Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs

文献类型： 外文期刊

第一作者： Wang, Chao

作者： Wang, Chao;Chen, Choulin;Lei, Bowen;Qin, Shenghua;Zhang, Yuanyuan;Li, Kui;Zhang, Song;Liu, Yuwen;Wang, Chao;Chen, Choulin;Lei, Bowen;Qin, Shenghua;Zhang, Yuanyuan;Li, Kui;Zhang, Song;Liu, Yuwen;Wang, Chao;Chen, Choulin;Lei, Bowen;Liu, Yuwen;Wang, Chao;Chen, Choulin;Lei, Bowen;Liu, Yuwen;Zhang, Yuanyuan;Zhang, Yuanyuan;Liu, Yuwen

作者机构：

期刊名称：GENETICS SELECTION EVOLUTION （ 影响因子：4.1； 五年影响因子：4.7 ）

ISSN： 0999-193X

年卷期： 2024 年 56 卷 1 期

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收录情况： SCI

摘要： Background Enhancer RNAs (eRNAs) play a crucial role in transcriptional regulation. While significant progress has been made in understanding epigenetic regulation mediated by eRNAs, research on the construction of eRNA-mediated gene regulatory networks (eGRN) and the identification of critical network components that influence complex traits is lacking.Results Here, employing the pig as a model, we conducted a comprehensive study using H3K27ac histone ChIP-seq and RNA-seq data to construct eRNA expression profiles from multiple tissues of two distinct pig breeds, namely Enshi Black (ES) and Duroc. In addition to revealing the regulatory landscape of eRNAs at the tissue level, we developed an innovative network construction and refinement method by integrating RNA-seq, ChIP-seq, genome-wide association study (GWAS) signals and enhancer-modulating effects of single nucleotide polymorphisms (SNPs) measured by self-transcribing active regulatory region sequencing (STARR-seq) experiments. Using this approach, we unraveled eGRN that significantly influence the growth and development of muscle and fat tissues, and identified several novel genes that affect adipocyte differentiation in a cell line model.Conclusions Our work not only provides novel insights into the genetic basis of economic pig traits, but also offers a generalizable approach to elucidate the eRNA-mediated transcriptional regulation underlying a wide spectrum of complex traits for diverse organisms.

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