Mechanism of translational regulation by miR-2 from sites in the 5′ untranslated region or the open reading frame

MicroRNAs (miRs) commonly regulate translation from target mRNA 3′ untranslated regions (UTRs). While effective miR-binding sites have also been identified in 5′ untranslated regions (UTRs) or open reading frames (ORFs), the mechanism(s) of miR-mediated regulation from these sites has not been defined. Here, we systematically investigate how the position of miR-binding sites influences translational regulation and characterize their mechanistic basis. We show that specific translational regulation is elicited in vitro and in vivo not only from the 3′UTR, but equally effectively from six Drosophila miR-2-binding sites in the 5′UTR or the ORF. In all cases, miR-2 triggers mRNA deadenylation and inhibits translation initiation in a cap-dependent fashion. In contrast, single or dual miR-2-binding sites in the 5′UTR or the ORF yield rather inefficient or no regulation. This work represents the first demonstration that 5′UTR and ORF miR-binding sites can function mechanistically similarly to the intensively investigated 3′UTR sites. Using single or dual binding sites, it also reveals a biological rationale for the high prevalence of miR regulatory sites in the 3′UTR.