Seedless 3' pairing enables miR-17 family miRNAs to seize let-7 target sites

MicroRNAs (miRNAs) are short noncoding RNAs that post-transcriptionally regulate gene expression. Their canonical function depends on a "seed" sequence at the miRNA 5' end that pairs with conserved sites in the 3' untranslated regions of target messenger RNAs to suppress gene expression. Although seed-mediated targeting is well characterized, the role of the miRNA 3' end remains poorly understood and is challenging to study. Here, we identify a noncanonical mechanism by which miR-106a, a member of the miR-17 family, competes with let-7a for binding to let-7 target sites despite their distinct seed sequences. This binding bypasses miR-106a seed pairing and instead relies on extensive complementarity at its 3' end, which shares sequence identity with the let-7a seed. Such binding of miR-106a does not itself silence these targets but shields them from let-7-mediated suppression, resulting in de-repression of let-7 targets. By contrast, miR-106b, which differs from miR-106a and the other miR-17 family members at its 3' end, lacks this de-repressive activity. These findings show that variation in miRNA 3' sequences can generate divergent functions within a miRNA family and underscore the need to account for 3'-end contributions when interpreting miRNA-target networks and considering the development of miRNA-based therapeutics.