Background: The processing of a microRNA results in an intermediate duplex of two potential mature products that derive from the two arms (5' and 3') of the precursor hairpin. It is often suggested that one of the sequences is degraded and the other is incorporated into the RNA-induced silencing complex. However, both precursor arms may give rise to functional levels of mature microRNA and the dominant product may change from species to species, from tissue to tissue, or between developmental stages. Therefore, both arms of the precursor have the potential to produce functional mature microRNAs.
Results: We have investigated the relationship between predicted mRNA targets of mature sequences derived from the 5' and 3' arms of the same pre-microRNAs. Using six state-of-the-art target prediction algorithms, we find that 5'/3' microRNA pairs target different sites in 3' untranslated regions of mRNAs. We also find that these pairs do not generally target overlapping sets of genes, or functionally related genes.
Conclusions: We show that alternative mature products produced from the same precursor microRNAs have different targeting properties and therefore different biological functions. These data strongly suggest that developmental or evolutionary changes in arm choice will have significant functional consequences.