Regulated localization of transposable element RNA during influenza A virus infection

Influenza A virus (IAV) infection triggers derepression of host transposable elements (TEs), which have the potential to form double-stranded (ds)RNAs and could enhance innate antiviral immunity. However, the contribution of TEs to stimulating such pathways during infection is unknown, and it remains unclear whether derepressed TEs actually form dsRNAs. Here, we perform strand-specific total RNA-Seq on nucleus-associated and cytosolic fractions from cells infected with wild-type IAV or an engineered IAV lacking NS1, a dsRNA-binding interferon-antagonist protein. Both infections globally increase levels of host TE RNAs with bioinformatic and experimental evidence for double-strandedness. However, NS1-deficient IAV leads to significantly more of these putative dsRNA-forming TEs accumulating in the cytosolic fraction. Co-precipitations identify that wild-type NS1, but not a dsRNA-binding mutant, associates with these TEs, and microscopy shows co-localization of wild-type NS1 with dsRNA in perinuclear regions. Our data reveal the double-stranded nature of some IAV-triggered host TEs and suggest that NS1-mediated sequestration could limit their engagement of cytosolic innate immune sensors.