EDC-3 and EDC-4 Regulate Embryonic mRNA Clearance and Biomolecular Condensate Specialization

Animal development is dictated by the selective and timely decay of mRNAs in developmental transitions, but the impact of mRNA decapping scaffold proteins in development is unknown. This study unveils the roles and interactions of the DCAP-2 decapping scaffolds EDC-3 and EDC-4 in the embryonic development of C. elegans. EDC-3 facilitates the timely removal of specific embryonic mRNAs, including cgh-1, car-1, and ifet-1 by reducing their expression, and preventing excessive accumulation of DCAP-2 condensates in somatic cells. We further uncover a novel role for EDC-3 in defining the boundaries between P-bodies, germ granules, and stress granules. Lastly, we show that EDC-4 counteracts EDC-3 and engenders the assembly of DCAP-2 with the GID (CTLH) complex, a ubiquitin ligase involved in maternal-to-zygotic transition (MZT). Our findings support a model wherein multiple RNA decay mechanisms temporally partake in the clearance of maternal and zygotic mRNAs throughout embryonic development. To investigate the transcriptome-wide effect of EDC-3 and EDC-4, we performed RNA-seq on 4 biological replicates of RNA extracted from mixed-stage C. elegans embryos of WT (N2 strain), edc-3(ok1427) (RB1311 strain), edc-4(qe49) (FD135 strain), and edc-3(ok1427); edc-4(qe49) (FD135 strain). Differential gene expression and GSEA analyses were done to determine the differentially expressed genes and biological pathways in the mutants compared to WT.

动物发育进程由发育转变过程中mRNA的选择性及时降解所调控，但mRNA脱帽支架蛋白在发育过程中的功能影响尚未明确。本研究揭示了DCAP-2脱帽支架蛋白EDC-3与EDC-4在秀丽隐杆线虫（Caenorhabditis elegans, C. elegans）胚胎发育中的作用与相互调控机制。EDC-3可通过降低特定胚胎mRNA的表达水平，及时清除包括cgh-1、car-1及ifet-1在内的靶标mRNA，并阻止体细胞中DCAP-2凝聚体的过度积累。本研究进一步发现EDC-3在界定P小体（processing bodies, P-bodies）、生殖颗粒与应激颗粒边界方面具有全新功能。最后，我们证实EDC-4可拮抗EDC-3的作用，并介导DCAP-2与GID（CTLH）复合物结合——该复合物是一种参与母源-合子转换（MZT）的泛素连接酶。我们的研究结果支持以下模型：多种RNA降解机制可在胚胎发育全程中时序性参与母源与合子mRNA的清除过程。为探究EDC-3与EDC-4的全转录组调控效应，我们对野生型（Wild Type, WT）、edc-3(ok1427)（RB1311品系）、edc-4(qe49)（FD135品系）及edc-3(ok1427); edc-4(qe49)（FD135品系）的混合阶段秀丽隐杆线虫胚胎提取的RNA进行了4次生物学重复的RNA测序（RNA-seq）。通过差异基因表达分析与基因集富集分析（Gene Set Enrichment Analysis, GSEA），我们鉴定了相较于野生型的各突变体中差异表达基因及相关生物学通路。