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Implications of RNA virus-produced miRNAs

MicroRNAs (miRNAs) are small noncoding RNAs that fine-tune protein expression through post-transcriptional regulation. Extensive deep sequencing efforts have identified hundreds of miRNAs from diverse eukaryotic lineages, in addition to a number of DNA virus-produced miRNAs. The absence of RNA virus-encoded miRNAs has led to the assumption that miRNA processing is deleterious to genomic integrity and therefore restricted to DNA-based organisms. However, we recently generated both cytoplasmic and nuclear RNA virus capable of producing a functional miRNA without loss of viral fitness. By exploiting the splicing activity of influenza A virus, we engineered the endogenous miR-124-2 locus into an intron of a viral gene product. Processing of viral-derived miR-124 followed canonical processing events and was comparable to its endogenous counterpart, while virus replication was unaffected. Furthermore, grafting the same locus into a duplicated non-essential subgenomic area of Sindbis virus, we can observe non-canonical cytoplasmic-based processing that is independent of any nuclear events. Although it remains unknown as to why there is little natural evidence of RNA virus-encoded miRNAs, successful generation of these vectors provide important insights into the relationship between miRNAs and RNA viruses and introduces a new delivery vehicle for the rapidly expanding therapeutic use of RNA interference (RNAi).