The Role of Target-Directed MicroRNA Degradation in Mammalian Development

Abstract

Pages vi-xvi are misnumbered as pages vii-xvii.MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression that play critical roles in development and disease. In animals, miRNAs canonically bind to partially complementary sites in messenger RNA 3′ untranslated regions, resulting in target repression. However, specialized targets, typically exhibiting extensive complementarity to the miRNA, can invert the regulatory logic and trigger degradation of the miRNA. Although this pathway, known as target-directed miRNA degradation (TDMD), has emerged as a potent mechanism of controlling miRNA levels, the biological role and scope of miRNA regulation by TDMD in mammals remains poorly understood. To address these questions, we generated mice with constitutive or conditional deletion of Zswim8, which encodes an essential TDMD factor. Loss of ZSWIM8 resulted in developmental defects in heart and lung, growth restriction, and perinatal lethality. Small RNA sequencing of embryonic tissues revealed widespread miRNA regulation by TDMD and greatly expanded the known catalog of miRNAs regulated by this pathway. These experiments also uncovered novel features of TDMD-regulated miRNAs, including their enrichment in co-transcribed clusters and examples in which TDMD underlies 'arm switching', a phenomenon wherein the dominant strand of a miRNA precursor changes in different tissues or conditions. Importantly, deletion of two TDMD-regulated miRNAs, miR-322 and miR-503, rescued growth of Zswim8 null embryos, directly implicating the TDMD pathway as a regulator of mammalian body size. Together, these data reveal the broad landscape of TDMD in mammals and demonstrate that regulation of miRNA abundance by this pathway is essential for normal mammalian development