Epigenetic regulation and maternal-to-zygotic transition in dwarf surf clam (Mulinia lateralis): Insights from chromatin state profiling and transcriptomics

Bivalve mollusks represent a taxonomically and economically significant clade within Mollusca. However, the regulatory mechanisms governing their embryonic development remain poorly characterized. The dwarf surf clam (Mulinia lateralis), characterized by a short generation time and high fecundity, has recently gained recognition as an ideal model system for bivalve embryological research. This study explored the epigenetic mechanisms driving embryogenesis in M. lateralis, with a particular focus on the maternal-to-zygotic transition (MZT), by integrating chromatin-state profiling and transcriptomic analysis. For the first time in this species, CUT&Tag was employed to generate high-resolution landscapes of histone modifications H3K4me1, H3K4me3, H3K27me3, and H3K27ac across key developmental stages. The resulting data revealed extensive reprogramming of histone marks, indicating dynamic shifts in chromatin architecture during early embryonic development. Integration with transcriptomic data identified the timing of MZT in M. lateralis between the morula and gastrula stages and highlighted a suite of candidate genes essential for embryogenesis. These findings provide mechanistic insight into chromatin-mediated control of bivalve embryogenesis and establish M. lateralis as a robust platform for epigenomic research in marine invertebrates, with implications for functional gene studies and aquaculture advancement.