Genome scale epigenomic analysis of response to acute stress in the
European sea bass (Dicentrarchus labrax, L.)
Abstract
Understanding the molecular basis of stress is of long standing interest
in biology and 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
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% (unique best hits). Sequencing reads mapped across all linkage
groups (LGs). 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 family effect was demonstrated, and 57 distinct
differentially methylated cytosines (DMCs) distributed on 17 of 24 LGs
were found between RBCs of pre- and post-stress individuals and located
close to 51 distinct stress-related genes. Thirty-eight of these genes
were previously reported as differentially expressed in the brain of
zebrafish, most of them involved in stress coping differences. Some
DMC-related genes appear as good candidates to study the stress
response, especially a set of them associated to the Brain Derived
Neurotrophic Factor (BDNF), a protein that favors stress adaptation and
fear memory. Limits to our study and future directions are presented,
including the use of RBCs as a surrogate to other target tissues, to
provide with classical physiological measurements a more complete
picture of the stress response in fish.