Epigenetic modifications, such as DNA methylation, can be regulated by nutrition and dietary factors. There has been a large increase in the use of sustainable plant-based protein sources in fish feed due to limitations of fishmeal resources, which are needed to sustain a rapidly growing aquaculture industry. With this major transition from marine ingredients to plant-based diets, fish are abruptly introduced to changes in dietary composition and exposed to a variety of phytochemicals, some of which known to cause epigenetic changes in mammals. However, the effect of plant ingredients on the epigenome of fish is barely understood. In the present study, the nutriepigenomic effects of the addition of pea, soy, and wheat gluten protein concentrate to aquafeeds were investigated using zebrafish as a model. A genome-wide analysis of DNA methylation patterns was performed by reduced representation bisulphite sequencing to examine global epigenetic alterations in the mid intestine after a 42-day feeding trial. We found that inclusion of 30% of wheat gluten, pea and soy protein concentrate in the diet induced epigenetic changes in the mid intestine of zebrafish. A large number of genes and intergenic regions were differentially methylated with plant-based diets. The genes concerned were related to immunity, NF‐κB system, ubiquitin-proteasome pathway, MAPK pathway, and the antioxidant defence system. Epigenetic regulation of several biological processes, including neurogenesis, cell adhesion, response to stress and immunity was also observed. Ultimately, the observed epigenetic changes may enable zebrafish to rapidly regulate inflammation and maintain intestinal homoeostasis when fed plant protein–based diets.

营养和饮食因素可以调节表观遗传修饰，例如DNA甲基化。由于鱼粉资源的局限性，鱼饲料中对可持续植物性蛋白质来源的使用已大大增加，而鱼粉资源是维持快速发展的水产养殖业所必需的。随着从海洋成分到以植物为基础的饮食的这一重大转变，鱼类被突然引入饮食组成的变化并暴露于多种植物化学物质中，其中一些已知会引起哺乳动物的表观遗传变化。然而，人们几乎不了解植物成分对鱼类表观基因组的影响。在本研究中，使用斑马鱼作为模型研究了将豌豆，大豆和小麦面筋蛋白浓缩物添加到水产饲料中的营养基因组学效应。在经过42天的喂养试验后，通过减少代表性的亚硫酸氢盐测序对DNA甲基化模式进行了全基因组分析，以检查肠道中部的整体表观遗传学变化。我们发现，饮食中包含30％的小麦面筋，豌豆和大豆浓缩蛋白会引起斑马鱼中肠的表观遗传变化。大量基因和基因间区域被植物性饮食甲基化。有关的基因与免疫力，NF-κB系统，泛素-蛋白酶体途径，MAPK途径和抗氧化防御系统有关。还观察到几种生物学过程的表观遗传学调控，包括神经发生，细胞粘附，对压力的反应和免疫。最终，