The Role of microRNAs During the Human Cellular Response to Negative-Strand RNA Virus Infection

The cellular response to virus infection is a complex orchestration of gene expression changes that results in the transcription and translation of hundreds of genes in order to generate a refractory state for virus replication. This process occurs through recognition of the invading virion by pre-existing cellular sensors that initiate signal transduction cascades to activate transcription factors such as NF-kappaB and interferon regulatory factors. The activated transcription factors translocate to the nucleus to initiate transcription of antiviral genes, including the type I interferon cluster. The combined function of these antiviral genes generates an antiviral state to inhibit virus replication. In addition to the well-characterized antiviral protein coding genes, a variety of non-coding RNAs are also generated, leading to the hypothesis that non-coding microRNAs are important regulators of gene expression during the cellular antiviral response. Specifically, this thesis work sought to determine if virus infection of mammalian cells altered microRNA expression in a manner similar to antiviral protein coding genes, and to determine if altered microRNA expression regulated the cellular response to virus infection. Work presented in this thesis describes three microRNA profiling experiments utilizing microarray and next generation sequencing technologies to identify differential microRNA expression during influenza A virus infection and Sendai virus infection. In addition to identifying changes in miRNA expression, corresponding mRNA targets were identified to determine the functional significance of virus induced microRNA expression. Specifically, influenza A virus infection was found to enhance expression of miR-132 and miR-1275 to target MAPK3, miR-146a and miR-1275 to target IRAK1, and miR-449b to regulate IFNbeta transcription through targeting of HDAC1. Sendai virus infection was found to increase miR-203 through the IFN-JAK-STAT pathway and regulate the interferon stimulated gene IFIT1/ISG56. This thesis provides experimental evidence for the function of 17 miRNAs during virus infection and a database of microRNA expression at steady state and during influenza A virus infection in A549 and BEAS-2B cells and Sendai virus infected A549 cells. This thesis describes an additional mechanism for gene expression control during the antiviral response and provides a foundation for future studies to investigate the regulation and function of virus induced microRNAs.