THE ROLE OF TAF1 AND CTCF IN HIV LATENCY

Despite the effectiveness of combination antiretroviral therapy (cART) in suppressing HIV-1 replication, it cannot eliminate the virus due to the persistence of a latent reservoir in long-lived CD4⁺ T cells. These transcriptionally silent proviruses evade immune clearance and represent a major barrier to HIV cure strategies. This dissertation investigates host-cell mechanisms that regulate latency, with the goal of identifying novel molecular targets that could be leveraged for therapeutic latency reversal.In Chapter 2, I examine the epigenomic landscape of latency using a primary CD4⁺ T cell model. Assay for transposase-accessible chromatin using sequencing (ATAC-seq) revealed a significant loss of chromatin accessibility across the HIV-1 provirus in latent cells, alongside a marked shift in transcription factor motif usage—namely increased Forkhead and KLF activity and reduced AP-1, RUNX, and GATA motifs indicating that lineage-specific transcriptional programs contribute to the maintenance of latency. Notably, chromatin insulator protein CTCF was enriched at differentially accessible sites, and its knockdown resulted in a moderate reduction of latent infection, implicating CTCF in the regulation of HIV-1 chromatin topology and gene silencing.Chapter 3 builds upon this work by identifying the transcription factor TAF1 as a selective regulator of HIV-1 latency through an epigenetic compound screen using the 2D10 cell line model. The TAF1 bromodomain inhibitor BAY-299 was found to induce HIV-1 expression in latently infected cells. Genetic depletion of TAF1 led to robust HIV-1 reactivation with minimal global transcriptional perturbation, supported by RNA-seq and CUT&RUN analyses. We hypothesize that TAF1 sequesters HIV-1 Tat, limiting its availability to initiate transcription from the viral LTR. Depletion of TAF1 increases Tat availability, driving viral gene expression. These findings suggest TAF1 as a promising target for latency reversal strategies. Together, these studies highlight two distinct, but complementary host regulatory pathways of chromatin insulation and core transcription factors contribute to HIV-1 latency. Both represent viable targets for novel therapeutic intervention.