数字农科院2.0

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

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

作者机构：

关键词： （1-1-1）Biological functions;Gene expression;Pig;TADs

期刊名称： BMC Genomics

ISSN： 1471-2164

年卷期： 2025 年 26 卷 1 期

页码：

收录情况： SCIE（2025版）

摘要： Background: Topologically 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. Results: Our 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. Conclusion: Our 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.

分类号：

  • 相关文献

[1]Cloning and Expression of the Chloroplast Copper/Zinc-Superoxide Dismutase Gene in Upland Cotton （Gossypium hirsutum L.）. Yu Shuxun,Fan Shuli,Song Meizhen. 2007

[2]Expression of the insulin-like growth factor system in skeletal muscle during embryonic and postnatal development in the first filial generation pigs from Erhualian and Yorkshire reciprocal crosses. Wang, Lijuan,Lin, Fei,Jiang, Baochun,Dong, Fulu,Liu, Honglin,Zhang, Guangmin. 2011

[3]Molecular characterization of the BTG2 and BTG3 genes in fetal muscle development of pigs. Feng, Zheng,Tang, Zhong-Lin,Li, Kui,Liu, Bang,Yu, Mei,Zhao, Shu-Hong. 2007

[4]Oral MSG administration alters hepatic expression of genes for lipid and nitrogen metabolism in suckling piglets. Chen, Gang,Zhang, Jun,Zhang, Yuzhe,Liao, Peng,Li, Tiejun,Yin, Yulong,Chen, Gang,Chen, Lixiang,Wang, Jinquan,Wu, Guoyao,Wu, Guoyao.

[5]Mapping and functional characterization of structural variation in 1060 pig genomes. Liu Yang,Hongwei Yin,Lijing Bai,Wenye Yao,Tan Tao,Qianyi Zhao,Yahui Gao,Jinyan Teng,Zhiting Xu,Qing Lin,Shuqi Diao,Zhangyuan Pan,Dailu Guan,Bingjie Li,Huaijun Zhou,Zhongyin Zhou,Fuping Zhao,Qishan Wang,Yuchun Pan,Zhe Zhang,Kui Li,Lingzhao Fang,George E. Liu. 2024

[6]cis-Regulatory variation affecting gene expression contributes to the improvement of maize kernel size. Li Y.-X., Lu J., He C., Wu X., Cui Y., Chen L., Zhang J., Xie Y., An Y., Liu X., Zhen S., Liu Y., Li C., Zhang D., Shi Y.-S., Song Y., Wang J., Li Y., Wang G., Fu J., Wang T.. 2022

[7]Individual-breed assignment analysis in swine populations by using microsatellite markers. Fan, B,Chen, YZ,Moran, C,Zhao, SH,Liu, B,Yu, M,Zhu, MJ,Xiong, TA,Lil, K. 2005

[8]Genome-Wide Association Study for Certain Carcass Traits and Organ Weights in a Large WhitexMinzhu Intercross Porcine Population. Liu Xin,Wang Li-gang,Liang Jing,Yan Hua,Zhao Ke-bin,Li Na,Zhang Long-chao,Wang Li-xian,Li Na. 2014

[9]Molecular characterization and association analysis of FBXO40 with partial hematological indexes in pig. Wang, Z. W.,Li, X. Y.,Tang, Z. L.,Yang, S. L.,Ying, Z. Z.,Fu, T.,Mu, Y. L.,Ao, H.,Li, K.,Wang, Z. W.,Li, X. Y.,Ying, Z. Z.,Fu, T.,Fan, B.. 2010

[10]The microRNA expression profile in porcine skeletal muscle is changed by constant heat stress. Hao, Y.,Liu, J. R.,Yang, P. G.,Feng, Y. J.,Cui, Y. J.,Yang, C. H.,Gu, X. H.,Liu, J. R.,Zhang, Y..

[11]Porcine LEM domain-containing 3: Molecular cloning, functional characterization, and polymorphism associated with ear size. Liang Jing,Li Na,Zhang Long-chao,Wang Li-gang,Liu Xin,Zhao Ka-bin,Yan Hua,Pu Lei,Zhang Yue-bo,Shi Hui-bi,Wang Li-xian,Li Na,Zhang Qin. 2016

[12]Genetic Variation of EPAS1 Gene in Tibetan Pigs and Three Low-Altitude Pig Breeds in China. Dong Kun-zhe,Yao Na,Shu Guo-tao,Zhao Qian-jun,Ma Yue-hui,Kang Ye,Zuo Qing-qing. 2014

[13]Effect of Graded Levels of Fiber from Alfalfa Meal on Nutrient Digestibility and Flow of Fattening Pigs. Chen Liang,Gao Li-xiang,Zhang Hong-fu. 2014

[14]Seroprevalence and genotypes of Toxoplasma gondii isolated from pigs intended for human consumption in Liaoning province, northeastern China. Wang, Dawei,Zhang, Guoxin,Yuan, Gaoming,He, Jianbin,Yang, Na,Liu, Yan,Jiang, Tiantian,Su, Chunlei. 2016

[15]Chromosome Mapping, Expression and Polymorphism Analysis of CRABP1 Gene in Pigs. Zhao Shuan-ping,Tang Zhong-lin,Zhou Rong,Li Kui,Zheng Jian-wei,Qu Chang-qing,Zhao Shuan-ping. 2014

[16]Effect of graded levels of fiber from alfalfa meal on apparent and standardized ileal digestibility of amino acids of growing pigs. Chen Liang,Gao Li-xiang,Liu Li,Ding Ze-ming,Zhang Hong-fu,Chen Liang. 2015

[17]Effect of graded levels of fiber from alfalfa meal on intestinal nutrient and energy flow, and hindgut fermentation in growing pigs. Chen, L.,Zhang, H. F.,Gao, L. X.,Zhao, F.,Lu, Q. P.,Sa, R. N.. 2013

[18]Effects of Long-Term Protein Restriction on Meat Quality, Muscle Amino Acids, and Amino Acid Transporters in Pigs. Yin, Jie,Li, Yuying,Zhu, Xiaotong,Han, Hui,Ren, Wenkai,Chen, Shuai,Bin, Peng,Liu, Gang,Li, Tiejun,Yin, Yulong,Yin, Jie,Li, Yuying,Zhu, Xiaotong,Han, Hui,Ren, Wenkai,Chen, Shuai,Bin, Peng,Liu, Gang,Li, Tiejun,Yin, Yulong,Yin, Jie,Li, Yuying,Zhu, Xiaotong,Han, Hui,Ren, Wenkai,Chen, Shuai,Bin, Peng,Liu, Gang,Li, Tiejun,Yin, Yulong,Yin, Jie,Li, Yuying,Zhu, Xiaotong,Han, Hui,Ren, Wenkai,Chen, Shuai,Bin, Peng,Liu, Gang,Li, Tiejun,Yin, Yulong,Yin, Jie,Li, Yuying,Han, Hui,Ren, Wenkai,Chen, Shuai,Bin, Peng,Huang, Xingguo,Fang, Rejun,Huang, Xingguo,Fang, Rejun,Li, Tiejun,Yin, Yulong,Wang, Bin,Wang, Kai,Sun, Liping.

[19]Timing of The First Zygotic Cleavage as a Developmental Potential Marker for Porcine Cloned Embryos. Luo Xue-Ming,Feng Chong,Long Chuan,Yan Jun,Pan Deng-Ke,Xiao Wei,Xue Zhen-Hua,Yun Peng. 2010

[20]Genome-wide profiling of Sus scrofa circular RNAs across nine organs and three developmental stages. Liang, Guoming,Yang, Yalan,Niu, Guanglin,Tang, Zhonglin,Li, Kui,Liang, Guoming,Yang, Yalan,Tang, Zhonglin,Li, Kui,Liang, Guoming,Yang, Yalan,Tang, Zhonglin.

作者其他论文 更多>>