Pervasive yet nonuniform contributions of Dcp2 and Cnot7 to maternal mRNA clearance in zebrafish

Abstract

mRNA degradation is a fundamental biological process that erases transcribed genetic information from cells. During maternal-to-zygotic transition of animal development, thousands of maternal mRNAs are degraded by multiple mechanisms including microRNAs and codonmediated decay. Enzymatic requirements for maternal mRNA clearance, however, are not fully understood. Here, we analyzed a contribution of the decapping enzyme Dcp2 to maternal mRNA clearance in zebrafish by over-expressing catalytically inactive Dcp2 and performing RNA-seq analysis. As expected, Dcp2 had a widespread role in maternal mRNA clearance. Interestingly, each mRNA showed differential dependency on Dcp2-mediated decapping and Cnot7-mediated deadenylation for degradation. Correlation analysis identified several mRNA features that were associated with the observed differential dependency. Our results show pervasive yet nonuniform contributions of the decapping enzyme Dcp2 and the deadenylase Cnot7 to maternal mRNA clearance.

Deadenylation by the CCR4‐NOT complex contributes to the turnover of hairy‐related mRNAs in the zebrafish segmentation clock

“…Although the degradation of mRNA generally proceeds from both 5 0 and 3 0 ends, our study demonstrates that the shortening of poly(A) tails by the CCR4-NOT deadenylase complex contributes substantially to the post-transcriptional regulation of hairy-related mRNAs compared with the decapping by Dcp2 in zebrafish segmentation clock. This observation is consistent with the differential contributions of the two decay machineries to maternal mRNA decay [23]. By using transgenic embryos, mRNAs derived from reporter genes fused to the 3 0 UTRs of her1, her7, and hes6 essentially recapitulated the turnover of endogenous transcripts predicted by the PAT assay (Fig.…”

“…The removal of 5 0 cap structure of mRNA also plays a critical role in the degradation of eukaryotic mRNA from 5 0 end. To examine whether the functional interferences of decapping may affect the somite segmentation as was observed in cnot7-DN mRNAinjected embryos, we overexpressed mRNA encoding a dominant negative form of the decapping enzyme, Dcp2 (Dcp2-DN), which has been shown to increase the stability of maternal RNAs in zebrafish [23]. Although the injection of dcp2-DN mRNA perturbed the embryogenesis at 24 hpf as described previously [23], we did not observe any defective segmentation of the somites in dcp2-DN mRNA-injected embryos ( Fig.…”

“…In general, mRNA decay has been thought to be initiated by shortening of the poly(A) tail from the 3′ end (deadenylation), the removal of 5′‐cap structure at the 5′ end (decapping), and the exonucleolytic digestion of mRNA body . Recent genome‐wide analysis revealed that maternally deposited mRNAs are differently removed by deadenylation and decappaing in zebrafish embryos .…”

Comparison of the somatic TADs and lampbrush chromomere-loop complexes in transcriptionally active prophase I oocytes

“…CNOT7 mRNA is a maternal RNA which translates to a key component of deadenylation machinery involved in maternal mRNA clearance (Ma et al . 2015; Mishima and Tomari 2017). Ortholog of FGF20 in Nile tilapia specifically expresses in female gonads and its mRNA accumulates in the cytoplasm of growing oocytes (Sun et al .…”

Zebrafish Ski7 tunes RNA levels during the oocyte-to-embryo transition

“…It has previously been shown that inherent RNA properties, such as transcript and polyA-tail length, codon usage and RNA structure influence RNA stability (Mishima & Tomari, 2016;Bazzini et al, 2016;Subtelny et al, 2014;Mishima & Tomari, 2017). To investigate whether Ski7 targets share specific transcript features that make them prone for Ski7-dependent regulation, we assessed whether shared period DEGs differ in their intrinsic RNA properties compared to unchanged genes.…”