A multi-tissue and -breed catalogue of chromatin conformations and their implications in gene regulation in pigs

文献类型： 外文期刊

第一作者： Yin, Hongwei

作者： Yin, Hongwei;Zhao, Qianyi;Yang, Liu;Yi, Guoqiang;Yao, Wenye;Bai, Lijing;Fang, Lingzhao;Yao, Wenye

作者机构：

关键词： Pig; TADs; Gene expression; Biological functions

期刊名称：BMC GENOMICS （ 影响因子：3.7； 五年影响因子：4.2 ）

ISSN： 1471-2164

年卷期： 2025 年 26 卷 1 期

页码：

收录情况： SCI

摘要： BackgroundTopologically associating domains (TADs) are functional units that organize chromosomes into 3D structures of interacting chromatin, and play a crucial role in regulating gene expression by constraining enhancer-promoter contacts. Evidence suggests that deletion of TAD boundaries can lead to aberrant expression of neighboring genes. In our study, we analyzed high-throughput chromatin conformation capture (Hi-C) datasets from publicly available sources, integrating 71 datasets across five tissues in six pig breeds.ResultsOur comprehensive analysis revealed 65,843 TADs in pigs, and we found that TAD boundaries are enriched for expression Quantitative Trait Loci (eQTL), splicing Quantitative Trait Loci (sQTL), Loss-of-Function variants (LoFs), and other regulatory variants. Genes within conserved TADs are associated with fundamental biological functions, while those in dynamic TADs may have tissue-specific roles. Specifically, we observed differential expression of the NCOA2 gene within dynamic TADs. This gene is highly expressed in adipose tissue, where it plays a crucial role in regulating lipid metabolism and maintaining energy homeostasis. Additionally, differential expression of the BMPER gene within dynamic TADs is associated with its role in modulating the activities of bone morphogenetic proteins (BMPs)-critical growth factors involved in bone and cartilage development.ConclusionOur investigations have shed light on the pivotal roles of TADs in governing gene expression and even influencing traits. Our study has unveiled a holistic interplay between chromatin interactions and gene regulation across various tissues and pig breeds. Furthermore, we anticipate that incorporating markers, such as structural variants (SVs), and phenotypes will enhance our understanding of their intricate interactions.

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