Abstract
Background MicroRNAs are endogenous ∼23nt RNAs which regulate mRNA targets mainly through perfect pairing with their seed region (positions 2-7). Several instances of bulge UTR sequence can also be recognized by miRNA as their target. But such non-Watson-Crick base pairings are incompletely understood.
Results We found a group of miRNAs which had very few conservative targets while potentially having a subclass of bulge message RNA targets. Compared with the canonical target, these bulge targets had a lower negative correlation with the miRNA expression, and either were downregulated in the miRNA overexpression experiment or upregulated in the miRNA knock-down experiment.
Conclusions We proved that the bulge target exists widely in certain groups of miRNAs and such non-canonical targets can be recoginized by miRNA. Incorporating these bulge targets, combined with evolutionary conservation, will reduce the false-positive rate of microRNA computational target prediction.