs directs histone methylation and transcriptional gene silencing in human cells. RNA. 2006;12:256-62.
76. Helene C, Giovannangeli C, Guieysse-Peugeot A, Praseuth D. Sequence-specific control of gene expression by antigene and clamp oligonucleotides. Ciba Found Symp. 1997;209:94-106.
77. Kwok T, Heinrich J, Jung-Shiu J, Meier M, Mathur S, Moelling K. Reduction of gene expression by a hairpin-loop structured oligodeoxynucleotide: alternative to siRNA and antisense. Biochim Biophys Acta. 2009;1790:1170-8.
78. Lisziewicz J, Sun D, Weichold F, et al. Antisense oligodeoxynucleotide phosphorothioate complementary to Gag mRNA blocks replication of human immunodeficiency virus type 1 in human peripheral blood cells. Proc Natl Acad Sci USA. 1994;91:7942-6.
79. Moelling K, Abels S, Jendis J, Matskevich A, Heinrich J. Silencing of HIV by hairpin-loop-structured DNA oligonucleotide. FEBS Lett. 2006;580:3545-50.
80. Peng H, Callison D, Li P, Burrell C. Long-term protection against HIV-1 infection conferred by tat or rev antisense RNA was affected by the design of the retroviral vector. Virology. 1996;220:377-89.