4.2 Freshwater transfer overall induces DNA hypomethylation inD. labrax gills
Studies on the effect of salinity on DNA methylation dynamics has been performed in plants (Rajkumar et al., 2019; Skorupa et al., 2021) and also in animals, but only in few teleost species (Artemov et al., 2017; Metzger and Schulte, 2018; Heckwolf et al., 2020, Zhang et al., 2022; Yang et al., 2023).
Our data showed that a freshwater transfer in fish gills overall induced hypomethylation of DNA across all chromosomes. Parallelly, a downregulation of the expression of two paralogs of DNA methyltransferase 3a was observed, which is consistent with this overall decrease in DNA methylation. Predominant DNA hypomethylation in fresh water vs seawater was observed in exons as well as in introns and all over the genome, where DMRs were detected. A salinity effect on DNA methylation level was also observed in threespine stickleback (G. aculeatus ) of a marine ecotype, where overall hypomethylation was observed in whole fish that were reared for 1 month at high salinity relative to those reared at low salinity (Metzger and Schulte, 2018), which is an inverse tendency than what we observed in D. labraxgills. It therefore seems that a medium-term (2 weeks in this study) as well as a long term salinity acclimation (1 month) can affect DNA methylation dynamics in fish tissues. In sea bass, the distribution of DMRs across genomic features (e.g., promoters, exons, introns and intergenic regions) did not differ from the relative proportions of these features in the genome (Tine et al., 2014) which means that fresh water induces methylation changes in all genomic features without targeting specific regions in the genome. Global hypomethylation has previously been shown following several stressors such as metal stress in zebrafish embryos (Bian and Gao., 2021), and salinity stress in the crustacean Daphnia magna (Jeremias et al., 2018). Global hypomethylation could be considered as a global response to a stressor, potentially playing a role in the modulation of transcription activity.