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. Overall design: 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（mRNA decapping scaffold proteins）在发育过程中的作用仍有待阐明。本研究揭示了秀丽隐杆线虫（C. elegans）胚胎发育中DCAP-2脱帽支架EDC-3与EDC-4的功能及其相互作用机制。EDC-3可通过降低cgh-1、car-1及ifet-1等特定胚胎mRNA的表达水平，促进其及时清除，并阻止体细胞内DCAP-2凝聚体（DCAP-2 condensates）的过度积累。本研究进一步发现EDC-3在界定P小体（P-bodies）、生殖颗粒（germ granules）与应激颗粒（stress granules）之间的边界方面具有全新功能。最后，本研究证实EDC-4可拮抗EDC-3的作用，并介导DCAP-2与GID（CTLH）复合物的组装——该复合物是一种参与母源到合子转变（MZT, maternal-to-zygotic transition）的泛素连接酶（ubiquitin ligase）。我们的研究结果支持如下模型：多种RNA降解机制在整个胚胎发育过程中时序性参与母源与合子mRNA的清除。

实验设计概述：为探究EDC-3与EDC-4的全转录组水平效应，我们对野生型（WT, N2菌株）、edc-3(ok1427)（RB1311菌株）、edc-4(qe49)（FD135菌株）及edc-3(ok1427); edc-4(qe49)（FD135菌株）秀丽隐杆线虫混合阶段胚胎提取的RNA开展了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（GSEA, Gene Set Enrichment Analysis），我们鉴定了各突变体相较于野生型的差异表达基因与富集的生物学通路。