HIV-1 latent infection triggers broader epigenomic changes in protein-coding and long non-coding RNAs than active infection of SupT1 cells (ATAC-Seq)

Latent HIV-1 infection poses a major challenge in complete viral remission and cure. HIV-1 latency is a multi-dimensional, dynamic process and many aspects of how the viral latency is established and maintained still remains incompletely characterized. Here, we have investigated the host chromatin organization and transcriptomic changes in active- and latently-infected SupT1 cells. We employed an in vitro model of HIV-1 latency in SupT1 cells using a dual-reporter virus, HIVGKO, which enables high purity sorting and characterization of active- and latently-infected cells. We found a significant divergence in chromatin organization and gene expression pattern between active and latent infection compared to uninfected cells. Latent infection results in a repressive reorganization of the host chromatin, while active infection leads to an overall increase in chromatin accessibility. A stronger correlation was also observed between chromatin accessibility and gene expression in latent infection, which was manifested in a greater alteration of the cellular transcriptome in latent than active infection, for both proteincoding and long-non-coding RNAs (lncRNAs). We identified a number of novel lncRNAs associated with either active and latent infection. A reversal in expression pattern of latency-associated lncRNAs following PMA-induced reactivation indicated their infection state-specific expression and potential roles in HIV-1 latency. Taken together, this integrated, comparative study revealed that latent HIV-1 infection requires a substantially greater alteration in cellular epigenome and transcriptome. Understanding of the distinct cellular states conducive to active and latent infection may support devising strategies for specific modulation of host cellular functions as a curative intervention for HIV-1. Four days post-infection (dpi), HIV GKO-infected SupT1 cells were flow sorted into the two populations: active (mKO2+GFP+) and latent (mKO2+GFP-) HIV-1- infected cells. RNA-sequencing was performed with total cellular RNA extracted from the flow-sorted uninfected, active- and latently infected SupT1 cells from two independent experiments.