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

Yunxia 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 ()
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Yunxia Zhao: Huazhong Agricultural University
Ye Hou: Huazhong Agricultural University
Yueyuan Xu: Huazhong Agricultural University
Yu Luan: Huazhong Agricultural University
Huanhuan Zhou: Huazhong Agricultural University
Xiaolong Qi: Huazhong Agricultural University
Mingyang Hu: Huazhong Agricultural University
Daoyuan Wang: Huazhong Agricultural University
Zhangxu Wang: Huazhong Agricultural University
Yuhua Fu: Huazhong Agricultural University
Jingjin Li: Huazhong Agricultural University
Saixian Zhang: Huazhong Agricultural University
Jianhai Chen: Huazhong Agricultural University
Jianlin Han: Chinese Academy of Agricultural Sciences (CAAS)
Xinyun Li: Huazhong Agricultural University
Shuhong Zhao: Huazhong Agricultural University

Nature Communications, 2021, vol. 12, issue 1, 1-17

Abstract: Abstract Although 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.

Date: 2021
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DOI: 10.1038/s41467-021-22448-x

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