A Rapid Genome-Wide MicroRNA Screen Identifies miR-14 as a Modulator of Hedgehog Signaling

Abstract

MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression by binding to sequences within the 3′UTR of mRNAs. Because miRNAs bind to short sequences with partial complementarity, target identification is challenging. To complement the existing target prediction algorithms, we devised a systematic “reverse approach” screening platform which allows the empirical prediction of miRNA-target interactions. Using Drosophila cells, we screened the 3′UTRs of the Hedgehog pathway genes against a genome-wide miRNA library and identified both predicted and many non-predicted miRNA-target interactions. We demonstrate that miR-14 is essential for maintaining the proper level of Hedgehog signaling activity by regulating its physiological target, hedgehog. Furthermore, elevated levels of miR-14 suppress Hedgehog signaling activity by co-targeting its apparent non-physiological targets, patched and smoothened. Altogether, our systematic screening platform is a powerful approach to identifying both physiological and apparent non-physiological targets of miRNAs, which are relevant in both normal and diseased tissues.