Research in the D’Orso lab focuses on understanding how gene regulatory programs operate using a wide arrays of experimental and computation approaches. Specifically, we focus on:
- Molecular mechanisms governing HIV-1 gene expression, latency and persistence.
- Molecular mechanisms of signal-induced transcription regulating cell fate.
- Molecular mechanisms of epigenetic silencing.
Ongoing projects for incoming trainees (students and postdocs):
Cell fate decisions are critical for key biological processes including development and differentiation. These cellular decisions are orchestrated through the precise spatio-temporal activation and deactivation of cell signaling-transcriptional programs. The goal of this project is to define how cell signaling and transcriptional molecules operate to facilitate this process. There is a need for advanced genetic tools to assess molecular functions and cellular phenotypes. Our lab is using acute factor depletion approaches combined with careful downstream mechanistic interrogation to explain phenotypes at the cellular and organismal levels in the context of human health and disease.
References: This is part of an ongoing investigation.
HIV-1 integrates semi-randomly in the human genome, thus generating proviral classes of active and silent genomes. We are interested in defining the mechanisms underlying transcriptional and epigenetic regulation of the HIV-1 proviral classes in immune cells. We want to understand how the euchromatin and heterochromatic genomic environments facilitate the recruitment of certain classes of epigenetic regulators for either HIV-1 proviral transcriptional activation or silencing. Unleashing the molecular rules controlling proviral fate will lead us not only to a better understanding of basic HIV-1 biology, but also inform about novel factors and signaling pathways that could be exploited therapeutically.
References: This is part of an ongoing investigation. Ruess et al., BBI 2022, PMID: 35250265
Genes are activated through recruitment of RNA polymerase II to their promoters or through the release of a promoter-proximal paused RNA polymerase II. The evolutionary selective pressures and functional advantages behind these disparate mechanisms remain poorly understood. Using genomics approaches we have recently discovered that the HIV-1 provirus is rapidly activated in response to ligands from the immune microenvironment through a mechanism of RNA polymerase II recruitment. We have identified a subset of immune genes which behave in a similar manner (here referred to as “HIV-1 like”). We have also devised high-resolution approaches combined with careful data analysis to measure and quantitate the behavior of RNA polymerase II at these genes. We now want to decipher the underlying mechanisms including the roles of chromatin accessibility, epigenetic marks, transcription factor binding and enhancer functions.
References: Shukla et al., manuscript in preparation.
To better examine the distribution and magnitude of transcription machinery and histone modifications throughout the HIV-1 provirus during latency and reactivation, we devised a high resolution and quantitative ChIP-seq approach in CD4+ T cell models of latency prior to and after cell stimulation. Using this approach, we made the unexpected observation that there is deposition of an epigenetic mark typically associated with gene repression in the 3’-end and flanking human genomic region of the provirus (referred to as “provirus 3’-end”) only upon immune cell stimulation. We are trying to: 1) elucidate the host enzymes implicated in epigenetic deposition, and 2) testing whether this epigenetic mark is important for viral gene expression and/or for host DNA damage sensing and repair.
References: This is part of an ongoing investigation.
