Microplastic exposure is associated with epigenomic effects in the model organism Pimephales promelas (fathead minnow)

Microplastics have evolutionary and ecological impacts across species, affecting organisms’ development, reproduction, and behavior along with contributing to genotoxicity and stress. As plastic pollution is increasing and ubiquitous, gaining a better understanding of organismal responses to microplastics is necessary. Gene methylation is a heritable form of molecular regulation that is influenced by environmental conditions, including exposure to pollutants, therefore determining epigenetic responses to microplastics will reveal potential chronic consequences of this pollutant. We performed an experiment across two generations of fathead minnows (Pimephales promelas) to elucidate transgenerational effects of microplastic exposure. We exposed the first generation of fish to four different treatments of microplastics: two concentrations of each of pre-consumer polyethylene (PE) and PE collected from Lake Ontario. We then raised the second generation from these parents with no microplasti..., Experimental Design
We used fathead minnow, a toxicological model organism, throughout this experiment to determine the effects of microplastics across life stages. Fish maintenance and handling followed protocols approved by the Ontario Ministry of Environment, Conservation, and Parks (MECP) Laboratory Services Animal Care Committee (approval number: ATU-004-19). We adapted rearing methods from a previously published fathead minnow life cycle experiment (Parrot 2005). We obtained fathead minnows from the breeding stock of the MECP. From eggs through 178 DPH, we raised fish under experimental conditions with four treatments and a negative control (CTRL). The treatments were: 1) a low, environmentally relevant concentration (100 particles/L) of pre-consumer PE (PL), 2) high, future scenario concentration (2000 particles/L) of pre-consumer PE (PH), 3) low concentration of PE gathered from Lake Ontario (EL), and 4) a high concentration of PE originating in Lake Ontario (EH). We reduced mic..., , # Data from: Microplastic exposure is associated with epigenomic effects in the model organism Pimephales promelas (fathead minnow)

[https://doi.org/10.5061/dryad.4tmpg4fhd](https://doi.org/10.5061/dryad.4tmpg4fhd)

Files contain metadata and the filtered R object (data is also given in CSV file format, final_filtration.csv) for methylation data from fathead minnows following a life cycle exposure experiment using microplastics.

## Description of the data and file structure

'sample_data_reduced.txt' file features a header for 'Sample_Name', 'treatment', 'plastic', 'concentration', 'sex', 'control', and 'generation'
One sample per row
Individuals are named according to treatment (i.e., 'BH' is env_high, 'BL' is env_low, 'CTRL' is control, 'CH' is pristine_high, 'CL' is pristine_low, the modification 'F1' is the second generation)

## Code/Software

Analyses are in R using the packages 'methylKit', 'bsseq', 'dmrseq', 'methylSig', and 'DSS'

the R package 'bsseq' is required to open 'fi...

微塑料（microplastics）对各类物种具有进化与生态影响，可干扰生物体的发育、繁殖与行为，并引发遗传毒性与应激反应。随着塑料污染愈发普遍且污染程度持续加剧，深入解析生物体对微塑料的响应机制已成为迫切需求。基因甲基化（gene methylation）是一种可遗传的分子调控形式，其表达受包括污染物暴露在内的多种环境条件影响，因此阐明生物体对微塑料的表观遗传响应，能够揭示该污染物潜在的慢性危害。

本研究针对黑头软口鲦（Pimephales promelas，fathead minnow）开展两代实验，以明确微塑料暴露的跨代效应。研究将第一代受试鱼暴露于四种不同的微塑料处理体系：分别为消费前聚乙烯（polyethylene, PE）的两个浓度梯度，以及从安大略湖采集的聚乙烯的两个浓度梯度。随后在无微塑料暴露的环境下，对由亲代繁育出的第二代鱼进行饲养……【实验设计】

我们全程使用毒理学模式生物黑头软口鲦开展实验，以探究微塑料对不同生命阶段的影响。鱼类的饲养与操作流程遵循安大略省环境、保护与公园部（Ontario Ministry of Environment, Conservation, and Parks, MECP）实验室服务动物护理委员会批准的方案（批准号：ATU-004-19）。本研究参考已发表的黑头软口鲦生命周期实验方法（Parrot 2005）对饲养方案进行调整。实验用黑头软口鲦均取自MECP的繁育种群。从鱼卵阶段至178日龄（days post hatching, DPH），我们将受试鱼饲养于四种处理组及一个阴性对照组（CTRL）的实验环境中。各处理组具体设置如下：1）低浓度环境相关剂量（100 particles/L）的消费前聚乙烯（PL）；2）高浓度未来场景剂量（2000 particles/L）的消费前聚乙烯（PH）；3）从安大略湖采集的聚乙烯低浓度组（EL）；4）源自安大略湖的聚乙烯高浓度组（EH）。本研究对实验样本进行了简化处理……

# 数据来源：微塑料暴露与模式生物黑头软口鲦（Pimephales promelas，fathead minnow）的表观基因组效应相关研究
[https://doi.org/10.5061/dryad.4tmpg4fhd](https://doi.org/10.5061/dryad.4tmpg4fhd)

本数据集包含元数据与经过滤处理的R对象（数据同时以CSV文件格式提供，文件名为final_filtration.csv），对应黑头软口鲦在经微塑料生命周期暴露实验后的甲基化测序数据。

## 数据与文件结构说明
'sample_data_reduced.txt' 文件包含表头字段：Sample_Name、treatment、plastic、concentration、sex、control与generation。
文件中每行代表一个独立样本。个体命名规则与处理组一一对应（例如：'BH'代表环境来源高浓度组，'BL'代表环境来源低浓度组，'CTRL'为对照组，'CH'代表 pristine高浓度组，'CL'代表 pristine低浓度组；后缀'F1'用于标注第二代个体）

## 分析软件
本分析使用R语言完成，所依赖的R包包括'methylKit'、'bsseq'、'dmrseq'、'methylSig'与'DSS'。
其中R包'bsseq'为打开[被截断的文件]所必需的工具……