Pig genome functional annotation enhances the biological interpretation of complex traits and human disease

文献类型： 外文期刊

第一作者： Pan, Zhangyuan

作者： Pan, Zhangyuan;Wang, Ying;Kern, Colin;Halstead, Michelle;Chanthavixay, Ganrea;Ross, Pablo;Zhou, Huaijun;Yao, Yuelin;Fang, Lingzhao;Yin, Hongwei;Bai, Lijing;Cai, Zexi;Sahana, Goutam;Su, Guosheng;Lund, Mogens SandO;Trakooljul, Nares;Wimmers, Klaus;Fredholm, Merete;Karlskov-Mortensen, Peter;Ernst, Catherine W.;Tuggle, Christopher K.

作者机构：

期刊名称：NATURE COMMUNICATIONS （ 影响因子：14.919； 五年影响因子：15.805 ）

ISSN：

年卷期： 2021 年 12 卷 1 期

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收录情况： SCI

摘要： The functional annotation of livestock genomes is crucial for understanding the molecular mechanisms that underpin complex traits of economic importance, adaptive evolution and comparative genomics. Here, we provide the most comprehensive catalogue to date of regulatory elements in the pig (Sus scrofa) by integrating 223 epigenomic and transcriptomic data sets, representing 14 biologically important tissues. We systematically describe the dynamic epigenetic landscape across tissues by functionally annotating 15 different chromatin states and defining their tissue-specific regulatory activities. We demonstrate that genomic variants associated with complex traits and adaptive evolution in pig are significantly enriched in active promoters and enhancers. Furthermore, we reveal distinct tissue-specific regulatory selection between Asian and European pig domestication processes. Compared with human and mouse epigenomes, we show that porcine regulatory elements are more conserved in DNA sequence, under both rapid and slow evolution, than those under neutral evolution across pig, mouse, and human. Finally, we provide biological insights on tissue-specific regulatory conservation, and by integrating 47 human genome-wide association studies, we demonstrate that, depending on the traits, mouse or pig might be more appropriate biomedical models for different complex traits and diseases. Annotating functional elements of the genome helps the interpretation of genetic variation. Here, the authors compile functional genomics data for the pig genome over 14 tissues with 15 different chromatin states, integrate the data with WGS and GWAS data, and compare conservation of regulatory elements across mouse and human tissues.

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