Biology subjects

Burgos, S. D.

Publications and source records attributed to Burgos, S. D..

4 recordsLinked to original sources

bioRxiv2026

RelB proximity proteomics and CRISPR screening define chromatin regulators of noncanonical NF-κB control of HIV latency and reactivation

Activation of the non-canonical NF-{kappa}B pathway via RelB/p52 signaling by SMAC mimetics such as AZD5582 is a promising strategy to induce HIV expression from latency, but the chromatin mechanisms linking RelB/p52 to proviral regulation remain poorly defined. Here, we combine RelB BioID proteomics, targeted HIV-CRISPR screening, and pharmacologic validation to identify ncNF-{kappa}B-associated regulators of HIV expression. RelB BioID revealed an extensive interaction network of chromatin and transcriptional regulators in basal and AZD5582-activated states. Basally associated RelB proteins included NSD2, SWI/SNF components, UHRF1, and DNMT1, while AZD5582-enriched proteins included p300, USP7, LSD1/KDM1A, NuRD components, SIN3A, and HBO1/KAT7. Functional screening using a custom guide RNA library targeting all BioID-identified factors identified regulators that promote HIV reactivation, including HBO1/KAT7, NSD2, and SIN3A, and regulators that restrict HIV expression, including p300, CHD4, and USP7. Because KAT7/HBO1 and p300 encode acetyltransferases with opposing screen phenotypes, we tested whether their catalytic activities contribute to HIV transcriptional regulation and found that, consistent with the CRISPR screen, KAT7/HBO1 inhibition reduced AZD5582-induced reactivation, whereas p300 inhibition enhanced it. Together, these data define a resource linking the RelB-associated chromatin landscape to HIV latency and reactivation.

cell biology↗

bioRxiv2025

A screen of chromatin-targeting compounds identifies TAF1 as a novel regulator of HIV latency

Antiretroviral therapy (ART) suppresses HIV replication but fails to eliminate the virus due to the persistence of a transcriptionally silent reservoir, which remains the primary barrier to a cure. HIV latency is maintained through chromatin-mediated repression, making epigenetic regulators attractive therapeutic targets. To identify new modulators of latency, we screened a focused library of 84 chromatin-targeting small molecules. This screen identified BAY-299, a bromodomain inhibitor selective for TAF1 and BRD1, as a latency-modulating compound. BAY-299 reactivated HIV expression and enhanced the efficacy of established latency-reversing agents (LRAs), including vorinostat, prostratin, and iBET-151, in cell line models. CRISPR/Cas9-mediated knockout experiments demonstrated that TAF1, but not BRD1, is essential for maintaining HIV latency and that TAF1 depletion selectively increases HIV transcription with minimal effects on host gene expression. Dual knockout of TAF1 and Tat revealed that the reactivation effect is partially Tat dependent. CUT&RUN analysis further showed that TAF1 depletion increases RNA Polymerase II occupancy across the HIV gene body, suggesting enhanced transcriptional elongation. These findings identify TAF1 as a novel regulator of HIV latency and demonstrate the utility of targeted chemical screening to uncover therapeutic vulnerabilities within the latent reservoir. ImportanceHIV remains incurable due to the persistence of a transcriptionally silent reservoir in infected cells that is not eliminated by antiretroviral therapy. This transcriptionally silent state, known as latency, is controlled by host cell factors that regulate access to the viral genome. In this study, we identified the host protein TAF1 as a key regulator that maintains HIV in a latent state. Using both genetic and chemical approaches, we demonstrated that reducing TAF1 levels selectively increases HIV gene expression without broadly disrupting host gene transcription. These findings highlight a previously unrecognized mechanism of HIV latency control and identify TAF1 as a potential therapeutic target. Understanding how host chromatin regulators contribute to latency is essential for developing strategies that aim to eliminate the persistent HIV reservoir.

microbiology↗

bioRxiv2022

A histone deacetylase network regulates epigenetic reprogramming and viral silencing in HIV infected cells

Approximately 70% of the HIV-1 latent reservoir originates from infections of CD4 T cells that occur in the months near the time of ART initiation, raising the possibility that interventions during this period might prevent reservoir seeding and reduce reservoir size. We identify class 1 histone deacetylase inhibitors (HDACi) as potent agents of latency prevention. Inhibiting HDACs in productively infected cells caused extended maintenance of HIV expression and this activity was associated with persistently elevated H3K9 acetylation and reduced H3K9 methylation at the viral LTR promoter region. HDAC inhibition in HIV-infected CD4 T cells during effector-to-memory transition led to striking changes in the memory phenotype of infected cells. Proviral silencing is accomplished through distinct activities of HDAC1/2 and HDAC3. Thus HDACs regulate a critical gateway process for HIV latency establishment and are required for the development of CD4 T-cell memory subsets that preferentially harbor long-lived, latent provirus.

molecular biology↗

bioRxiv2020

Epigenomic characterization of latent HIV infection identifies latency regulating transcription factors.

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 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.

microbiology↗