The unprecedented access to annotated genomes now facilitates the investigation of the molecular basis of epigenetic phenomena in phenotypically diverse animals. In this critical review, we describe the roles of molecular epigenetic mechanisms in regulating mitotically and meiotically stable spatiotemporal gene expression, phenomena that provide the molecular foundation for the intra-, inter-, and trans-generational emergence of physiological phenotypes. By focusing principally on emerging comparative epigenetic roles of DNA-level and transcriptome-level epigenetic mark dynamics in the emergence of phenotypes, we highlight the relationship between evolutionary conservation and innovation of specific epigenetic pathways, and their interplay as a priority for future study. This comparative approach is expected to significantly advance our understanding of epigenetic phenomena, as animals show a diverse array of strategies to epigenetically modify physiological responses. Additionally, we review recent technological advances in the field of molecular epigenetics (single-cell epigenomics and transcriptomics and editing of epigenetic marks) in order to (1) investigate environmental and endogenous factor dependent epigenetic mark dynamics in an integrative manner; (2) functionally test the contribution of specific epigenetic marks for animal phenotypes via genome and transcript-editing tools. Finally, we describe advantages and limitations of emerging animal models, which under the Krogh principle, may be particularly useful in the advancement of comparative epigenomics and its potential translational applications in animal science, ecotoxicology, ecophysiology, climate change science and wild-life conservation, as well as organismal health.

现在，对注释基因组的前所未有的访问便利了对表型多样的动物中表观遗传现象的分子基础的研究。在这篇重要的综述中，我们描述了分子表观遗传机制在调节有丝分裂和减数分裂稳定的时空基因表达中的作用，这些现象为生理表型的代内，代间和跨代出现提供了分子基础。通过主要关注新兴比较在表型的出现中，DNA水平和转录组水平表观遗传标记动力学的表观遗传作用，我们着重指出了进化保护与特定表观遗传途径创新之间的关系，并将它们之间的相互作用作为未来研究的重点。由于动物表现出多种表观遗传修饰生理反应的策略，因此这种比较方法有望大大提高我们对表观遗传现象的理解。此外，我们综述了分子表观遗传学领域的最新技术进展（单细胞表观基因组学和转录组学以及表观遗传学标记的编辑），以便（1）以综合方式研究环境和内源性因子依赖性表观遗传学标记动力学；（2）通过基因组和转录编辑工具功能性测试特定表观遗传标记对动物表型的贡献。最后，我们描述了新兴动物模型的优点和局限性，这些优点和局限性在克罗格（Krogh）原理下，可能对比较基因组学的发展及其在动物科学，生态毒理学，生态生理学，气候变化科学和野生生物保护中的潜在转化应用特别有用，以及机体健康。