5. Conclusion
We have investigated salinity-induced DNA methylation and its role in plasticity and gene expression in gills of euryhaline European sea bass. This study highlighted that genes with low methylation levels in first exons, first introns and promoters are generally highly expressed. We also showed that fresh water triggers an overall hypomethylation of the genome. Our investigation showed that pathways involved in tight junctions are highly enriched in upregulated genes displaying hypomethylated promoters. We also identified other pathways as lipid metabolism, calcium signaling and regulation of actin cytoskeleton that were enriched for gene expression and DNA methylation changes in either promoters or first exons/introns. Numerous key genes involved in transepithelial ion transport of gill ionocytes also show methylation and gene expression changes. Interestingly, mitochondria metabolism is strongly activated, suggesting a modulation of metabolite availability as substrate for chromatin-modifying enzymes. We recommend further investigation of methylation dynamics in environmentally challenged fish in order to determine the role of methylation changes in phenotypic plasticity, acclimation and adaptation.