4.3 Hypermethylation triggered by freshwater transfer overall induces downregulation of genes
Despite an overall DNA hypomethylation in the sea bass genome, we observed an interesting trend for hypermethylated genes to be silenced at a very high percentage, notably in first introns. When considering genes that were hypermethylated in first introns and show differential expression between salinities, 81% of the genes were downregulated, and only 19% were upregulated, which is intriguing. Genes that were downregulated and hypermethylated in promoters, first exons or first introns belonged to different KEGG categories (Table 7S). Among those, we identified several genes involved in cell-cell adhesion and regulation of actin cytoskeleton as tropomyosin and a change in integrin turnover. It is known that integrins assembling to the cytoskeleton is important in cell-cell adhesion (Delon and Brown., 2007). There is in fact an extensive remodeling of gills in euryhaline teleosts following salinity transfer, that involves cell proliferation and turnover pathways, leading to epithelial remodeling. In D. labrax as in other species, the density and subtypes of gill ionocytes is increased in the freshwater environment (Masroor et al., 2018). We identified several genes involved in the calcium signaling pathway. Calcium is an ubiquitous second messenger regulating numerous cellular processes, including proliferation, cellular metabolism, and cell death. In mammal studies linked to cancer research, the SERCA pump (encoded byatp2a ), which sequesters Ca2+ into the endoplasmic reticulum (ER), as well as other calcium regulated genes, showed altered expression patterns that coincided with increased promoter methylation (Bertocci et al., 2022). In D. labrax , the hypermethylation of the gene encoding for SERCA might contribute to its significantly lower expression in FW (log2FC: -0,38), which could lead to increased cytoplasmic calcium availability. We did not measure any expression difference in plasma membrane Ca2+ ATPase (pmca ) between salinity conditions, which is an important pump expressed in gill ionocytes to take up Ca2+ from FW environments.