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

Abstract

Summary 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.

Overview of MicroRNA Biology

“…Another example of a microRNA affecting multiple proteins to fine-tune pathway function is observed in miR-14 signaling. Basal levels of miR-14 in Drosophila cells allow targeting of Hedgehog, a signaling protein involved in development, differentiation and proliferation 39 . However, increased miR-14 allows targeting of Patched and Smoothened, both members of the Hedgehog signaling pathway for a net decrease in Hedgehog signaling.…”

Regulation of physiological processes by microRNAs in insects

“…Several studies have shown that dme-miR-8 regulates multiple peptide hormones in the fat body, contributing to cell growth [9–11]. dme-miR-14 was shown to target Hedgehog (Hg), a core component of the highly conserved Hg signaling pathway important for various developmental processes [12]. This miRNA also functions in the degradation of the larval salivary gland during pupal development by regulating autophagy in salivary gland cells through the modulation of inositol 1,4,5-trisphosphate kinase 2 ( ip3k2 ) [13]*.…”

TGF-β1-induced miR-202 mediates drug resistance by inhibiting apoptosis in human osteosarcoma

“…MicroRNAs (miRNAs) are a group of 22-25 nucleotide non-coding RNAs that emerged as critical components of gene regulatory networks regulating various biological processes, including cell growth, differentiation, apoptosis and metastasis (Kim et al 2014). They can cause mRNA degradation or inhibit protein translation through binding to complementary sequences in the 3′-untranslated region A growing evidence during the last several years suggests that microRNAs play a key role in cancer drug resistance by inhibiting apoptosis (Chan et al 2012).…”