Department of Animal Sciences and Aquatic Ecology, Ghent University, Coupure Links 653, Ghent 9000, Belgium.
Department of Animal Sciences and Aquatic Ecology, Ghent University, Coupure Links 653, Ghent 9000, Belgium.
Environ Pollut. 2023 Aug 1;330:121737. doi: 10.1016/j.envpol.2023.121737. Epub 2023 Apr 28.
Environmental epigenetics has become a key research focus in global climate change studies and environmental pollutant investigations impacting aquatic ecosystems. Specifically, triggered by environmental stress conditions, intergenerational DNA methylation changes contribute to biological adaptive responses and survival of organisms to increase their tolerance towards these conditions. To critically review epigenetic analytical approaches in ecotoxicological aquatic research, we evaluated 78 publications reported over the past five years (2016-2021) that applied these methods to investigate the responses of aquatic organisms to environmental changes and pollution. The results show that DNA methylation appears to be the most robust epigenetic regulatory mark studied in aquatic animals. As such, multiple DNA methylation analysis methods have been developed in aquatic organisms, including enzyme restriction digestion-based and methyl-specific immunoprecipitation methods, and bisulfite (in)dependent sequencing strategies. In contrast, only a handful of aquatic studies, i.e. about 15%, have been focusing on histone variants and post-translational modifications due to the lack of species-specific affinity based immunological reagents, such as specific antibodies for chromatin immunoprecipitation applications. Similarly, ncRNA regulation remains as the least popular method used in the field of environmental epigenetics. Insights into the opportunities and challenges of the DNA methylation and histone variant analysis methods as well as decreasing costs of next generation sequencing approaches suggest that large-scale epigenetic environmental studies in model and non-model organisms will soon become available in the near future. Moreover, antibody-dependent and independent methods, such as mass spectrometry-based methods, can be used as an alternative epigenetic approach to characterize global changes of chromatin histone modifications in future aquatic research. Finally, a systematic guide for DNA methylation and histone variant methods is offered for ecotoxicological aquatic researchers to select the most relevant epigenetic analytical approach in their research.
环境表观遗传学已成为全球气候变化研究和影响水生生态系统的环境污染物调查的一个关键研究焦点。具体而言，在环境胁迫条件下，代际 DNA 甲基化变化会引发生物适应性反应，从而提高生物体对这些条件的耐受性，使其得以存活。为了批判性地回顾生态毒理学水生研究中的表观遗传分析方法，我们评估了过去五年（2016-2021 年）报告的 78 篇应用这些方法来研究水生生物对环境变化和污染的反应的出版物。结果表明，DNA 甲基化似乎是水生动物中研究最广泛的表观遗传调控标记。因此，已经在水生生物中开发了多种 DNA 甲基化分析方法，包括基于酶限制消化和甲基特异性免疫沉淀的方法，以及亚硫酸氢盐（不）依赖的测序策略。相比之下，由于缺乏基于物种特异性亲和力的免疫试剂，例如用于染色质免疫沉淀应用的特异性抗体，只有少数水生研究（约 15%）专注于组蛋白变体和翻译后修饰。同样，ncRNA 调控仍然是环境表观遗传学领域中使用最少的方法。深入了解 DNA 甲基化和组蛋白变体分析方法的机遇和挑战，以及下一代测序方法成本的降低，表明在模型和非模型生物中进行大规模的环境表观遗传学研究将在不久的将来成为可能。此外，基于抗体的和非抗体的方法，如基于质谱的方法，可以作为未来水生研究中描述染色质组蛋白修饰整体变化的替代表观遗传方法。最后，为生态毒理学水生研究人员提供了 DNA 甲基化和组蛋白变体方法的系统指南，以帮助他们在研究中选择最相关的表观遗传分析方法。
