A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome
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...
| Main Authors: | , , , , , , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Springer
2021
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/113497 |
| _version_ | 1855525079094394880 |
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| author | 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 Han Jianlin Xinyun Li Shuhong Zhao |
| author_browse | Daoyuan Wang Han Jianlin Huanhuan Zhou Jianhai Chen Jingjin Li Mingyang Hu Saixian Zhang Shuhong Zhao Xiaolong Qi Xinyun Li Ye Hou Yu Luan Yueyuan Xu Yuhua Fu Yunxia Zhao Zhangxu Wang |
| author_facet | 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 Han Jianlin Xinyun Li Shuhong Zhao |
| author_sort | Yunxia Zhao |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | 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. |
| format | Journal Article |
| id | CGSpace113497 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1134972024-05-01T08:17:20Z 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 Han Jianlin Xinyun Li Shuhong Zhao swine genetics genomes animal breeding 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. 2021-04-13 2021-04-22T19:11:05Z 2021-04-22T19:11:05Z Journal Article https://hdl.handle.net/10568/113497 en Open Access Springer 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. 2021. A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome. Nature Communications 12:2217 |
| spellingShingle | swine genetics genomes animal breeding 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 Han Jianlin Xinyun Li Shuhong Zhao A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome |
| title | A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome |
| title_full | A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome |
| title_fullStr | A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome |
| title_full_unstemmed | A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome |
| title_short | A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome |
| title_sort | compendium and comparative epigenomics analysis of cis regulatory elements in the pig genome |
| topic | swine genetics genomes animal breeding |
| url | https://hdl.handle.net/10568/113497 |
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