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Identification and Conservation Analysis of Cis-Regulatory Elements in Pig Liver
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-...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6562536/ https://www.ncbi.nlm.nih.gov/pubmed/31067820 http://dx.doi.org/10.3390/genes10050348 |
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author | Luan, Yu Zhang, Lu Hu, Mingyang Xu, Yueyuan Hou, Ye Li, Xinyun Zhao, Shuhong Zhao, Yunxia Li, Changchun |
author_facet | Luan, Yu Zhang, Lu Hu, Mingyang Xu, Yueyuan Hou, Ye Li, Xinyun Zhao, Shuhong Zhao, Yunxia Li, Changchun |
author_sort | Luan, Yu |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-6562536 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-65625362019-06-17 Identification and Conservation Analysis of Cis-Regulatory Elements in Pig Liver Luan, Yu Zhang, Lu Hu, Mingyang Xu, Yueyuan Hou, Ye Li, Xinyun Zhao, Shuhong Zhao, Yunxia Li, Changchun Genes (Basel) Article 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. MDPI 2019-05-07 /pmc/articles/PMC6562536/ /pubmed/31067820 http://dx.doi.org/10.3390/genes10050348 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Luan, Yu Zhang, Lu Hu, Mingyang Xu, Yueyuan Hou, Ye Li, Xinyun Zhao, Shuhong Zhao, Yunxia Li, Changchun Identification and Conservation Analysis of Cis-Regulatory Elements in Pig Liver |
title | Identification and Conservation Analysis of Cis-Regulatory Elements in Pig Liver |
title_full | Identification and Conservation Analysis of Cis-Regulatory Elements in Pig Liver |
title_fullStr | Identification and Conservation Analysis of Cis-Regulatory Elements in Pig Liver |
title_full_unstemmed | Identification and Conservation Analysis of Cis-Regulatory Elements in Pig Liver |
title_short | Identification and Conservation Analysis of Cis-Regulatory Elements in Pig Liver |
title_sort | identification and conservation analysis of cis-regulatory elements in pig liver |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6562536/ https://www.ncbi.nlm.nih.gov/pubmed/31067820 http://dx.doi.org/10.3390/genes10050348 |
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