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).