A strategy to characterize the global histone PTM landscape within tissues of non-model organisms

Histone post-translational modifications (PTMs) are epigenetic marks that play a critical role in the expression and maintenance of DNA, but they remain largely uninvestigated in non-model organisms due to technical challenges. To begin alleviating this issue, we developed a workflow for histone PTM analysis in the Mozambique tilapia (Oreochromis mossambicus), being a widespread and environmentally hardy fish, using mass spectrometry methods. By incorporating multiple protein digestion methods into the preparation of each sample, we reliably quantified 503 biologically relevant histone PTMs. All of these histone PTMs, collectively referred to as the global histone PTM landscape, were characterized in the gills, kidney, and testes of this fish. By comparing the global histone PTM landscape between the three tissues, we found that 90.46% of histone PTMs were tissue-dependent. The workflow and tools for histone PTM analysis described in this study are now publicly available and enable comprehensive investigation into the influence of environmental stress on histone PTMs in non-model organisms. Given the functionality and flexibility of histone PTMs, we anticipate that the study of histone PTMs in ecologically relevant contexts will provide ground-breaking insights into comparative physiology and evolution.

组蛋白翻译后修饰（Histone post-translational modifications, PTMs）是一类关键的表观遗传标记，在DNA的表达与维持过程中发挥核心作用，但受限于技术难题，这类修饰在非模式生物中的研究仍未得到广泛深入的开展。为缓解这一研究困境，本研究针对分布广泛且环境耐受性优异的莫桑比克罗非鱼（Oreochromis mossambicus），开发了一套基于质谱技术的组蛋白PTM分析流程。该流程在每份样品制备中整合多种蛋白质消化方法，最终可稳定定量503个具有生物学相关性的组蛋白PTM。这些被统称为全局组蛋白PTM图谱的修饰，已在该物种的鳃、肾脏与睾丸组织中完成系统表征。通过比对三种组织间的全局组蛋白PTM图谱，研究发现90.46%的组蛋白PTM呈现组织依赖性。本研究中开发的组蛋白PTM分析流程与工具现已公开可用，可为探究环境胁迫对非模式生物组蛋白PTM的影响提供全面的研究支撑。鉴于组蛋白PTM具有多样的功能与调控灵活性，我们预计在生态相关情境下开展的组蛋白PTM研究，将为比较生理学与进化研究带来突破性见解。