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.