A proteomic glimpse into the initial global epigenetic changes during HIV infection

Abstract

HIV-1 replication requires the insertion of viral DNA into the host genome, which is catalyzed by HIV-1 integrase. This integration event can lead to vast changes in the chromatin landscape and gene transcription. In this study, we sought to correlate the extensive changes of histone post-translation modification (PTM) abundances with the equally dynamic shifts in host transcriptional activity. To fully capture the changes that were occurring during the course of HIV-infection, we performed time-courses in which we extracted both histones and mRNA from HIV-infected, UV-inactivated HIV-infected and mock-infected SUP-T1 cells. We then analyzed the alterations to histone PTM profiles using nanoLC-MS/MS, as well as the expression of chromatin-associated enzymes, such as histone deacetylases, acetyltransferases, demethylases, methyltransferases and histone chaperone proteins. As expected, we observed major changes in histone PTM abundances, which we linked to massive fluctuations in mRNA expression of associated chromatin enzymes. However, we find few differences between HIV and HIVUV (UV-inactivated) infection, which suggests that initial histone PTM changes during HIV infection are from the host in response to the infection, and not due to the HIV virus manipulating the transcriptional machinery. We believe that these preliminary experiments can provide a basis for future forays into targeted manipulations of histone PTM-regulated aspects of HIV progression through its replication cycle.

Characterization of histone post-translational modifications during virus infection using mass spectrometry-based proteomics

“…The role of histone PTMs during virus infection has only recently come into prominence with the recognition that viral manipulation of host cells necessarily hijacks chromatin signaling [11-13]. Many studies have focused on histone PTMs associated with viral genomes at various stages during infection [14-18] where others have investigated specific histone PTM changes on host genomes, largely through antibody-based approaches [19-21], or investigating the effect of specific viral proteins [22,23].…”

Epigenetic crosstalk in chronic infection with HIV-1

“…Indeed, there is preliminary data that HIV-1 infection also alters levels of several histone PTMs [125,126]. One study showed that HIV-1 infection ex vivo is accompanied by strong fluctuations in histone PTM levels as demonstrated by mass spectrometry and transcriptional profiling of PTM-associated enzymes [126]. In accordance with the findings on increased CpG methylation upon infection, a second report suggested that global repressive histone marks, such as H3K9me3 and H3K27me3 increase [125].…”

“…Based on our understanding of epigenetic regulation as a complex interplay of different features, it would be astonishing if methylome changes would not be accompanied by genome-wide changes of further epigenetic marks. Indeed, there is preliminary data that HIV-1 infection also alters levels of several histone PTMs [125,126]. One study showed that HIV-1 infection ex vivo is accompanied by strong fluctuations in histone PTM levels as demonstrated by mass spectrometry and transcriptional profiling of PTM-associated enzymes [126].…”

Proteomics in the investigation of HIV‐1 interactions with host proteins

“…The histone PTMs of HIV-1 infection were also examined by nano-LC-MS/MS. Major changes in histone PTM abundances were linked to massive fluctuations in mRNA expression of associated chromatin enzymes [26]. Unlike the numerous epigenetic studies performed for many diseases, especially in cancer, the investigation of HIV-1 induced PTM proteomic regulation has been rather limited.…”