Environmental influences on the epigenome and transcriptome of the European sea bass

Abstract

Temperature is an environmental factor known to influence both DNA methylation and gene expression in many types of animals, whereas farming conditions can alter the morphology and the gene expression in fish. Here, we explored the effects of temperature and farming on the genome-wide DNA methylation and the transcriptome of adult European sea bass (Dicentrarchus labrax). For this purpose, we used Reduced Representation Bisulfite Sequencing (RRBS) and and RNA sequencing to measure DNA methylation and gene expression levels, respectively. Temperature effects were evaluated using 3-year-old fish that were raised either at low (17 C) or high (21 C) temperature during the thermosensitive period, while farming effects were evaluated comparing fish raised at low temperature with wild fish. Cytosines in the CpG context were affected in all comparisons, with more differentially methylated cytosines (DMC) found in the muscle of farmed fish and fewer but still more than ~12000 in the testis of high temperature fish. Focusing on genes that contained DMCs in their known regulatory regions, especially the promoter and the first exon, we performed enrichment tests of gene ontology (GO) terms to gather functional information In addition, we found genes that not only contained DMCs in their regulatory elements but also were differentially expressed. Together, these data show that environmental factors acting during the early development have long lasting effects on both the epigenome and the transcriptome of the sea bass, since these effects are detected later in life. It remains to be determined their actual functional consequences