Using Single-Cell Data to Decipher Mechanisms of NF-kB-chromatin-mediated HIV Transcriptional Regulation

Yale University, New Haven CT

Investigators

Abstract

1264246 Miller-Jensen, Kathryn Genetically identical cells can display significant phenotypic heterogeneity as a result of random fluctuations (noise) in gene expression, which is modulated by transcription factor binding and chromatin modifications at each gene promoter. The interaction of chromatin and transcription factors is especially evident among mammalian retroviruses, such as the human immunodeficiency virus-1 (HIV), which integrate semi-randomly into the genome of their host's DNA and depend on host regulatory factors to initiate viral gene expression and complete replication. In the case of HIV, noisy viral gene expression results in transcriptional delays that may be a precursor for latent infections. Latent HIV currently prevents complete eradication of the virus in a patient, and reversing viral latency via activation of the latent HIV reservoir is a promising therapeutic strategy. However, an incomplete understanding of the complex mechanisms underlying chromatin- and transcription factor-mediated regulation of HIV hinders progress. To address this knowledge gap, the proposed project integrates experimental and computational approaches to study how the canonical transcription factor NF-kB and the local chromatin environment at the viral integration site together regulate activation of the latent HIV LTR promoter. The inability to target and purge latent (i.e., silent) HIV-infected cells is currently the biggest obstacle to a cure, and this proposal seeks to address this significant public health problem. By integrating single-cell experiments and computational modeling, this research will improve understanding of how protein-DNA interactions called chromatin regulate HIV-1 transcription, and will further progress towards eradication of the latent viral reservoir. This work may also advance knowledge of mechanisms of chromatin-mediated transcriptional regulation more broadly, with the potential to impact immunology, development, and cancer. In addition, two educational initiatives are proposed to broaden participation of under-represented minority engineering students in interdisciplinary research through summer research fellowships; and to contribute to transformative teaching approaches at the interface of the biological and physical sciences through design of a new discussion session for an interdisciplinary graduate course.