ChIP-Seq; H3K27ac; RNA-Seq; XIST; complex traits; pig; Biochemistry, Genetics and Molecular Biology (all); Environmental Science (all); Agricultural and Biological Sciences (all); General Agricultural and Biological Sciences; General Environmental Science; General Biochemistry, Genetics and Molecular Biology
Abstract :
[en] The limited knowledge of genomic noncoding and regulatory regions has restricted our ability to decipher the genetic mechanisms underlying complex traits in pigs. In this study, we characterized the spatiotemporal landscape of putative enhancers and promoters and their target genes by combining H3K27ac-targeted ChIP-Seq and RNA-Seq in fetal (prenatal days 74-75) and adult (postnatal days 132-150) tissues (brain, liver, heart, muscle and small intestine) sampled from Asian aboriginal Bama Xiang and European highly selected Large White pigs of both sexes. We identified 101,290 H3K27ac peaks, marking 18,521 promoters and 82,769 enhancers, including peaks that were active across all tissues and developmental stages (which could indicate safe harbor locus for exogenous gene insertion) and tissue- and developmental stage-specific peaks (which regulate gene pathways matching tissue- and developmental stage-specific physiological functions). We found that H3K27ac and DNA methylation in the promoter region of the XIST gene may be involved in X chromosome inactivation and demonstrated the utility of the present resource for revealing the regulatory patterns of known causal genes and prioritizing candidate causal variants for complex traits in pigs. In addition, we identified an average of 1,124 super-enhancers per sample and found that they were more likely to show tissue-specific activity than ordinary peaks. We have developed a web browser to improve the accessibility of the results ( http://segtp.jxau.edu.cn/pencode/?genome=susScr11 ).
Disciplines :
Genetics & genetic processes
Author, co-author :
Zhu, Yaling; State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China ; Laboratory Animal Research Center, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China
Zhou, Zhimin; State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China ; Laboratory Animal Research Center, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, China
Huang, Tao; State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
Zhang, Zhen; State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
Li, Wanbo; State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
Ling, Ziqi; State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
Jiang, Tao; State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
Yang, Jiawen; State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
Yang, Siyu; State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
Xiao, Yanyuan; State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
Charlier, Carole ; Université de Liège - ULiège > GIGA > GIGA Medical Genomics - Unit of Animal Genomics ; State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
Georges, Michel ; Université de Liège - ULiège > GIGA > GIGA Cardiovascular Sciences - Molecular Biomimetic and Protein Engineering Laboratory ; State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
Yang, Bin; State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China. binyang@live.cn
Huang, Lusheng; State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China. lushenghuang@hotmail.com
This work was supported by the National Natural Science Foundation of China (31790413 and 31760657). We are grateful to colleagues in State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University for sample collection.
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