Stronger parental than temperature effects on methylation in juvenile brown trout (Salmo trutta)

Epigenetic modifications, particularly DNA methylation, are increasingly recognized as mechanisms underlying phenotypic plasticity and potential mediators of transgenerational responses to environmental change. We investigated the persistence of early life temperature-induced DNA methylation changes and the role of parental life history in shaping methylation patterns in juvenile brown trout (Salmo trutta). Fertilized eggs from crosses of anadromous and resident trout were incubated under natural or elevated temperatures (by +3°C) until first feeding, after which all fish were reared under common conditions. Whole-genome bisulfite pooled sequencing was conducted on juveniles 10.5 months post-fertilization. We found weak and inconsistent evidence for persistent temperature-induced methylation changes, with little overlap among different parental cross types. In contrast, parental life history, particularly maternal origin, significantly influenced offspring methylation patterns. Maternal..., , # Stronger parental than temperature effects on methylation in juvenile brown trout (Salmo trutta)

File: methylation_merged.tsv.gz

Description:

* CpG sites and their methylation in 8 samples.
* Combined coverage ranges between 120 and 800.
* No missing values are allowed.

Format:

* The first 5 columns are information columns for the CpG sites.
* chr: chromosome.
* start: 1-based starting position of C in the CpG site.
* end: 1-based ending position of C in the CpG site.
* strand: strand of the CpG site. \"+\" and \"-\" indicate forward and reverse strands, respectively. \"*\" indicates that the complementary CpGs were merged.
* context: context of C. It can be one of CpG, CHG and CHH, where H represents A, T or G. For the current file, this column only contains CpG because this study only focuses on C's of CpG context. C's of CHG or CHH are hardly methylated in vertebrates.
* The 6th column onwards specify the methylation in each sample. Each entry in the sample columns consis...,

表观遗传修饰（Epigenetic modifications），尤其是DNA甲基化（DNA methylation），正日益被认定为表型可塑性（phenotypic plasticity）的核心调控机制，亦是环境变化引发跨代响应的潜在介导因子。本研究聚焦于早期温度诱导的DNA甲基化变化的持久性，以及亲本生活史对幼年褐鳟（Salmo trutta）甲基化模式的塑造作用。实验采用溯河型与陆封型褐鳟的杂交受精卵，分别置于自然温度或升温3℃（+3°C）的环境中孵化至首次摄食阶段，随后所有幼鱼均在统一饲养条件下培育。于受精后10.5个月对幼体开展全基因组亚硫酸氢盐混合测序（whole-genome bisulfite pooled sequencing）。研究发现，温度诱导的甲基化变化持久性证据微弱且不一致，不同亲本杂交类型间的甲基化位点重叠度极低。与之相对，亲本生活史，尤其是母本来源，显著影响子代的甲基化模式。母本……# 幼年褐鳟（Salmo trutta）甲基化受亲本影响强于温度影响
文件：methylation_merged.tsv.gz
数据集描述：
* 涵盖8个样本中的CpG位点（CpG site）及其甲基化水平
* 合并后的测序覆盖度范围为120至800
* 不允许存在缺失值
数据格式：
* 前5列为CpG位点的信息列：
* chr：染色体编号
* start：CpG位点中胞嘧啶（C）的1起始坐标
* end：CpG位点中胞嘧啶（C）的1终止坐标
* strand：CpG位点的链方向："+"与"-"分别代表正链与负链，"*"表示互补CpG位点已合并
* context：胞嘧啶的序列上下文类型，可分为CpG、CHG与CHH，其中H代表A、T或G。本文件仅包含CpG类型，因本研究仅聚焦于CpG背景的胞嘧啶，而脊椎动物中CHG与CHH背景的胞嘧啶几乎不发生甲基化
* 第6列及之后为各样本的甲基化水平信息，样本列中的每个条目……