Roles of convergent RNA polymerase II transcription to HIV-1 latency and reactivation

The National Institute of Allergy and Infectious Diseases awarded The University of Texas Southwestern Medical Center $249,000 on July 16, 2026, under the Allergy and Infectious Diseases Research program (CFDA 93.855) to investigate the role of convergent RNA polymerase II transcription in HIV-1 latency and reactivation.

The research aims to define how convergent POL II transcription—specifically antisense and downstream forms originating from the 5'-LTR—regulates sense HIV-1 transcription during latency maintenance and viral reactivation. The investigator will employ genetic assays for HIV-1 proviral genome engineering and high-resolution genomic assays in immortalized cell models of latency, with cross-validation in primary cell models. Work will test whether convergent POL II influences HIV-1 transcription across basal, host, and viral phases of the multi-phase transcription program, both with and without Tat function. The project focuses on understanding the latency-reactivation switch to inform cure strategies for HIV-1 infection.

Performance occurs in Dallas, Texas. The period of performance runs through June 30, 2028. This is a Project Grant, an assistance type supporting investigator-initiated research.

Abstract

Although HIV-1 infection can be controlled through long-term treatment with anti-retroviral therapy (art), a true cure has been intangible. Reservoir cells endure over time and support latent HIV-1 reactivation upon therapy cessation, yet little is known about the underlying molecular mechanisms. Our lab has recently identified previously unprecedented mechanistic details in the process of RNA polymerase (POL II) transcription, which might have implications for the regulation of latency maintenance and reactivation in reservoir cells. Specifically, we found a form of convergent POL II (antisense and downstream of the 5'-LTR) that we will explore in this research proposal to help fill this knowledge GAP, and provide key insights into HIV-1 biology as well as cure strategies. The major goal of this grant application is to define the role(s) of the convergent POL II form to the process of sense HIV-1 transcription from the 5'-LTR during latency and reactivation. We will accomplish this goal by leveraging genetic assays for HIV-1 proviral genome engineering and high-resolution genomic assays in immortalized cell models of latency with cross-validation in primary cell models to bolster physiologic relevance. We will explore the central hypothesis that the convergent POL II form is required to maintain proper dynamics of sense HIV-1 transcription to facilitate the latency-reactivation switch. We will test if the convergent POL II form influences HIV-1 transcription in the various phases of the multi-phase HIV-1 transcription program (basal, host and viral) with and without TAT function. We propose to build on our recent findings to gain a deeper understanding of how convergent POL II controls HIV-1 transcription for latency reactivation in the host and viral phases of the HIV-1 transcriptional program. These goals are reflected in two specific aims: assess the function of convergent POL II pausing to HIV-1 transcription latency and reactivation (aim 1), and cross validate the presence of convergent POL II in a primary cell model of latency (aim 2). If successful, this project will yield a better understanding of the underlying molecular mechanisms by which sense and convergent POL II forms operate (jointly or independently) to promote HIV-1 transcription during latency reactivation, collectively having a sustained impact in the field. In keeping with niaid's mission of ending the HIV-1 epidemic, our long-term objective is to leverage these basic discoveries to help devise novel and alternative cure strategies. We envision that the fundamental knowledge gained by this research could be used in future studies beyond the scope (e.g., by exploiting the convergent POL II form) to permanently silence transcription to achieve the long-awaited HIV-1 remission.