Genome scale epigenomic analysis of response to acute stress in the European sea bass
Understanding the molecular basis of stress is crucial in biology and of long standing interest in fish science. We tackled this question by modifying the epiGBS (epiGenotyping By sequencing) technique to screen for cytosine methylation and explore the genome-wide epigenomic response to a three months repeated acute stress challenge in the European sea bass (Dicentrarchus labrax). Following a minimally invasive sampling using nucleated red blood cells (RBCs), our modified epiGBS protocol retrieved 501,108,033 sequencing reads after trimming, with a mean mapping efficiency of 73.0% for unique best hits. Sequencing reads were shown to map across all linkage groups (LGs) of sea bass. A total of 47,983 CpG coordinates with a minimum 30X read depth was retained for differential methylation analysis between pre- and post-stress fish. A strong family effect was demonstrated, and fifty-seven distinct differentially methylated cytosines (DMCs) distributed on 17 of 24 LGs were found between RBCs of pre- and post-stress individuals. Twelve of them were located in intergenic regions, one in a repeated element; and forty four in gene bodies. Overall, DMCs were found inside or in the vicinity of 51 distinct genes shown previously to be related to stress. Thirty-eight of these genes were previously reported as differentially expressed in the brain of zebrafish, most of them involved in stress coping differences. Overall design: 74 samples of sea bass (paired-end sequencing) analyzed with epiGBS