Genome-wide epigenomic stress response in the European sea bass (Dicentrarchus labrax, L.)

Abstract Background While the stress response inspired genome-wide epigenetic studies in vertebrate models, it remains mostly ignored in fish. We modified the epiGBS (epiGenotyping By sequencing) technique to explore changes in genome-wide cytosine methylation to a repeated acute stress challenge in the nucleated red blood cells (RBCs) of the European sea bass (Dicentrarchus labrax). This species is widely studied in both the natural and farmed environments, including issues regarding health and welfare. Results We retrieved 501,108,033 sequencing reads after trimming, with a mean mapping efficiency of 73.0% (unique best hits). Fifty-seven differentially methylated cytosines (DMCs) close to 51 distinct stress-related genes distributed on 17 of 24 linkage groups (LGs) were detected between RBCs of pre- and post-stress individuals. Literature surveys indicated that thirty-eight of these genes were previously reported as differentially expressed in the brain of zebrafish, most of them involved in stress coping differences. DMC-related genes associated to the Brain Derived Neurotrophic Factor, a protein that favors stress adaptation and fear memory, are especially relevant. Conclusion We provide an improved epiGBS protocol with increased multiplexing and sequencing capacities that offer new opportunities to improve data acquisition and to investigate important biological processes at a genome-wide level, such as the stress response. Minimally invasive RBCs deserve more attention to investigate the epigenetic response to stress without sacrificing fish.