Abstract
Epigenetic modifications, like DNA methylation, generate phenotypic
diversity in fish and ultimately lead to adaptive evolutionary
processes. Euryhaline marine species that migrate between salinity
contrasted habitats have received little attention regarding the role of
salinity on whole-genome DNA methylation. Investigation of
salinity-induced DNA methylation in fish will help to better understand
the potential role of this process in salinity acclimation. Using whole
genome bisulfite sequencing, we compared DNA methylation patterns in
European sea bass (Dicentrarchus labrax ) juveniles in seawater
and after freshwater transfer. We targeted the gill as a crucial organ
involved in plastic responses to environmental changes. To investigate
the function of DNA methylation in gills, we performed RNAseq and
assessed DNA methylome-transcriptome correlations. We showed a negative
correlation between gene expression levels and DNA methylation levels in
promoters, first introns and exons. A significant effect of salinity on
DNA methylation dynamics with an overall DNA hypomethylation in
freshwater-transferred fish compared to seawater controls was
demonstrated. This suggests a role of DNA methylation changes in
salinity acclimation. Genes involved in key functions as metabolism, ion
transport and transepithelial permeability (junctional complexes) were
differentially methylated and expressed between salinity conditions.
Expression of genes involved in mitochondrial metabolism was increased
as well as the expression of DNA methyltransferases 3a. This study
reveals novel aspects on the link of DNA methylation and gene expression
patterns.