Final Report Summary - NCRNAVIR (Roles of non-coding RNAs in viral infections in mammals)
It is now a long time since RNA was solely recognized as the carrier of genetic information. The importance of non-coding RNAs (ncRNAs), small and large, is growing exponentially in modern biology. Among these ncRNAs, 19 to 30 nucleotides RNA molecules have recently emerged as critical regulators of gene expression and as part of a defense system against invading nucleic acids. These small RNAs are invariably found at the core of RNA silencing pathways, and serve as guide to target effector complexes to the regulated transcripts. Different classes of small RNAs have been defined based on their origin and properties, and among them micro (mi) RNAs, and small interfering (si) RNAs are the most studied across organisms. Viruses interact extensively with the RNA silencing machinery. Thus in plant and insect organisms, they are directly targeted and degraded in siRNAs by the ribonuclease Dicer or by Dicer-like protein. The situation is slightly more complicated in mammals, where a more sophisticated innate immune response has replaced this antiviral mechanism. Nevertheless, there are interactions between viruses and mammalian RNA silencing pathways, which mainly involve miRNAs. On one hand, miRNAs of cellular origin can regulate (both positively and negatively) viral RNAs, and on the other hand, some viruses have hijacked the miRNA biogenesis apparatus to express their own miRNAs. This project aimed at characterizing the full scope of interactions between mammalian viruses and the RNA silencing machinery, and to reconcile the apparent contradictions between a negative impact mediated by cellular miRNAs, and a positive usurpation by the expression of viral miRNAs. We used RNA and DNA viruses to identify cellular miRNAs that have antiviral or proviral properties, and correlate these finding with the changes in cellular miRNA profiles induced by viral. This allowed to identify one case where a virus, namely the mouse cytomegalovirus, can deploy a counter method to trigger degradation of an antiviral cellular miRNAs. We deciphered the underlying mechanism at the molecular level. During this project, we also studied miRNAs of viral origin, and we could elucidate the role of some of them, such as the ones encoded by the Kaposi’s sarcoma herpesvirus. But, we also started to investigate how viral miRNAs accumulation is regulated, and in particular how the RNA secondary structure affect its processing. Finally, we also studied how viruses affect the RNA silencing machinery, and respond to it. We found that there is a crosstalk between this ancient defense system and the more recently evolved interferon pathway. Altogether, the results of this research project did advance our knowledge of how and why viruses interact with RNA silencing.