A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome

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dc.creatorYunxia Zhao
dc.creatorYe Hou
dc.creatorYueyuan Xu
dc.creatorYu Luan
dc.creatorHuanhuan Zhou
dc.creatorXiaolong Qi
dc.creatorMingyang Hu
dc.creatorDaoyuan Wang
dc.creatorZhangxu Wang
dc.creatorYuhua Fu
dc.creatorJingjin Li
dc.creatorSaixian Zhang
dc.creatorJianhai Chen
dc.creatorHan Jianlin
dc.creatorXinyun Li
dc.creatorShuhong Zhao
dc.date2021-04-13
dc.date2021-04-22T19:11:05Z
dc.date2021-04-22T19:11:05Z
dc.date.accessioned2026-06-27T16:49:24Z
dc.descriptionAlthough major advances in genomics have initiated an exciting new era of research, a lack of information regarding cis-regulatory elements has limited the genetic improvement or manipulation of pigs as a meat source and biomedical model. Here, we systematically characterize cis-regulatory elements and their functions in 12 diverse tissues from four pig breeds by adopting similar strategies as the ENCODE and Roadmap Epigenomics projects, which include RNA-seq, ATAC-seq, and ChIP-seq. In total, we generate 199 datasets and identify more than 220,000 cis-regulatory elements in the pig genome. Surprisingly, we find higher conservation of cis-regulatory elements between human and pig genomes than those between human and mouse genomes. Furthermore, the differences of topologically associating domains between the pig and human genomes are associated with morphological evolution of the head and face. Beyond generating a major new benchmark resource for pig epigenetics, our study provides basic comparative epigenetic data relevant to using pigs as models in human biomedical research.
dc.identifierhttps://hdl.handle.net/10568/113497
dc.identifier.urihttp://hdl.handle.net/123456789/134189
dc.languageen
dc.publisherSpringer
dc.rightsOpen Access
dc.sourceYunxia Zhao, Ye Hou, Yueyuan Xu, Yu Luan, Huanhuan Zhou, Xiaolong Qi, Mingyang Hu, Daoyuan Wang, Zhangxu Wang, Yuhua Fu, Jingjin Li, Saixian Zhang, Jianhai Chen, Jianlin Han, Xinyun Li and Shuhong Zhao. 2021. A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome. Nature Communications 12:2217
dc.subjectswine
dc.subjectgenetics
dc.subjectgenomes
dc.subjectanimal breeding
dc.titleA compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome
dc.typeJournal Article

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Instituto Internacional de Investigaciones Pecuarias (ILRI)