Comp Biochem Physiol Part D Genomics Proteomics 2025 Feb 23;55:101456. doi: 10.1016/j.cbd.2025.101456.

Joint profiling of DNA methylomics and transcriptomic reveals roles of demethylation in regeneration of coelomocytes after evisceration in sea cucumber Apostichopus japonicus.

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Generally, there is a large number of deaths for sea cucumber along with evisceration after which a weakly immune state occurs because of a poor resistance against a variety of pathogens and environmental stress. The regeneration of coelomocytes plays an important role in the remodeling of the immune defense system after evisceration with the decrease of methylation modification. In this study, the whole DNA methylation of coelomocytes is detected post evisceration in Apostichopus japonicus to explore the process of cell regeneration. Our results found that total methylation level reached a lowest point at 12 h (9.8 %), which was followed by increased at 24 h. The transcriptomic and DNA methylomic analysis indicated a total of 215 genes were identified by selecting the significant hypomethylation within the 2-kilobase region of the transcriptional start site upstream. The KEGG pathway enrichment analyses of the 215 genes showed that signal transduction, signaling molecules and interaction were significantly enriched. The genes were enriched in the top 20 signaling pathway, such as IGF1R, Notch2 and HSPA1s. Taken together, this study provides new clues for deciphering the coelomocytes regeneration after evisceration of A. japonicus by DNA demethylation.

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