Viral microRNA genomics and target validation

•Most viral microRNAs show little or no sequence similarity to other viral microRNAs or cellular microRNAs.•There is no single quintessential target prediction method, integration of various methods is key to filter and prioritize potential miRNA targets for further analysis.•Secondary target validation assays are difficult to perform in a high-throughput fashion.

A subset of viruses express their own microRNAs (miRNAs) and one way to understand the functions of these microRNAs is to identify the targets of these miRNAs. Sequence analysis and mRNA expression profiling were some of the first techniques to identify targets of viral miRNAs. More recently, proteomics and sequencing of RNA by crosslinking and immunoprecipitation (CLIP) methods have been insightful and discovered many miRNA targets that may be missed using other methods. We are now at a point where numerous validated miRNA targets have been described and integration of these genomic datasets will provide a richer understanding of miRNA targeting and viral infection, persistence, and pathogenesis.