Needed: large scale experimental validation of predicted microRNA targets.
The importance of microRNAs—short noncoding RNAs that inhibit mRNA expression—is as big as their size is small. They are thought to regulate at least 30% of all human genes and have a crucial role in normal and disease development. The relatively easy part in studying microRNAs is to find new ones and to establish their profiles in a cell or tissue using techniques such as microarrays, reverse-transcriptase PCR and sequencing. The challenging part is to match a microRNA to its mRNA target, as the interaction is not only based on the complementarity of the sequence but on many other factors.
MicroRNA finds its targets.
Given the much larger number of mRNAs compared to microRNAs, the most efficient way to find a match is by computational means. Several researchers have developed algorithms relying not only on sequence but on other factors such as evolutionary conservation, sequences surrounding the binding site and, most recently, mRNA structure and accessibility as well as expression levels of both mRNA and micro RNA. The real crux of the matter, though, is the experimental validation of these predicted targets. Currently the wet-lab validation of an in silico target is still cumbersome. What is needed is a large-scale assay that allows rapid and definitive identification of an mRNA targeted by a microRNA. Various efforts toward that goal are under way, some making use of the microRNA-mRNA pair in vivo by using the microRNA as a primer and extending the sequence further (J. Mol. Biol.358, 983–986; 2006), others trying to isolate and characterize the microRNA-mRNA-ribonucleoprotein complex (RNA13, 1198–1204; 2007). Although these assays allow validation of specific targets, they are not at a scale yet that will allow rapid and comprehensive validation of all microRNA targets—and to go from large scale in silico predictions to large-scale in vitro validation will be a welcome breakthrough in the field of microRNA biology.
