The miRNA target prediction field has developed rapidly over the last few years. New entrants like miRanda, PicTar, DIANA, and RNA22 have acted as oracles to the target seeking research community, but have often left scientists with more questions than answers, so experimental validation is still required.
Taking advantage of the fact that Arognaute-mediated mRNA cleavage takes place at a precise location relative to the small RNA guiding it, Penn State researchers have found a way to map the degradation products of mRNAs to the miRNAs that targeted them for degradation.
They start by mapping the 5’ ends of uncapped polyA-tailed RNA (the “degradome”) to transcribed RNA (the “transcriptome”), generating 26 nt “query sequences” — 13 nt on either side of the 5’ end of the degradome sequences. Query sequences are aligned with a database of small RNAs and voila! miRNA::mRNA target pairs. The method, dubbed CleaveLand, apparently works with any species and is free to download! Check out all the details at Bioinformatics, January 2009