Comparative analysis of genome-scale, base-resolution DNA methylation profiles across 580 animal species

We mapped DNA methylation in 580 animal species (535 vertebrates, 45 invertebrates), resulting in 2443 genome-scale, base-resolution DNA methylation profiles of primary tissue samples from various organs. Reference-genome independent analysis of this comprehensive dataset defined a “genomic code” of DNA methylation, which allowed us to predict global and locus-specific DNA methylation from the DNA sequence within and across species. This code appears broadly conserved throughout vertebrate evolution, with two major transitions – once in the first vertebrates and again with the emergence of reptiles. Beyond the central role of species-specific DNA sequence composition, our dataset identified the tissue type and the individual as two main sources of DNA methylation variability within species. Tissue type was the dominant factor in fish, birds, and mammals, while in invertebrates, reptiles, and amphibians both factors were similarly strong. Cross-species comparisons focusing on heart and liver tissues supported a highly conserved role of DNA methylation for tissue type and identity and cross-mapping based promoter methylation analysis revealed divergence at specific genes. In summary, this study establishes a large resource of vertebrate and invertebrate DNA methylomes, it showcases the power of reference-free epigenome analysis in species for which no reference genomes are available, and it contributes an epigenetic perspective to the study of vertebrate evolution.本研究对580个动物物种（其中脊椎动物535种、无脊椎动物45种）的DNA甲基化（DNA methylation）进行了图谱绘制，最终获得了来自不同器官的原代组织样本的2443份基因组规模（genome-scale）、单碱基分辨率（base-resolution）的DNA甲基化谱。通过对该综合数据集开展不依赖参考基因组（reference-genome independent）的分析，本研究定义了DNA甲基化的"基因组编码（genomic code）"，借此可从物种内及跨物种的DNA序列中预测全局及位点特异性的DNA甲基化水平。该编码在脊椎动物演化过程中整体呈现保守性，共经历两次重大转变——首次发生在早期脊椎动物阶段，第二次则伴随爬行动物的出现而产生。除物种特异性DNA序列组成所发挥的核心作用外，本数据集还明确了组织类型与个体差异是物种内DNA甲基化变异的两大主要来源。在鱼类、鸟类与哺乳类中，组织类型是主导性的甲基化变异影响因素；而在无脊椎动物、爬行动物及两栖类中，两类因素的影响强度相当。以心脏与肝脏组织为对象的跨物种比较分析证实，DNA甲基化在调控组织类型与组织特性方面具有高度保守的作用；而基于跨物种比对的启动子甲基化分析则揭示了特定基因的甲基化分化现象。综上，本研究构建了涵盖脊椎动物与无脊椎动物的大规模DNA甲基化组资源，展示了针对无参考基因组物种开展不依赖参考基因组的表观基因组（epigenome）分析的可行性与优势，并为脊椎动物演化研究提供了表观遗传学视角。