Epigenomic characterization of latent HIV infection identifies latency regulating transcription factors

Abstract

SummaryTranscriptional 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 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.

Vpr shapes the proviral landscape and polyclonal HIV-1 reactivation patterns in cultured cells

“…Because identifying latent cells is challenging, many experimental latency systems include reporter genes and/or delete viral genes believed to be unnecessary for silencing and reactivation (33,34,52). For example, two prominent studies that used barcoded proviruses to track virus dissemination in animals used vpr-proviruses (33,52).…”

“…For these reasons, some latency models use vpr-defective proviruses to allow the survival of cells harboring transcriptionally active proviruses. Cultured over time to allow proviral transcriptional silencing, these cells can then be used for reactivation studies (31)(32)(33)(34).…”