Comparative Analysis of Promoters and Enhancers in the Pituitary Glands of the Bama Xiang and Large White Pigs
The epigenetic regulation of gene expression is implicated in complex diseases in humans and various phenotypes in other species. There has been little exploration of regulatory elements in the pig. Here, we performed chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) t...
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doaj-d4ca43a42d54451db0de9157f63b8a292021-07-23T13:42:47ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-07-011210.3389/fgene.2021.697994697994Comparative Analysis of Promoters and Enhancers in the Pituitary Glands of the Bama Xiang and Large White PigsZhimin Zhou0Yaling Zhu1Yaling Zhu2Zhen Zhang3Tao Jiang4Ziqi Ling5Bin Yang6Wanbo Li7Wanbo Li8State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, ChinaState Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, ChinaLaboratory Animal Research Center, School of Basic Medical Sciences, Anhui Medical University, Hefei, ChinaState Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, ChinaState Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, ChinaState Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, ChinaState Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, ChinaState Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, ChinaKey Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, ChinaThe epigenetic regulation of gene expression is implicated in complex diseases in humans and various phenotypes in other species. There has been little exploration of regulatory elements in the pig. Here, we performed chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) to profile histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 27 acetylation (H3K27ac) in the pituitary gland of adult Bama Xiang and Large White pigs, which have divergent evolutionary histories and large phenotypic differences. We identified a total of 65,044 non-redundant regulatory regions, including 23,680 H3K4me3 peaks and 61,791 H3K27ac peaks (12,318 proximal and 49,473 distal), augmenting the catalog of pituitary regulatory elements in pigs. We found 793 H3K4me3 and 3,602 H3K27ac peaks that show differential activity between the two breeds, overlapping with genes involved in the Notch signaling pathway, response to growth hormone (GH), thyroid hormone signaling pathway, and immune system, and enriched for binding motifs of transcription factors (TFs), including JunB, ATF3, FRA1, and BATF. We further identified 2,025 non-redundant super enhancers from H3K27ac ChIP-seq data, among which 302 were shared in all samples of cover genes enriched for biological processes related to pituitary function. This study generated a valuable dataset of H3K4me3 and H3K27ac regions in porcine pituitary glands and revealed H3K4me3 and H3K27ac peaks with differential activity between Bama Xiang and Large White pigs.https://www.frontiersin.org/articles/10.3389/fgene.2021.697994/fullChIP-Seqpituitary glandpigsH3K4me3H3K27acdifferential peak activity |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Zhimin Zhou Yaling Zhu Yaling Zhu Zhen Zhang Tao Jiang Ziqi Ling Bin Yang Wanbo Li Wanbo Li |
spellingShingle |
Zhimin Zhou Yaling Zhu Yaling Zhu Zhen Zhang Tao Jiang Ziqi Ling Bin Yang Wanbo Li Wanbo Li Comparative Analysis of Promoters and Enhancers in the Pituitary Glands of the Bama Xiang and Large White Pigs Frontiers in Genetics ChIP-Seq pituitary gland pigs H3K4me3 H3K27ac differential peak activity |
author_facet |
Zhimin Zhou Yaling Zhu Yaling Zhu Zhen Zhang Tao Jiang Ziqi Ling Bin Yang Wanbo Li Wanbo Li |
author_sort |
Zhimin Zhou |
title |
Comparative Analysis of Promoters and Enhancers in the Pituitary Glands of the Bama Xiang and Large White Pigs |
title_short |
Comparative Analysis of Promoters and Enhancers in the Pituitary Glands of the Bama Xiang and Large White Pigs |
title_full |
Comparative Analysis of Promoters and Enhancers in the Pituitary Glands of the Bama Xiang and Large White Pigs |
title_fullStr |
Comparative Analysis of Promoters and Enhancers in the Pituitary Glands of the Bama Xiang and Large White Pigs |
title_full_unstemmed |
Comparative Analysis of Promoters and Enhancers in the Pituitary Glands of the Bama Xiang and Large White Pigs |
title_sort |
comparative analysis of promoters and enhancers in the pituitary glands of the bama xiang and large white pigs |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Genetics |
issn |
1664-8021 |
publishDate |
2021-07-01 |
description |
The epigenetic regulation of gene expression is implicated in complex diseases in humans and various phenotypes in other species. There has been little exploration of regulatory elements in the pig. Here, we performed chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) to profile histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 27 acetylation (H3K27ac) in the pituitary gland of adult Bama Xiang and Large White pigs, which have divergent evolutionary histories and large phenotypic differences. We identified a total of 65,044 non-redundant regulatory regions, including 23,680 H3K4me3 peaks and 61,791 H3K27ac peaks (12,318 proximal and 49,473 distal), augmenting the catalog of pituitary regulatory elements in pigs. We found 793 H3K4me3 and 3,602 H3K27ac peaks that show differential activity between the two breeds, overlapping with genes involved in the Notch signaling pathway, response to growth hormone (GH), thyroid hormone signaling pathway, and immune system, and enriched for binding motifs of transcription factors (TFs), including JunB, ATF3, FRA1, and BATF. We further identified 2,025 non-redundant super enhancers from H3K27ac ChIP-seq data, among which 302 were shared in all samples of cover genes enriched for biological processes related to pituitary function. This study generated a valuable dataset of H3K4me3 and H3K27ac regions in porcine pituitary glands and revealed H3K4me3 and H3K27ac peaks with differential activity between Bama Xiang and Large White pigs. |
topic |
ChIP-Seq pituitary gland pigs H3K4me3 H3K27ac differential peak activity |
url |
https://www.frontiersin.org/articles/10.3389/fgene.2021.697994/full |
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