Cross-Species Comparative DNA Methylation Reveals Novel Insights into Complex Trait Genetics among Cattle, Sheep, and Goats

文献类型： 外文期刊

第一作者： Chen, Siqian

作者： Chen, Siqian;Shi, Shaolei;Tang, Yongjie;Zhang, Jinning;Li, Wenlong;Ding, Xiangdong;Wang, Yachun;Liu, Jianfeng;Zhang, Shengli;Yu, Ying;Liu, Shuli;Liu, Shuli;Yin, Hongwei;Liu, Gang;Qu, Kaixing;Fang, Lingzhao

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关键词： DNA hypomethylation; DNA hypermethylation; multitissue transcriptome; epigenetic regulation; GWAS enrichment

期刊名称：MOLECULAR BIOLOGY AND EVOLUTION （ 影响因子：10.7； 五年影响因子：15.1 ）

ISSN： 0737-4038

年卷期： 2024 年 41 卷 2 期

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收录情况： SCI

摘要： The cross-species characterization of evolutionary changes in the functional genome can facilitate the translation of genetic findings across species and the interpretation of the evolutionary basis underlying complex phenotypes. Yet, this has not been fully explored between cattle, sheep, goats, and other mammals. Here, we systematically characterized the evolutionary dynamics of DNA methylation and gene expression in 3 somatic tissues (i.e. brain, liver, and skeletal muscle) and sperm across 7 mammalian species, including 3 ruminant livestock species (cattle, sheep, and goats), humans, pigs, mice, and dogs, by generating and integrating 160 DNA methylation and transcriptomic data sets. We demonstrate dynamic changes of DNA hypomethylated regions and hypermethylated regions in tissue-type manner across cattle, sheep, and goats. Specifically, based on the phylo-epigenetic model of DNA methylome, we identified a total of 25,074 hypomethylated region extension events specific to cattle, which participated in rewiring tissue-specific regulatory network. Furthermore, by integrating genome-wide association studies of 50 cattle traits, we provided novel insights into the genetic and evolutionary basis of complex phenotypes in cattle. Overall, our study provides a valuable resource for exploring the evolutionary dynamics of the functional genome and highlights the importance of cross-species characterization of multiomics data sets for the evolutionary interpretation of complex phenotypes in cattle livestock.

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