Identification of virally encoded microRNAs

RNA silencing is a widespread phenomenon that regulates gene expression at different levels. Small RNA molecules are at the core of all RNA silencing pathways and can be grouped in distinct families depending on their chemical properties and their mode of action. Among these small RNAs, microRNAs (miRNAs) represent one of the most extensively studied classes in animals. These tiny endogenous RNAs regulate gene expression posttranscriptionally by cleaving the targeted transcript or by interfering with its translation. miRNAs are found in plants and animals and have been identified in mammalian viruses. This indicates that mammalian viruses exploit the host RNA silencing machinery to produce miRNAs that have the potential to act both on the infected host genome and on the viral genome. The techniques used for identification of viral miRNAs mostly parallel what is used for identifying cellular miRNAs. The use of prediction algorithms followed by validation has been successful. A more direct and nonbiased way of identifying viral miRNAs consists of cloning and sequencing small RNA libraries from virally infected cells or tissues.