Yeast Genetic Analysis Reveals the Involvement of Chromatin Reassembly Factors in Repressing HIV-1 Basal Transcription

Abstract

Rebound of HIV viremia after interruption of anti-retroviral therapy is due to the small population of CD4+ T cells that remain latently infected. HIV-1 transcription is the main process controlling post-integration latency. Regulation of HIV-1 transcription takes place at both initiation and elongation levels. Pausing of RNA polymerase II at the 5′ end of HIV-1 transcribed region (5′HIV-TR), which is immediately downstream of the transcription start site, plays an important role in the regulation of viral expression. The activation of HIV-1 transcription correlates with the rearrangement of a positioned nucleosome located at this region. These two facts suggest that the 5′HIV-TR contributes to inhibit basal transcription of those HIV-1 proviruses that remain latently inactive. However, little is known about the cell elements mediating the repressive role of the 5′HIV-TR. We performed a genetic analysis of this phenomenon in Saccharomyces cerevisiae after reconstructing a minimal HIV-1 transcriptional system in this yeast. Unexpectedly, we found that the critical role played by the 5′HIV-TR in maintaining low levels of basal transcription in yeast is mediated by FACT, Spt6, and Chd1, proteins so far associated with chromatin assembly and disassembly during ongoing transcription. We confirmed that this group of factors plays a role in HIV-1 postintegration latency in human cells by depleting the corresponding human orthologs with shRNAs, both in HIV latently infected cell populations and in particular single-integration clones, including a latent clone with a provirus integrated in a highly transcribed gene. Our results indicate that chromatin reassembly factors participate in the establishment of the equilibrium between activation and repression of HIV-1 when it integrates into the human genome, and they open the possibility of considering these factors as therapeutic targets of HIV-1 latency.

Author Summary

Acquired immunodeficiency syndrome (AIDS) is caused by the human immunodeficiency virus (HIV). Drugs used for anti-viral therapy are very efficient in controlling the presence of viral particles in infected patients. However, if this therapy is interrupted, rebound of viremia occurs due to the small population of cells that remain latently infected. A specific region of the HIV genome (the beginning of the transcribed region) plays an important role in viral expression and may contribute to its silent state in latently infected cells. We reconstructed a minimal HIV system in yeast to perform a genetic analysis of the role played by that specific region of the viral genome. We found that the repressive role played by this region is mediated by a group of proteins (chromatin reassembly factors) so far associated with other functions during gene expression. We confirmed that this group of factors plays a role in controlling HIV-1 basal transcription in human cells.