<i>Plagl1</i> and <i>Lrrc58</i> control mammalian body size by triggering target-directed microRNA degradation of miR-322 and miR-503

Precise control of microRNA (miRNA) expression is critical during development. An important mechanism of miRNA regulation is target-directed microRNA degradation (TDMD), a pathway in which the binding of miRNAs to specialized trigger RNAs induces ubiquitylation and decay of associated argonaute (AGO) proteins by the ZSWIM8 ubiquitin ligase. Concomitant release of miRNAs results in their rapid turnover. ZSWIM8-deficient mice exhibit reduced body size, cardiopulmonary and neurodevelopmental defects, and perinatal lethality. Despite widespread dysregulation of miRNAs in these animals, the vast majority of presumptive trigger RNAs that induce decay of ZSWIM8-regulated miRNAs remain undefined. Here, using AGO cross-linking and sequencing of hybrids (AGO-CLASH), a high-throughput method for identifying miRNA binding sites, we report the identification of <i>Plagl1</i> as a TDMD trigger for miR-322-5p and <i>Lrrc58</i> and <i>Malat1</i> as TDMD triggers for miR-503-5p in mouse embryonic fibroblasts (MEFs). In mice, deletion of the miR-322-5p and miR-503-5p trigger sites in the <i>Plagl1</i> and <i>Lrrc58</i> 3' UTRs, respectively, abrogated TDMD of these miRNAs and resulted in miR-322/503-dependent embryonic growth restriction, recapitulating a key feature of the <i>Zswim8</i> ^-<i>/</i>- phenotype. Thus, <i>Plagl1</i> and <i>Lrrc58</i> act as triggers for degradation of miR-322-5p and miR-503-5p, revealing a noncoding function for these mRNAs as regulators of mammalian body size.