The role of host cell non-protein coding RNAs during influenza A virus infection

Influenza A virus (IAV) is the cause of seasonal epidemics and pandemic outbreaks and thus represents a global threat to public health. Since virus propagation strongly depends on the host cell machinery, it is crucial to understand virus-host interactions in detail to develop new antiviral strategies. A growing body of evidence clearly demonstrates functions during cell homeostasis and disease for the vast amount of cellular non-protein coding ribonucleic acid (RNA), including the recently identified diverse class of long non-coding RNAs (lncRNAs). However, their impact on infection processes remains elusive. In this study, the differential expression of several classes of human lncRNAs during influenza A/WSN/33 infection was investigated using lncRNAmicroarrays. Additional infection experiments revealed that a certain transcript, called lincRNAACTR3, is not only strongly up-regulated by A/WSN/33, but is distinctly induced by different IAV strains and vesicular stomatitis virus, in contrast to influenza B virus. Using an IAV mutant lacking the NS1 gene, a decreased lincRNA-ACTR3 expression was observed, implicating a possible role for this viral factor in lincRNA-ACTR3 induction. Most importantly, this study revealed that siRNA-mediated depletion of lincRNA-ACTR3 leads to a significant decrease in the amount of IAV progeny, thereby assigning a crucial role for lincRNA-ACTR3 during productive IAV replication. Together with its observed nuclear distribution, messenger RNA expression analysis in lincRNA-ACTR3 knockdown conditions suggested a gene-regulatory role for lincRNA-ACTR3 during IAV infection. Thus, I demonstrated for the first time that a lncRNA is functionally relevant during pathogenesis of IAV infection, providing insight into its features, regulation and function during the infection process. In addition, the relevance of microRNA (miRNA)-mediated gene regulation during IAV infection was addressed on a high-throughput scale. Investigating the role of human miRNA expression by applying miRNA mimic and inhibitor libraries showed that several miRNAs impaired viral replication considerably. Computationally predicted targets of identified miRNA families significantly overlapped with known host dependency genes revealed by previous RNA-interference (RNAi) screens, indicating an inhibition of IAV replication based on miRNA function. To validate the importance of miRNA-mediated gene regulation implicated in IAV pathogenesis, miRNA expression during infection was investigated by deep sequencing. Evaluation and correlation of all datasets suggested that members of the miR-449 family are induced by IAV, and are possibly implicated in control of cell cycle and cell death pathways. Taken together, this study highlights the impact of the non-coding transcriptome on the outcome of infectious diseases.