DMS-seq and SHAPE-seq of flu virion, vRNP, and vRNA

To reveal the secondary structure of influenza A virus genome RNA in virion, DMS-seq and SHAPE-seq were performed. Flu virion, viral ribonucleoprotein complex (vRNP), and viral RNA (vRNA) were treated with DMS or NAI. By bioinformatics analysis, we identified pseudoknot structure in vRNA even in virion and vRNP. To analyze the role of the pseudoknot structure for virus propagation, we created a recombinant virus which has mutations in the pseudoknot region. To confirm the unwinding of the pseudoknot region in the recombinant virus, we also performed DMS-seq and SHAPE-seq analysis using the recombinant virus and determined the secondary structure of vRNA in the recombinant virus.