Temperature and farming conditions provoke changes in the epigenome of the European sea bass

Abstract

The early developmental environment an organism experiences may have a long term impact on the phenotype. Fish represent good animal models for the study of the integration of environmental information via epigenetic mechanisms. Both temperature and farming conditions are shown to be related with lasting changes in gene expression and the phenotype. Here, we used adult European sea bass (Dicentrarchus labrax) subjected to two temperatures (17oC or 21oC) during the thermosensitive period and also, we compared farmed and wild fish. From one hand we explored the DNA methylome using next generation sequencing (NGS) technology and from the other hand we studied specific histone modifications and variants in key genes. In order to measure DNA methylation levels, we prepared and sequenced Reduced Representation Bisulfite Sequencing (RRBS) libraries. Temperature provoked changes in ~3500 cytosines in testis and ~12000 cytosines in muscle, whereas farming conditions affected ~4000 cytosines in testis and ~15000 cytosines in muscle. The great majority of these differentially methylated cytosines arisen both by temperature and farming conditions were physically located in proximity to genes and their regulatory elements including the transcription start sites (TSS). For the purposes of identifying enrichment of two histone modifications and one variant related to regulation of gene expression, we measured the expression of two genes (drmt1 in testis and myog in muscle) and performed ChIP-qPCR experiments using antibodies for both transcriptional activation (H3K4me3 and H2A.Z) and inactivation (H3K9me3) epigenetic markers. In addition, we used RNA-seq to establish possible relationships between epigenetic and gene expression changes. In this study, we have demonstrated that the environmental information received during early development in the sea bass has broad consequences on the epigenome that are revealed later in life