数字农科院2.0

Integrative Genomic, Transcriptomic and Epigenomic Analysis Reveals cis-regulatory Contributions to High-Altitude Adaptation in Tibetan Pigs

文献类型： 外文期刊

作者： Dingwang Lai;Xiaolu Qu;Zhen Wang;Sang He;Xingzheng Li;Qi Bao;Guangming Sun;Jian Zhang;Yanbin Zhu;Guoqiang Yi

作者机构：

关键词： （1-1-1）H3K27ac HiChIP;high-Altitude adaptation;lung tissue;multi-omics integration;Tibetan pigs

期刊名称： Molecular Biology and Evolution

ISSN： 0737-4038

年卷期： 2025 年 42 卷 7 期

页码：

收录情况： SCIE（2025版）

摘要： The Qinghai-Tibet Plateau, characterized by its extreme environmental conditions, presents significant challenges to life, making it an ideal region for studying adaptation and evolution. Tibetan pigs, known for their high genetic diversity and exceptional adaptability to high altitudes, serve as excellent models for investigating high-Altitude adaptation. While previous studies have extensively identified genetic determinants associated with high-Altitude adaptation, the molecular mechanisms, particularly cis-regulatory patterns, remain poorly understood. Here, we conducted a selective sweep analysis using 484 genomes from Chinese and Western pig breeds across various altitudes, revealing 38.56 Mb of genomic regions under selection in Tibetan pigs. Enrichment analysis identified the lung as the primary functional tissue involved in high-Altitude adaptation, supported by tissue-specific transcriptional and regulatory patterns observed between Tibetan and Meishan pigs (low altitude). By integrating genomic, RNA-seq, ATAC-seq, and H3K27ac HiChIP data, we constructed comprehensive enhancer-promoter regulatory maps of candidate genes and pinpointed promising genetic determinants associated with high-Altitude adaptation, including SNPs in EPAS1, KLF13, SPRED1, and CFD. These loci were predicted to influence chromatin accessibility and the interactions of regulatory elements, with altered binding strength of relevant transcription factors. Further in vitro experiments confirmed that these loci function as allele-specific enhancers, modulating the expression of target genes. Our findings elucidate the regulatory basis of high-Altitude adaptation in Tibetan pigs and provide valuable insights for exploring hypoxia-related diseases in livestock and humans.

分类号：

  • 相关文献

[1]Post-transcriptional regulation through alternative splicing in the lungs of Tibetan pigs under hypoxia. Yanan Yang,Haonan Yuan,Qiaoli Yang,Yuan Cai,Yue Ren,Yongqing Li,Caixia Gao,Shengguo Zhao. 2022

[2]The Expression Regulatory Network in the Lung Tissue of Tibetan Pigs Provides Insight Into Hypoxia-Sensitive Pathways in High-Altitude Hypoxia. Yanan Yang,Haonan Yuan,Tianliang Yang,Yongqing Li,Caixia Gao,Ting Jiao,Yuan Cai,Shengguo Zhao. 2021

[3]Single-cell omics: A new direction for functional genetic research in human diseases and animal models. Siyuan Kong,Rongrong Li,Yunhan Tian,Yaqiu Zhang,Yuhui Lu,Qiaoer Ou,Peiwen Gao,Kui Li,Yubo Zhang. 2023

[4]Effects of spatial heterogeneity of perfluoroether carboxylic acids in leaves on differential metabolic damage in wheat leaves and the underlying mechanisms. Mei, Jianxiong,Wang, Hao,Liu, Miao,He, Zeying,Liu, Bingjie,Wang, Xuexin,Wang, Jishi,Geng, Yue,Zhang, Yanwei. 2025

[5]Integration of Light and Circadian Signaling in Plant Gene Regulatory Networks: Implications for Photomorphogenesis and Stress Adaptation. Muhammad Mujahid,Alia Ambreen,Yusra Zarlashat,Zareen Sarfraz,Muhammad Sajid Iqbal,Abdul Waheed,Muhammad Shahid Iqbal. 2025

[6]Key Challenges in Plant Microbiome Research in the Next Decade. Ayomide Emmanuel Fadiji,Adegboyega Adeniji,Adedayo Ayodeji Lanrewaju,Afeez Adesina Adedayo,Chinenyenwa Fortune Chukwuneme,Blessing Chidinma Nwachukwu,Joshua Aderibigbe,Iyabo Olunike Omomowo. 2025

[7]Green manure enhances ecological pest management by triggering systemic resistance in rice through reshaped rhizosphere microbiome. Jiaqi Sun,Yangyang Hou,Yueqiu Liu,Lei Zhang,Dianjie Xie,Lin Ma,Jixing Xia,Yue Qi,Jiale You,Thomas W. Sappington,Yuhu Lv,Xingfu Jiang. 2025

[8]Integrated Transcriptomic and Metabolomic Insights into the Molecular Mechanisms of Albino Leaf Formation in Sweetpotato. Dai, Xibin,Li, Yongping,Zhao, Lingxiao,Xiao, Shizhuo,Zhou, Zhilin,Zhang, An,Zhao, Donglan,Yuan, Rui,Wang, Yao,Wang, Jie,Li, Qinglian,Ning, Tong,Zhu, Guopeng,Cao, Qinghe. 2025

[9]Association of novel single-nucleotide polymorphisms of the vascular endothelial growth factor-A gene with high-altitude adaptation in yak (Bos grunniens). Wu, X. Y.,Liang, C. N.,Ding, X. Z.,Guo, X.,Bao, P. J.,Chu, M.,Liu, W. B.,Yan, P.,Wu, X. Y.,Liang, C. N.,Ding, X. Z.,Guo, X.,Bao, P. J.,Chu, M.,Liu, W. B.,Yan, P.. 2013

[10]Chromosome-level genome assemblies of four wild peach species provide insights into genome evolution and genetic basis of stress resistance. Cao, Ke,Peng, Zhen,Zhao, Xing,Li, Yong,Liu, Kuozhan,Arus, Pere,Fang, Weichao,Chen, Changwen,Wang, Xinwei,Wu, Jinlong,Fei, Zhangjun,Wang, Lirong. 2022

[11]Comparative Transcriptome Analysis of Gayal (Bos frontalis), Yak (Bos grunniens), and Cattle (Bos taurus) Reveal the High-Altitude Adaptation. Jun Ma,Tianliu Zhang,Wenxiang Wang,Yan Chen,Wentao Cai,Bo Zhu,Lingyang Xu,Huijiang Gao,Lupei Zhang,Junya Li,Xue Gao. 2022

[12]Genome-Wide Selection Signals Reveal Candidate Genes Associated with Plateau Adaptation in Tibetan Sheep. Yufang Song,Chao Yuan,Xuejiao An,Tingting Guo,Wentao Zhang,Zengkui Lu,Jianbin Liu. 2024

[13]Recent selection and introgression facilitated high-altitude adaptation in cattle. Lyu, Yang,Wang, Fuwen,Cheng, Haijian,Han, Jing,Dang, Ruihua,Xia, Xiaoting,Wang, Hui,Zhong, Jincheng,Lenstra, Johannes A.,Zhang, Hucai,Han, Jianlin,Machugh, David E.,Medugorac, Ivica,Upadhyay, Maulik,Leonard, Alexander S.,Ding, He,Yang, Xiaorui,Wang, Ming-Shan,Quji, Suolang,Zhuzha, Basang,Quzhen, Pubu,Wangmu, Silang,Cangjue, Nima,Wa, Da,Ma, Weidong,Liu, Jianyong,Zhang, Jicai,Huang, Bizhi,Qi, Xingshan,Li, Fuqiang,Huang, Yongzhen,Ma, Yun,Wang, Yu,Gao, Yuanpeng,Lu, Wenfa,Lei, Chuzhao,Chen, Ningbo. 2024

[14]Insight into the meat quality differences of Tibetan sheep from different altitudes based on metabolomics. Ruisi Liu,Jianing Fu,Shaobo Li,Minghui Gu,Liang Li,Le Xu,Jiangying Yu,Dequan Zhang,Li Chen. 2026

[15]Genome-wide selection signal analysis reveals the adaptability of Tibetan sheep to high altitudes. Song, Yufang,Yuan, Chao,Guo, Tingting,Chen, Bowen,Wang, Fan,Lu, Zengkui,Liu, Jianbin. 2025

[16]First report of seroprevalence of swine influenza a virus in Tibetan pigs in Tibet, China. Liu, Guo-Hua,Zhou, Dong-Hui,Cong, Wei,Zhang, Xiao-Xuan,Huang, Si-Yang,Zhu, Xing-Quan,Liu, Guo-Hua,Zhu, Xing-Quan,Shi, Xin-Chun,Danba, Ciren. 2014

[17]Seroprevalence and risk factors associated with Haemophilus parasuis infection in Tibetan pigs in Tibet. Zhang, Nian-Zhang,Zhou, Dong-Hui,Huang, Si-Yang,Wang, Meng,Shi, Xin-Chun,Zhu, Xing-Quan,Shi, Xin-Chun,Ciren, Danba,Zhu, Xing-Quan. 2014

[18]First Report of Chlamydiaceae Seroprevalence in Tibetan Pigs in Tibet, China. Zhang, Nian-Zhang,Zhou, Dong-Hui,Shi, Xin-Chun,Huang, Si-Yang,Wu, Song-Ming,Zhu, Xing-Quan,Shi, Xin-Chun,Ciren, Danba,Zhu, Xing-Quan,Zhu, Xing-Quan. 2013

[19]First Report of Actinobacillus pleuropneumoniae Prevalence in Tibetan Pigs in Tibet, China. Shi, X. C.,Mu, Y.,Shi, X. C.,Zhang, N. Z.,Zhou, D. H.,Xu, M. J.,Wu, S. M.,Zhu, X. Q.,Danba, C.,Ga, G.,Zhu, X. Q.. 2012

[20]Different feeding patterns affect meat quality of Tibetan pigs associated with intestinal microbiota alterations. Yanbin Zhu,Cidan-yangji,Guangming Sun,Chengzeng Luo,Jiujun Duan,Bin Shi,Teng Ma,Shanlong Tang,Ruqing Zhong,Liang Chen,Basang-wangdui,Hongfu Zhang. 2022

作者其他论文 更多>>