The Role of RNA Binding Proteins in Regulating Infection and Double-stranded RNA Sensing

Abstract

RNA binding proteins (RBPs) interact with double or single-stranded RNA and regulate numerous stages of RNA metabolism. My thesis investigates Fused-in-sarcoma (FUS) and TAR DNA-binding protein (TDP-43), two ubiquitous RBPs that are involved in similar RNA processes including RNA splicing, transcription, and transport. Mutations and mislocalization of these proteins are associated with several diseases with the most notable being amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Here, I demonstrate that FUS and TDP-43 negatively regulate viral infection and a double-stranded RNA (dsRNA) sensing immune response, respectively. FUS depletion in Kaposi’s sarcoma-associated herpesvirus (KSHV) latently infected primary effusion lymphoma (PEL) and an epithelial cell-based model significantly enhanced viral reactivation and the generation of infectious virions. FUS binds the viral episome at several lytic genes and interacts with RNA polymerase II to negatively impact Serine-2 phosphorylation of its C-terminal domain, decreasing nascent viral RNA synthesis to restrict KSHV reactivation. Furthermore, I determine that TDP-43 restricts a lethal retinoic acid-inducible gene I (RIG-I)-dependent immune response to endogenous dsRNA. Loss of TDP-43 resulted in immunostimulatory dsRNA accumulation and induced a robust type I and III interferon response in neuroblastoma and renal cell carcinoma cell lines. The immunostimulatory dsRNA was identified as RNA polymerase III transcripts, including 7SL and Alu retrotransposons, and I demonstrate that the RNA binding activity of TDP-43 is required to prevent immune stimulation. Collectively, I conclude that RBPs function beyond their canonical role in regulating RNA metabolism and are involved in restricting viral infection and activation of an innate immune response.