Whole genome methylation array reveals the down-regulation of IGFBP6 and SATB2 by HIV-1

Sci Rep. 2015 Jun 3:5:10806. doi: 10.1038/srep10806.


Nowadays, the knowledge in DNA methylation-mediated gene regulation has shed light on the understanding of virus-host interplay in the context of genome alteration. It has also been shown that HIV is able to change the DNA methylation pattern by DNA methyltransferases and such changes can be correlated with the progression of AIDS. In this study, we have investigated the relationship between genome-wide DNA methylation pattern and HIV infection using the methylated DNA immunoprecipitation--microarray method. A pair of monozygotic twins was recruited: one of the twins was infected with HIV while the other was not. Based on data from the microarray experiment, 4679 differentially methylated regions in the HIV positive subject with the significant peak values were identified. Selected genes were then validated in human T lymphocyte CEM*174 cell line and HIV/AIDS patients by comparing with normal subjects. We found that IGFBP6 and SATB2 were significantly down-regulated in HIV-infected CEM*174 cells and 3 different cohorts of HIV/AIDS patients while their promoters were predominantly hyper-methylated compared with normal controls. This study also provides a resource for the identification of HIV-induced methylation and contributes to better understanding of the development of HIV/AIDS.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Cell Line
  • CpG Islands
  • DNA Methylation*
  • Down-Regulation
  • Epigenesis, Genetic
  • Epigenomics*
  • Female
  • Gene Expression Profiling
  • Gene Expression Regulation*
  • Genome, Human*
  • HIV Infections / genetics*
  • HIV Infections / virology
  • HIV-1 / physiology*
  • Humans
  • Insulin-Like Growth Factor Binding Protein 6 / genetics*
  • Matrix Attachment Region Binding Proteins / genetics*
  • Promoter Regions, Genetic
  • Reproducibility of Results
  • T-Lymphocytes / metabolism
  • T-Lymphocytes / virology
  • Transcription Factors / genetics*
  • Twins, Monozygotic
  • Viral Load


  • Insulin-Like Growth Factor Binding Protein 6
  • Matrix Attachment Region Binding Proteins
  • SATB2 protein, human
  • Transcription Factors