ABSTRACT

Phenotypic plasticity is a key component of the ability of organisms to respond to changing environmental conditions. In this study, we aimed to study the establishment of DNA methylation marks in response to an environmental stress in rainbow trout and to assess whether these marks depend on the genetic background. The environmental stress chosen here was temperature, a known induction factor of epigenetic marks in fish. To disentangle the role of epigenetic mechanisms such as DNA methylation in generating phenotypic variations, nine rainbow trout isogenic lines with no genetic variability within a line were used. For each line, half of the eggs were incubated at standard temperature (11°C) and the other half at high temperature (16°C), from eyed-stage to hatching. In order to gain a first insight into the establishment of DNA methylation marks in response to an early temperature regime (control 11°C vs. heated 16°C), we have studied the expression of 8 dnmt3 (DNA methyltransferase) genes, potentially involved in de novo methylation, and analysed global DNA methylation in the different rainbow trout isogenic lines using LUMA (LUminometric Methylation Assay). Finally, finer investigation of genome-wide methylation patterns was performed using EpiRADseq, a reduced-representation library approach based on the ddRADseq (Double Digest Restriction Associated DNA) protocol, for six rainbow trout isogenic lines. We have demonstrated that thermal history during embryonic development alters patterns of DNA methylation, but to a greater or lesser extent depending on the genetic background.

摘要

表型可塑性是生物体对不断变化的环境条件作出反应的能力的关键组成部分。在这项研究中，我们旨在研究 DNA 甲基化标记在虹鳟鱼环境压力下的建立，并评估这些标记是否依赖于遗传背景。这里选择的环境压力是温度，这是鱼类表观遗传标记的已知诱导因素。为了解开诸如 DNA 甲基化等表观遗传机制在产生表型变异中的作用，使用了九个虹鳟同基因系，在一个系内没有遗传变异性。对于每条线，一半的鸡蛋在标准温度（11°C）下孵化，另一半在高温（16°C）下孵化，从眼睛阶段到孵化。dnmt3（DNA 甲基转移酶）基因，可能参与从头甲基化，并使用 LUMA（LUminometric Methylation Assay）分析了不同虹鳟鱼同基因系中的全局 DNA 甲基化。最后，使用 EpiRADseq（一种基于 ddRADseq（双消化限制相关 DNA）协议的减少表示库方法）对六个虹鳟鱼同基因系进行更精细的全基因组甲基化模式研究。我们已经证明胚胎发育过程中的热历史会改变 DNA 甲基化的模式，但或多或​​少取决于遗传背景。