Multi-omics analysis reveals critical cis-regulatory roles of transposable elements in livestock genomes
文献类型： 外文期刊
作者： Wang, Chao 1 ; Lei, Bowen 1 ; Bao, Yongzhou 1 ; Wang, Zhen 1 ; Chen, Choulin 1 ; Zhang, Yuanyuan 1 ; Qin, Shenghua 1 ; Sun, Tao 1 ; Tang, Zhonglin 1 ; Liu, Yuwen 1 ;
作者机构： 1.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Shenzhen Branch, Guangdong Lab Lingnan Modern Agr,Key Lab Livestock, Shenzhen 518124, Peoples R China
2.Huazhong Agr Univ, Key Lab Agr Anim Genet Breeding & Reprod, Minist Educ, Wuhan 430070, Peoples R China
3.Huazhong Agr Univ, Key Lab Swine Genet & Breeding, Minist Agr & Rural Affairs, Wuhan 430070, Peoples R China
4.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Res Ctr Anim Genome, Innovat Grp Pig Genome Design & Breeding, Shenzhen 518124, Peoples R China
5.Henan Univ, Sch Life Sci, Kaifeng 475004, Peoples R China
6.Henan Univ, Shenzhen Res Inst, Shenzhen 518000, Peoples R China
7.Chinese Acad Agr Sci, Kunpeng Inst Modern Agr Foshan, Foshan 528226, Peoples R China
关键词： Highlights; Animals; Genomic analysis; Molecular
期刊名称：ISCIENCE （ 影响因子：4.1； 五年影响因子：4.7 ）
ISSN：
年卷期： 2025 年 28 卷 3 期
页码：
收录情况： SCI
摘要： Transposable elements (TEs) are important sources of genetic and regulatory variation, yet their functional roles in domesticated animals remain insufficiently explored. To address this gap, we comprehensively annotated TE types, ages, and distributions in the genomes of pig (Sus scrofa), cattle (Bos taurus), and chicken (Gallus gallus). Our analysis revealed species-specific patterns in TE abundance, amplification, and activity in modern genomes. By integrating transcriptomic and epigenomic data, we explored the impact of specific TE types on cis-regulatory elements (CREs) and constructed a TE expression atlas across five tissues in all three species. Our findings underscored the critical roles of tissue-specific TE expression and chromatin accessibility in regulating tissue-specific biological processes. Most notably, we developed a computational framework to uncover TE-mediated gene regulatory networks (TE-GRNs). Our findings provide valuable insights into the regulatory functions of TEs in livestock and offer a robust approach for studying TE-GRNs in diverse biological contexts.
- 相关文献
作者其他论文 更多>>
-
Role of ultrasound and pectin in regulating the foaming properties and baking applications of liquid egg white
作者：Ali, Sadaqat;Jin, Haobo;Yang, Yaqin;Zhang, Yuanyuan;Wang, Yanli;Li, Erjiao;Fan, Xiang;Song, Yanbin;Sun, Yunxin;Cai, Zhaoxia;Sheng, Long;Ali, Sadaqat;Cai, Zhaoxia;Sheng, Long;Ali, Sadaqat;Cai, Zhaoxia;Sheng, Long
关键词：Liquid egg white; Pectin; Ultrasound
-
Uncovering Molecular Mechanisms of Feed Efficiency in Pigs Through Multi-Omics Analysis of the Jejunum
作者：Zhang, Saixian;Qi, Xiaolong;Li, Jingjin;Liu, Yuwen;Zhang, Saixian;Xiang, Yue;Jian, Yaobang;Zhao, Qiulin;Sun, Jiahui;Huang, Yi;Xu, Jing;Zheng, Zhuqing;Fu, Liangliang;Li, Xinyun;Zhang, Saixian;Xiang, Yue;Jian, Yaobang;Zhao, Qiulin;Sun, Jiahui;Huang, Yi;Xu, Jing;Zheng, Zhuqing;Fu, Liangliang;Li, Xinyun
关键词：feed efficiency; pigs; jejunum; RNA-seq; ATAC-seq; lipid metabolism; immune response
-
Oocytes maintain low ROS levels to support the dormancy of primordial follicles
作者：Qin, Shaogang;Chi, Xinyue;Zhu, Zijian;Gao, Meng;Zhao, Ting;Zhang, Jingwen;Zheng, Wenying;Chen, Ziqi;Zhou, Bo;Xia, Guoliang;Wang, Chao;Chen, Chuanhe;Zhang, Tuo;He, Meina;Zhang, Lifan;Wang, Wenji
关键词：ferroptosis; primary ovarian insufficiency; primordial follicle; ROS; SOD1
-
Pre-Season Precipitation and Temperature Have a Larger Influence on Vegetation Productivity than That of the Growing Season in the Agro-Pastoral Ecotone in Northern China
作者：Zhang, Yuanyuan;Wang, Qingtao;Zhang, Yuanyuan;Ma, Changhui;He, Lei;Zhang, Xueyuan;He, Lei;Zhang, Xueyuan;Guo, Zecheng;Guo, Xiaonan;Wei, Baocheng
关键词：vegetation productivity; climate change; land cover change; precipitation patterns; pre-season climate; APENC
-
Systemic factors associated with antler growth promote complete wound healing
作者：Guo, Qianqian;Zhang, Guokun;Ren, Jing;Li, Jiping;Wang, Zhen;Ba, Hengxing;Ye, Zihao;Li, Chunyi;Guo, Qianqian;Zheng, Junjun;Wang, Ying
关键词：
-
Disturbing egg yolk protein structure via pH-shifting treatment for interface reorganization: Improving solubility to enhance oil-water interface adsorption and emulsification properties
作者：Yang, Yaqin;Jin, Haobo;Chen, Bao;Zhang, Yuanyuan;Cai, Zhaoxia;Sheng, Long;Yang, Yaqin;Cai, Zhaoxia;Sheng, Long;Yang, Yaqin;Cai, Zhaoxia;Sheng, Long
关键词：Egg yolk protein; pH-shifting; Oil-water interface; Protein conformation; Emulsifying properties
-
An efficient allotriploid-mediated system of generating genomic introgression from Brassica oleracea to B. rapa
作者：Gu, Aixia;Li, Xiaomin;Wang, Zengfeng;Wang, Yanhua;Xuan, Shuxin;Ma, Wei;Hong, Yiguo;Zhao, Yalei;Chen, Xueping;Luo, Shuangxia;Liu, Yuanming;Liu, Shengyi;Zhao, Jianjun;Shen, Shuxing;Li, Xiaomin;Wang, Zengfeng;Liu, Shengyi;Zhang, Yuanyuan
关键词：allotriploid; Brassica crops; genome introgression; homoeologous recombination; interspecific hybridization; trait variation
