Sources of variation of DNA methylation in rainbow trout: combined effects of temperature and genetic background

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 <i>dnmt3</i> (DNA methyltransferase) genes, potentially involved in <i>de novo</i> 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.

表型可塑性（phenotypic plasticity）是生物体应对环境条件变化的核心能力组成部分。本研究以虹鳟为对象，旨在探究生物体响应环境胁迫时DNA甲基化（DNA methylation）标记的建立模式，并评估此类标记是否依赖于遗传背景。本研究选取的环境胁迫因子为温度——这是已被证实可诱导鱼类表观遗传标记（epigenetic marks）形成的常见诱因。为厘清DNA甲基化等表观遗传机制在表型变异产生过程中的作用，本研究选用了9个虹鳟同基因系（isogenic lines）——每个品系内部不存在遗传变异。针对每个品系，将其半数受精卵从眼发育期至孵化阶段置于标准温度（11℃）下培养，剩余半数则置于高温（16℃）环境中培养。为初步解析胚胎早期温度处理（对照11℃与热处理16℃）下DNA甲基化标记的建立规律，本研究检测了8个可能参与<i>de novo</i>（从头）甲基化过程的<i>dnmt3</i>（DNA甲基转移酶，DNA methyltransferase）基因的表达水平，并采用LUMA（LUminometric Methylation Assay，荧光光度甲基化检测法）技术分析了不同虹鳟同基因系的全基因组DNA甲基化水平。最后，为对全基因组甲基化模式开展更精细的解析，本研究针对6个虹鳟同基因系，采用了基于ddRADseq（双酶切限制性位点相关DNA测序，Double Digest Restriction Associated DNA）流程的简化基因组文库方法EpiRADseq。本研究证实，胚胎发育阶段的热暴露历史会改变DNA甲基化模式，且这种改变程度因遗传背景的不同而存在显著差异。