ZSWIM8 destabilizes many murine microRNAs and is required for proper embryonic growth and development

Abstract

MicroRNAs (miRNAs) pair to sites in mRNAs to direct the degradation of these RNA transcripts. Conversely, certain RNA transcripts can direct the degradation of particular miRNAs. This target-directed miRNA degradation (TDMD) requires the ZSWIM8 E3 ubiquitin ligase. Here, we report the function of ZSWIM8 in the mouse embryo.Zswim8–/– embryos were smaller than their littermates and died near the time of birth. This highly penetrant perinatal lethality was apparently caused by a lung sacculation defect attributed to failed maturation of alveolar epithelial cells. Some mutant individuals also had heart ventricular septal defects. These developmental abnormalities were accompanied by aberrant accumulation of >50 miRNAs observed across 12 tissues, which often led to enhanced repression of their mRNA targets. These ZSWIM8-sensitive miRNAs were preferentially produced from genomic miRNA clusters, and in some cases, ZSWIM8 caused a switch in the dominant strand or isoform that accumulated from a miRNA hairpin—observations suggesting that TDMD provides a mechanism to uncouple co-produced miRNAs from each other. Overall, our findings indicate that the regulatory influence of ZSWIM8, and presumably TDMD, in mammalian biology is widespread and consequential, and posit the existence of many yet-unidentified transcripts that trigger miRNA degradation.

Turnover of RNA-binding Proteins and MicroRNAs by intrinsically disordered region-directed ZSWIM8 ubiquitin ligase during brain development

“…From a different route focusing on IDR protein degradation in neonatal brains, we arrived at the same conclusion that ZSWIM8 monitors miRBPs and finely controls the expression and function of their associated miRNAs (e.g., MiR7). All of the upregulated miRNAs we found in the Zswim8 f/f ;N-Cre brain were also shown to be increased in whole-body ZSWIM8 knockouts (31,32). These results, together with other recent findings from worm, fly and human cell culture systems (30,(63)(64)(65)(66) further corroborate the physiological relevance of ZSWIM8 in regulating miRNAs and miRBPs.…”

“…We also cannot rule out the possibility that other entities of the AGO-miRNA complex (e.g., other RBPs) in the cell may also contribute to ZSWIM8 binding. AGO2 and miRNAs form the RISC complex to downregulate target mRNA expression, while ZSWIM8 degrades AGO2 and consequentially deprotects the bound miRNAs, leading to TDMD (31)(32)(33)(34). Loss of ZSWIM8 disrupts this self-limiting system, thus leads to aberrant expression of miRNAs such as MiR7.…”

“…Given that whole-body and brain-specific knockout of ZSWIM8 lead to developmental lethality in mice (29,31,32), we predict that ZSWIM8 may have a much broader substrate specificity in mammals.…”

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).…”

“…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.…”