Viruses and microRNAs: a toolbox for systematic analysis.

RNA silencing is emerging as a novel layer of regulation of virus-host interaction. Since individual small RNAs can probably repress dozens if not hundreds of target mRNA molecules, and transcripts, on the other hand, may be recognized by multiple regulatory small RNAs, a dense and complex interaction network of microRNAs (miRNAs) and their targets arises. A comprehensive analysis of miRNA functions thus not only requires systematic approaches employing high-throughput technologies but also calls for the development of improved experimental technologies and a profound bioinformatic analysis. Integration of complementary approaches will enhance our understanding of the mutual regulation of virus and host. Focusing on herpesviruses, we here describe currently available technologies and summarize present results obtained by high-throughput approaches. These techniques can be broadly applied to other virus families and pathways employing other classes of small regulatory RNAs and therefore are powerful universal tools for research on virus-host interaction.