Influenza non-structural protein 1 (NS1) localization plays a key role in the anatagonism of host antiviral processes.

The influenza virus is opportunistic by nature and is capable of subverting cellular signalling pathways for the benefit of viral replication. The function of non-structural protein 1 (NS1) as a core component for the influenza virus to interfere with host antiviral activity has been well cited in literature. However, the mechanism as to how NS1 is capble of subverting the host's innate immune system is unknown. NS1 has a unique capability to migrate between both the cytoplasm and nucleus of infected cells. To assess if NS1 interference operates a stratagy pertaining to a mechanism involved with nuclear-located signalling processes we designed two mutant virsus; WSNdelNS1 which encodes a deletion to prevent complete NS1 expression and WSN3M which encodes a NS1-variant that is defective in NS1 nuclear-translocation, thus preventing NS1 from entering the nuclus of infected cells. Overall design: We infected A549 cells with wildtype (native) influenza A/WSN/1933 (H1N1) or with a mutant virus deficient in encoding fully-functional NS1 (WSNdelNS1 or WSN3M). These infection experiements were used to perform RNA-Seq analysis to assess for significant changes in the transcriptome of infected cells in response wildtype/mutant influenza infection. We complemented this analysis with PolII/PolII-s2p/PolII-s5p ChIP-Seq in order to observe if changes in PolII densities and their variants reflect the transcriptomic profiles generated from our RNA-Seq analysis. Intergration of both RNA-Seq and ChIP-Seq datasets presented a unique profile of gene expression and PolII transcription initiation and elongation dynamics during the early stages of influenza infection.