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Author ORCID Identifier


Open Access Dissertation

Document Type


Degree Name

Doctor of Philosophy (PhD)

Degree Program


Year Degree Awarded


Month Degree Awarded


First Advisor

Mandy Muller

Subject Categories

Molecular Biology | Virology


During viral infection, virus and host clash for control of the cell in a conflict that ultimately drives the evolution of both sides and has lasting consequences in the form of pathogenesis. At the heart of this struggle is a contest for control of cellular gene expression, a struggle epitomized by an evolutionary tug-of-war for supremacy over RNA fate. During lytic replication, Kaposi’s sarcoma-associated herpesvirus (KSHV) triggers a massive RNA decay event known as viral “Host Shutoff” which decimates greater than 70% of the host transcriptome, simultaneously suppressing the cellular anti-viral response and freeing host resources for viral replication. However, despite the magnitude of SOX targeting, we and others have shown that there remains a smaller subset of mRNAs that actively evade SOX cleavage via a protective RNA element within their 3’UTR known as a “SOX resistant element” or SRE. Among these active “escapees”, we identified C19ORF66 (recently renamed Shiftless), and the overarching goal of this dissertation is to understand the role of Shiftless during KSHV lytic replication following its escape from viral host shutoff. In the first chapter, using RNA-seq, we identified multiple cellular mRNA capable of escaping viral host shutoff, including C19ORF66. Further investigation revealed that Shiftless is a potent anti-KSHV factor that restricts KSHV lytic reactivation from latency and nearly every step of lytic replication therein. Then, in the second chapter, we defined two complementary mechanisms by which Shiftless inhibits KSHV lytic replication. First, we show that Shiftless broadly restricts viral gene expression by restricting the expression of critical viral early genes including KSHV ORF50 and ORF57. Surprisingly, we also found SHFL profoundly impacts global gene translation, an effect reflected by changes in global RNA dynamics. Collectively, these studies emphasize the complex struggle between KSHV and its host for control of cellular gene expression. In this pursuit, we have revealed novel insights into the crossroads between the host anti-viral response and the regulation of RNA fate during viral infection.