Epigenetic analysis of HIV-1 proviral genomes from infected individuals

Predominance of unmethylated CpG's

Stefanie Weber, Barbara Weiser, Kimdar S. Kemal, Harold Burger, Christina M. Ramirez, Klaus Korn, Kathryn Anastos, Rupert Kaul, Colin Kovacs, Walter Doerfler

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Efforts to cure HIV-1 infections aim at eliminating proviral DNA. Integrated DNA from various viruses often becomes methylated de novo and transcriptionally inactivated. We therefore investigated CpG methylation profiles of 55 of 94 CpG's (58.5%) in HIV-1 proviral genomes including ten CpG's in each LTR and additional CpG's in portions of gag, env, nef, rev, and tat genes. We analyzed 33 DNA samples from PBMC's of 23 subjects representing a broad spectrum of HIV-1 disease. In 22 of 23 HIV-1-infected individuals, there were only unmethylated CpG's regardless of infection status. In one long term nonprogressor, however, methylation of proviral DNA varied between 0 and 75% over an 11-year period although the CD4+ counts remained stable. Hence levels of proviral DNA methylation can fluctuate. The preponderance of unmethylated CpG's suggests that proviral methylation is not a major factor in regulating HIV-1 proviral activity in PBMC's. Unmethylated CpG's may play a role in HIV-1 immunopathogenesis.

Original languageEnglish (US)
Pages (from-to)181-189
Number of pages9
JournalVirology
Volume449
DOIs
StatePublished - Jan 20 2014

Fingerprint

Epigenomics
HIV-1
Genome
DNA Methylation
Methylation
rev Genes
tat Genes
nef Genes
gag Genes
env Genes
DNA Viruses
DNA
CD4 Lymphocyte Count
HIV Infections
Infection

Keywords

  • Bisulfite sequencing
  • Epigenetics of HIV-1 proviral DNA
  • Escape from proviral DNA methylation
  • Fluctuation of CpG methylation in one LTNP individual
  • Integrated HIV-1 DNA in PBMC's from infected individuals
  • Methylation analysis of integrated HIV-1 genomes
  • Predominance of unmethylated CpG's in PBMC's
  • Wide spectrum of infection outcome

ASJC Scopus subject areas

  • Virology

Cite this

Weber, S., Weiser, B., Kemal, K. S., Burger, H., Ramirez, C. M., Korn, K., ... Doerfler, W. (2014). Epigenetic analysis of HIV-1 proviral genomes from infected individuals: Predominance of unmethylated CpG's. Virology, 449, 181-189. https://doi.org/10.1016/j.virol.2013.11.013

Epigenetic analysis of HIV-1 proviral genomes from infected individuals : Predominance of unmethylated CpG's. / Weber, Stefanie; Weiser, Barbara; Kemal, Kimdar S.; Burger, Harold; Ramirez, Christina M.; Korn, Klaus; Anastos, Kathryn; Kaul, Rupert; Kovacs, Colin; Doerfler, Walter.

In: Virology, Vol. 449, 20.01.2014, p. 181-189.

Research output: Contribution to journalArticle

Weber, S, Weiser, B, Kemal, KS, Burger, H, Ramirez, CM, Korn, K, Anastos, K, Kaul, R, Kovacs, C & Doerfler, W 2014, 'Epigenetic analysis of HIV-1 proviral genomes from infected individuals: Predominance of unmethylated CpG's', Virology, vol. 449, pp. 181-189. https://doi.org/10.1016/j.virol.2013.11.013
Weber, Stefanie ; Weiser, Barbara ; Kemal, Kimdar S. ; Burger, Harold ; Ramirez, Christina M. ; Korn, Klaus ; Anastos, Kathryn ; Kaul, Rupert ; Kovacs, Colin ; Doerfler, Walter. / Epigenetic analysis of HIV-1 proviral genomes from infected individuals : Predominance of unmethylated CpG's. In: Virology. 2014 ; Vol. 449. pp. 181-189.
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