Jovanovic, M. et al. Genome Res. advance online publication (19 April 2012).

It is known that microRNAs, short, non-coding RNA transcripts, play an important role in regulating gene expression. What is still being debated is their mechanism of action and how to best identify their direct targets. In an effort to identify and validate microRNA targets, Jovanovic et al. combined RNA-binding protein immunoprecipitation (RIP), in which they affinity-purified mRNAs associated with the microRNA silencing complex, with selective reaction monitoring–mass spectrometry (SRM-MS) in Caenorhabditis elegans that expressed either wild-type or mutant microRNA of interest. SRM-MS allowed them to quantify the targets at the protein level. By comparing mRNA and protein abundance between wild-type and mutant worms, the researchers could distinguish between direct and indirect targets and differentiate between targets regulated at the level of translation or mRNA degradation.