Hu Yisi, Yuan Shenli, Du Xin, Liu Jiang, Zhou Wenliang, Wei Fuwen
CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
University of Chinese Academy of Sciences, Beijing 100049, China.
Innovation (Camb). 2023 Apr 28;4(3):100434. doi: 10.1016/j.xinn.2023.100434. eCollection 2023 May 15.
DNA methylation is an epigenetic modification that plays a crucial role in various regulatory processes, including gene expression regulation, transposable element repression, and genomic imprinting. However, most studies on DNA methylation have been conducted in humans and other model species, whereas the dynamics of DNA methylation across mammals remain poorly explored, limiting our understanding of epigenomic evolution in mammals and the evolutionary impacts of conserved and lineage-specific DNA methylation. Here, we generated and gathered comparative epigenomic data from 13 mammalian species, including two marsupial species, to demonstrate that DNA methylation plays critical roles in several aspects of gene evolution and species trait evolution. We found that the species-specific DNA methylation of promoters and noncoding elements correlates with species-specific traits such as body patterning, indicating that DNA methylation might help establish or maintain interspecies differences in gene regulation that shape phenotypes. For a broader view, we investigated the evolutionary histories of 88 known imprinting control regions across mammals to identify their evolutionary origins. By analyzing the features of known and newly identified potential imprints in all studied mammals, we found that genomic imprinting may function in embryonic development through the binding of specific transcription factors. Our findings show that DNA methylation and the complex interaction between the genome and epigenome have a significant impact on mammalian evolution, suggesting that evolutionary epigenomics should be incorporated to develop a unified evolutionary theory.
DNA甲基化是一种表观遗传修饰，在各种调控过程中发挥着关键作用，包括基因表达调控、转座元件抑制和基因组印记。然而，大多数关于DNA甲基化的研究是在人类和其他模式物种中进行的，而哺乳动物中DNA甲基化的动态变化仍未得到充分探索，这限制了我们对哺乳动物表观基因组进化以及保守和谱系特异性DNA甲基化的进化影响的理解。在这里，我们从13种哺乳动物物种（包括两种有袋类物种）中生成并收集了比较表观基因组数据，以证明DNA甲基化在基因进化和物种性状进化的几个方面发挥着关键作用。我们发现启动子和非编码元件的物种特异性DNA甲基化与身体图案等物种特异性性状相关，这表明DNA甲基化可能有助于建立或维持塑造表型的基因调控中的种间差异。为了获得更广泛的视角，我们研究了88个已知的哺乳动物印记控制区域的进化历史，以确定它们的进化起源。通过分析所有研究哺乳动物中已知和新发现的潜在印记的特征，我们发现基因组印记可能通过特定转录因子的结合在胚胎发育中发挥作用。我们的研究结果表明，DNA甲基化以及基因组与表观基因组之间的复杂相互作用对哺乳动物进化有重大影响，这表明进化表观基因组学应被纳入以发展统一的进化理论。
