Characterization of the virus-host RNA-RNA interactome across important human pathogenic RNA viruses.

Viruses make extensive use of host cell machinery, however, most systematic studies of virus-host interactions focused on proteins with less attention to nucleic acids. RNA plays important roles in storing, conveying, and regulating genetic information. Our understanding of functional interactions between viral and host RNA is dominated by interactions with micro-RNAs (miRNAs), such as the interaction between hepatitis C virus (HCV) and the liver specific miR-122, critical for viral replication. Methodological developments, however, allow for broader exploration of the RNA interaction landscape beyond that of miRNAs. We here set out to identify virus-host RNA interactions by optimizing RNA antisense purification to systematically map RNA-RNA interactions (RAP-RNA) for viral RNA. After using the HCV/miR-122 interaction for validation, we applied RAP-RNA to determine the RNA interactomes for three important human pathogens; HCV, yellow fever virus (YFV) and chikungunya virus (CHIKV). Comparing virus-host RNA interactomes, we observed patterns of mRNAs encoding factors involved in translation and the proteasome, mitochondrial (mt)RNAs, small nucleolar (sno)RNAs and small nuclear (sn)RNAs, thereby providing a more comprehensive understanding of cellular RNA interactions for RNA viruses. Experimental targeting of selected HCV interactors did not lead to significant impact on viral infection, suggesting that the majority of virus-host RNA interactions are not critical for the virus. In contrast, transcription data were consistent with a possible role in viral stabilization of host RNA interactors. These findings may guide future research directions, e.g., for the role of snoRNAs and snRNAs in viral RNA regulation, with potential to provide further insight to viral exploitation of host factors.