4.1 Gene expression and DNA methylation are inversely correlated in promoters, first exons and first introns
First, we determined if there is a correlation between gene expression and DNA methylation levels in different genomic regions using gill homogenates from the same individuals for both analyses. In D. labrax , we observed a global DNA methylation all over the genome, with a depletion at the promoters and transcription start sites. This is consistent with previous observations in vertebrates (Aliaga et al., 2019; Suzuki and Bird, 2008). An inverse correlation between gene expression and DNA methylation levels was found in promoters, first introns and first exons. This inverse correlation has previously been highlighted by Anastasiadi et al. (2018) who compared DNA methylation levels in muscles and testes of D. labrax, and later by Liu et al. (2022) in Anguilla anguilla muscles for first exons. The presence of unmethylated CpG islands in the proximity of the TSS is consistent with the role of first introns and first exons in the regulation of gene expression. Additionally to promoters, first introns and first exons could thus be involved in transcriptional regulation as highlighted for first introns in humans (Li et al., 2012). We showed that the rest of the introns and exons were highly methylated (>75 %) and did not show any correlation with gene expression, as previously observed in previous studies (Anastasiadi et al., 2018).