Identification and Conservation Analysis of Cis-Regulatory Elements in Pig Liver
1
Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
2
The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
*
Authors to whom correspondence should be addressed.
Genes 2019, 10(5), 348; https://doi.org/10.3390/genes10050348
Received: 2 April 2019
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Revised: 29 April 2019
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Accepted: 1 May 2019
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Published: 7 May 2019
(This article belongs to the Section Animal Genetics and Genomics)
The liver plays a key role in metabolism and affects pig production. However, the functional annotation of noncoding regions of the pig liver remains poorly understood. We revealed the landscape of cis-regulatory elements and their functional characterization in pig liver. We identified 102,373 cis-regulatory elements in the pig liver, including enhancers, promoters, super-enhancers, and broad H3K4me3 domains, and highlighted 26 core transcription regulatory factors in the pig liver as well. We found similarity of cis-regulatory elements among those of pigs, humans, and cattle. Despite the low proportion of functionally conserved enhancers (~30%) between pig and human liver tissue, ~78% of the pig liver enhancer orthologues sequence could play an enhancer role in other human tissues. Additionally, we observed that the ratio of consistent super-enhancer-associated genes was significantly higher than the ratio of functionally conserved super-enhancers. Approximately 54% of the core regulation factors driven by super-enhancers were consistent across the liver from these three species. Our pig liver annotation and functional characterization studies provide a system and resource for noncoding annotation for future gene regulatory studies in pigs. Furthermore, our study also showed the high level functional conservation of cis-regulatory elements in mammals; it also improved our understanding of regulation function of mammal cis-regulatory elements.
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Keywords:
cis-regulatory elements; pig liver; conservation
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MDPI and ACS Style
Luan, Y.; Zhang, L.; Hu, M.; Xu, Y.; Hou, Y.; Li, X.; Zhao, S.; Zhao, Y.; Li, C. Identification and Conservation Analysis of Cis-Regulatory Elements in Pig Liver. Genes 2019, 10, 348. https://doi.org/10.3390/genes10050348
AMA Style
Luan Y, Zhang L, Hu M, Xu Y, Hou Y, Li X, Zhao S, Zhao Y, Li C. Identification and Conservation Analysis of Cis-Regulatory Elements in Pig Liver. Genes. 2019; 10(5):348. https://doi.org/10.3390/genes10050348
Chicago/Turabian StyleLuan, Yu, Lu Zhang, Mingyang Hu, Yueyuan Xu, Ye Hou, Xinyun Li, Shuhong Zhao, Yunxia Zhao, and Changchun Li. 2019. "Identification and Conservation Analysis of Cis-Regulatory Elements in Pig Liver" Genes 10, no. 5: 348. https://doi.org/10.3390/genes10050348
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