Epigenomic characterization of latent HIV infection identifies latency regulating transcription factors [article]

Stuart R Jefferys, Sam D Burgos, Jackson Peterson, Sara R Selitsky, Anne-Marie Turner, Lindsey I James, David M Margolis, Joel Parker, Edward P Browne
2020 bioRxiv   pre-print
Transcriptional silencing of HIV generates a reservoir of latently infected cells, but the mechanisms that lead to this outcome are not well understood. We characterized a primary cell model of HIV latency, and observed that latency is a stable, heritable viral state that is rapidly reestablished after stimulation. Using Assay of Transposon-Accessible Chromatin sequencing (ATACseq) we found that latently infected cells exhibit reduced proviral accessibility, elevated activity of Forkead and
more » ... of Forkead and Kruppel-like factor transcription factors (TFs), and reduced activity of AP-1, RUNX and GATA TFs. Latency reversing agents caused distinct patterns of chromatin reopening across the provirus. Furthermore, depletion of a chromatin domain insulator, CTCF inhibited HIV latency, identifying this factor as playing a key role in the initiation or enforcement of latency. These data indicate that HIV latency develops preferentially in cells with a distinct pattern of TF activity that promotes a closed proviral structure and inhibits viral gene expression.
doi:10.1101/2020.07.24.220012 fatcat:frgbb57alvfu3exjdrkuxgyete