Epigenomic of the stress response 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

解析胁迫的分子基础是生物学领域的关键议题，在鱼类科学中同样拥有长期的研究价值与关注度。本研究通过改良epiGBS（epiGenotyping By sequencing，基于测序的表观基因分型技术）技术，对胞嘧啶甲基化进行筛选，并探究欧洲海鲈（Dicentrarchus labrax）历经3个月反复急性胁迫刺激后的全基因组表观基因组响应。本研究采用有核红细胞（RBCs）开展微创采样，经序列修剪质控后，改良的epiGBS实验方案共获得501,108,033条测序读段，唯一最佳比对的平均比对效率为73.0%。测序读段可比对至海鲈的全部连锁群（LGs）。最终保留共计47,983个最低测序深度达30X的CpG位点坐标，用于开展胁迫前后海鲈个体的差异甲基化分析。研究证实存在显著的家系效应，在胁迫前后个体的有核红细胞中，共发现分布于24个连锁群中17个的57个独立差异甲基化胞嘧啶（DMCs）。其中12个位于基因间区，1个位于重复序列元件内，剩余44个位于基因本体区域。总体而言，这些差异甲基化胞嘧啶分布于51个已知与胁迫相关的基因内部或其邻近区域。其中38个基因此前已有报道在斑马鱼大脑中存在差异表达，且多数与胁迫应对差异相关。实验总体设计：采用epiGBS技术对74份海鲈样本（双端测序）进行分析。