Prediction of targets for microRNAs

MicroRNAs (miRNAs) are small 20-22 nt long RNAs which function as post-transcriptional regulators altering the expression of genes either by blocking translation or by destabilizing mRNAs (for recent reviews see, e.g., Zhang et al. (J Cell Physiol, 210:279-289) and Engels and Hutvagner (Oncogene, 25:6163-6169)). A central problem in miRNA biology is to identify the mRNAs regulated by miRNAs - the miRNA targets. A large number (>10) of bioinformatics methods have been developed to address this question, but unfortunately the scarcity of experimentally validated targets makes it hard to objectively judge the performance of the methods (for an attempt see Sethupathy et al. (Nat Methods, 3:881-886). Nevertheless, here I will give some guidelines on how to use the existing tools to find miRNA targets.