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

• Published in: Nature communications Vol. 12; no. 1; p. 2217
• Main Authors: Zhao, Yunxia, Hou, Ye, Xu, Yueyuan, Luan, Yu, Zhou, Huanhuan, Qi, Xiaolong, Hu, Mingyang, Wang, Daoyuan, Wang, Zhangxu, Fu, Yuhua, Li, Jingjin, Zhang, Saixian, Chen, Jianhai, Han, Jianlin, Li, Xinyun, Zhao, Shuhong
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 13.04.2021; Nature Publishing Group; Nature Portfolio
• Subjects: 38; 38/15; 38/23; 38/91; 45; 631/208/177; 631/208/191; Animal models; Animals; Chromatin Immunoprecipitation Sequencing; Conservation; Epigenesis, Genetic; Epigenetics; Epigenomics; Gene Expression; Genetic improvement; Genome; Genome, Human; Genomes; HEK293 Cells; Humanities and Social Sciences; Humans; Meat; Mice; multidisciplinary; Receptors, G-Protein-Coupled - metabolism; Regulatory sequences; Regulatory Sequences, Nucleic Acid; Ribonucleic acid; RNA; RNA-Seq; Science; Science (multidisciplinary); Swine; Swine - genetics; Transcriptome
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-021-22448-x

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. To date, little is known about the regulatory landscape of the pig genome. Here, the authors characterize cis -regulatory elements in the pig genome using RNA-seq, ChIP-Seq and ATAC-seq, finding a higher degree of usage conservation between pig and human than mouse and human.