3.5 Changes in DNA methylation and gene expression profiles are identified in specific gene pathways
Enrichment analyses of gene ontology terms (GO-terms) were done in both analyses (transcriptome and methylome) to identify the enriched GO terms. Venn diagrams in Fig. 7 show the numbers and percentages of unique and common GO terms between DMRs (in genes and promoters) and DEGs. For the ‘biological process’ category (Fig. 7A), the results showed 17% of common GO terms between DMRs and DMGs. Among them, we identified categories involved in metabolism as ‘carbohydrate derivative biosynthetic process’, ‘lipid biosynthesis process’ and ‘mitochondrial transport’. Concerning the ’molecular function’ category (Fig. 7B), 14% of enriched GO terms were common between DMRs and DEGs. Among these GO terms we identified main categories involved in active ion transport, as ‘ATPase-coupled transmembrane transporter activity’. Several genes encoding for ATPases such as different subunits of Na+/K+-ATPase (atp1a1 ,atp1a3b ) and the V-H+-ATPase (atp6v1b2 ,atp6v1d ) were upregulated in FW and showed differential methylation patterns between salinities (Table 1). We also identified genes encoding for other main ion transporters or channels that showed differential methylation and were upregulated (as one clcn2paralog, clcn3 , several K+ channels:kcnh5 , kcnk5 , kcnt1 ) or downregulated in FW (scn4a Na+ channel, atp6v1e1b subunit of V-H+-ATPase, chloride channels cftr and one of the clcn2 paralog, potassium channel kcnma1 , and an ammonium channel rhcg ). The gene encoding for Aquaporin 3, a glyceroporin, was strongly upregulated in FW (log2FC=3.3) and hypomethylated at the promoter and gene body levels. We also identified in the category ‘cytokine receptor activity’ the gene encoding for prolactin receptor (prlr ), being upregulated in FW and hypomethylated at the promoter and gene body levels (Table 1). Finally, among the 28% of common GO terms with enriched DMRs and DEGs in the ‘cellular component’ category (Fig. 7C), we observed those associated with ‘bicellular tight junction’ and ‘outer membrane’. Numerous genes encoding for tight junction proteins and claudins appeared as being mainly upregulated in FW and hypomethylated at the promoter level (detailed below).
Interestingly, two genes encoding for DNA methyltransferase 3a (dnmt3a ) were both downregulated in FW and showed differential methylation patterns (Table 1). One gene was hypomethylated and the other was hypermethylated at the level of the gene body. Methylcytosine dioxygenase 3 (tet3 ), a DNA demethylase, was downregulated in FW.