Integrated Analysis of ATAC-Seq and RNA-Seq Reveals the Signal Transduction Regulation of the Molting Cycle in the Muscle of Chinese Mitten Crab (Eriocheir sinensis)

Molting is a critical physiological process for the growth and development of Eriocheir sinensis. Any disruption in this process can significantly affect both survival rates and crab quality. The regulatory mechanisms of molting vary across different stages of the molting cycle and remain poorly understood. In this study, ATAC-seq and RNA-seq were combined to identify the integrated differentially expressed genes (IDEGs) in muscle across adjacent stages of the molting cycle. A total of 17, 491, 84, and 491 IDEGs were identified in the comparisons of inter-molt_vs_pre-molt, pre-molt_vs_molt, molt_vs_post-molt, and post-molt_vs_inter-molt stages, respectively. GO enrichment analysis of these IDEGs revealed several key signaling pathways involved in each adjacent molting stage. The GPCR signaling, steroid hormone-mediated signaling, and smoothened signaling pathways were all active across three molting transitions (pre-molt_vs_molt, molt_vs_post-molt, and post-molt_vs_inter-molt). Among them, the GPCR pathway played a dominant role throughout the process. Further structural analysis and RT-qPCR validation identified eight GPCRs involved in molting regulation: GRM7 and moody were specific to the post-molt_vs_inter-molt stage; Kpna6, ADRB2, and SSTR2 were unique to the pre-molt_vs_molt stage; FMRFaR and gpr161 functioned in both post-molt_vs_inter-molt and pre-molt_vs_molt stages; and mth2 was active in both post-molt_vs_inter-molt and molt_vs_post-molt stages. These findings improve the understanding of molting regulation and provide potential targets for further genetic improvement in E. sinensis.