Finding microRNA targets in plants: current status and perspectives

MicroRNAs (miRNAs), a class of ~20-24 nt long non-coding RNAs, have critical roles in diverse biological processes including development, proliferation, stress response, etc. With the development and availability of experimental technologies and computational approaches, the field of miRNA biology has advanced tremendously over the last decade. By sequence complementarity, miRNAs have been estimated to regulate certain mRNA transcripts. Although it was once thought to be simple and straightforward to find plant miRNA targets, this viewpoint is being challenged by genetic and biochemical studies. In this review, we summarize recent progress in plant miRNA target recognition mechanisms, principles of target prediction, and introduce current experimental and computational tools for plant miRNA target prediction. At the end, we also present our thinking on the outlook for future directions in the development of plant miRNA target finding methods.