Functional Characterization of Herpesvirus-Activated Noncoding Retrotransposon RNAs

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The advancement of sequencing technologies has resulted in the discovery of numerous types of non-coding RNAs (ncRNA) that play important role in both tissue homeostasis and disease pathology. Additionally, several studies have identified host and pathogen-encoded ncRNA whose expression patterns are associated with viral pathogenesis, host defense and activation from latency. One specific class of ncRNA that has been shown to modulate viral replication and inflammatory responses in mouse and human cells, respectively, are the short interspersed nuclear elements (SINEs), termed B1-B4 in mice and Alu in humans. These repetitive elements are epigenetically silenced in healthy somatic cells but can be induced and transcribed by RNA polymerase III (Pol3) upon exposure to various cellular stresses , including infection with a variety of DNA viruses. Recent studies suggest that SINE ncRNA expression can influence viral and host gene expression and NFκB signaling during infection with the murine gammaherpesvirus MHV68, a close relative of Kaposi's sarcoma-associated herpesvirus. Additional studies have linked SINE expression to increased transcription of interferon-stimulated genes (ISG) . Given that SINE ncRNAs accumulate in the nucleus and the cytoplasm, how their gene regulatory and signaling activities are coordinated in each compartment is a fundamental question in the field. We will address this by first constructing a SINE locus activation map in cells infected with alpha or gammaherpesviruses, which will be used to identify direct SINE ncRNA-driven gene expression signatures in the nucleus and their consequences for viral replication. We will then identify which components of the innate immune pathway in the cytoplasm are involved in sensing natively transcribed SINE ncRNAs. Collectively, these results will provide new mechanistic insights into how these “self” ncRNAs function to influence the gene expression landscape during DNA virus infection.