Characterization of the virus-host RNA-RNA interactome across different RNA viruses

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).