UC Berkeley

Gene expression is generally thought of as a linear pathway, beginning with transcription and processing of messenger RNA (mRNA), followed by export to the cytoplasm for translation and decay. Viruses have long been a key to discovering novel pathways and regulation in cells in their modulation of these pathways and gene expression is no different. Here we describe how infection with gammaherpesviruses is characterized by widespread mRNA degradation that leads to reduced RNA Polymerase II (Pol II) occupancy of host promoters by chromatin immuno- precipitation and sequencing (ChIP-seq) of infected cells. Pol II occupancy depends on RNA decay as infection with a decay-deficient virus does not broadly alter Pol II occupancy. In contrast to host promoters, viral promoters continue to recruit Pol II and transcribe their genes even at late stages in infection. This transcriptional escape of viral genes is all the more notable in light of a massive reduction in components of Pol II and general transcription factors (GTF) protein levels that we describe during infection. We further isolate the transcriptional capacity of viral genes to their presence on the replicating viral genome.

In Chapter 1 of this thesis we provide an overview of RNA decay, transcription and the literature that investigates mechanistic links between these two processes. This situates our work as distinct from the majority of literature that finds RNA decay and transcription are modulated to maintain constant RNA levels in a cell; instead, during pathogenic stress RNA decay feeds forward to further inhibit transcription. Chapter 2 characterizes the transcriptional repression phenotype during murine herpesvirus 68 infection and highlights how viral genes are able to robustly transcribe their genome irrespective of widespread decay. In Chapter 3 we further investigate the protein depletions of Pol II subunits and GTFs that exacerbate transcriptional repression of the host that we uncover in Chapter 2. Chapter 4 delves into the dual roles of SOX, the viral nuclease that instigates RNA decay, as both an RNase and a DNase.

In summary, this dissertation links disparate stages of the gene expression pathway and provides mechanistic details for how this occurs during MHV68 infection.