Target-directed microRNA degradation regulates developmental microRNA expression and embryonic growth in mammals

Abstract

MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression that play critical roles in development and disease. Target-directed miRNA degradation (TDMD), a pathway in which miRNAs that bind to specialized targets with extensive complementarity are rapidly decayed, has emerged as a potent mechanism of controlling miRNA levels. Nevertheless, 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 ofZswim8, which encodes an essential TDMD factor. Loss ofZswim8resulted in developmental defects in the heart and lungs, 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 cotranscribed 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 miRNAs, miR-322 and miR-503, rescued growth ofZswim8-null embryos, directly implicating the TDMD pathway as a regulator of mammalian body size. These data illuminate the broad landscape and developmental role of TDMD in mammals.

Evidence of target-mediated miRNA degradation inDrosophilaovarian cell culture

“…The suppression of TDMD stabilizes multiple miRNAs in variable tissues and cell cultures (Shi et al 2023;Jones et al 2023;Han et al 2020;Shi et al 2020). Similarly, we revealed the repertoire of miRNAs repressed with the involvement of Dora in OSCs, including miR-7-5p (Figure 2B,C).…”

“…This likely indicates that some TDMD targets exist for both miR-10 strands. It was shown that the destabilization of one of the miRNA strands by TDMD may facilitate its antisense counterpart to be dominantly loaded and preserved in the complex with Ago and thus may be the mechanism of regulating 'arm switching' (Shi et al 2023;Jones et al 2023). The control of stability of mature miRNAs and, related to this, the determination of active strands by degradation of their counterparts allow TDMD to affect the content of cellular miRNA pool.…”

“…In Drosophila embryos, suppression of miRNA-310/313 by TDMD is required for embryonic cuticle development (Kingston et al 2022). Recent screening of murine miRNAs destabilized by TDMD in different tissues revealed that it can be involved in the regulation of body size and embryonic development (Shi et al 2023;Jones et al 2023). The conservative nature of TDMD implies that it might regulate some ancient and general molecular pathways, but it has not been reported yet.…”

“…Although TDMD is found in various species (Jones et al 2023;Shi et al 2023;Kleaveland et al 2018;Bitetti et al 2018;Shi et al 2020;Kingston and Bartel 2021;Kingston et al 2022), the molecular details of TDMD are described only for mammals. To highlight the molecular mechanism of TDMD in Drosophila, here we investigated the Dora protein, the Drosophila ortholog of mammalian ZSWIM8, in OSC cell culture derived from ovarian somatic tissues.…”

Target‐directed microRNA degradation: Mechanisms, significance, and functional implications

“…Similar studies were conducted back-to-back, again by the Bartel and Mendell groups, detailing ZSWIM8 lossof-function during mouse development (Jones et al, 2023;Shi et al, 2023). Each group independently reached the same conclusion, that ZSWIM8 loss-of-function mice displayed low birth weight, cyanosis, and significantly underdeveloped cardiopulmonary systems, resulting in perinatal lethality (Jones et al, 2023;Shi et al, 2023). Given the tissue-specific alterations observed, and the potential for tissue-specific expression of miRNAs and triggers alike, detailed examination of altered miRNA abundance was conducted in a variety of mouse tissues.…”