1. A pig BodyMap transcriptome reveals diverse tissue physiologies and evolutionary dynamics of transcription
- Author
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Mengnan He, Zhongxu Chen, Zhiqing Huang, Jingdong Yin, Zhengli Chen, Yan Li, Bo Zeng, Yuhao Wang, Yiren Gu, Vadim N. Gladyshev, Diyan Li, Lixuan Gui, Qianzi Tang, Xuewei Li, Silu Hu, Jideng Ma, Guisen Li, Xun Wang, Mingzhou Li, Linyuan Shen, Fei Liu, Keren Long, Xuming Zhou, Bo Zhang, Long Jin, Li Zhu, Guoqing Tang, and Yanzhi Jiang
- Subjects
0301 basic medicine ,Swine ,Transcriptional regulatory elements ,Molecular Conformation ,Gene regulatory network ,General Physics and Astronomy ,Transcriptome ,0302 clinical medicine ,Myofibrils ,Gene Regulatory Networks ,Promoter Regions, Genetic ,Phylogeny ,Multidisciplinary ,Biological Evolution ,Mitochondria ,Experimental models of disease ,Enhancer Elements, Genetic ,Adipose Tissue ,miRNAs ,RNA, Long Noncoding ,Science ,Computational biology ,Biology ,Article ,General Biochemistry, Genetics and Molecular Biology ,Cell Line ,Evolution, Molecular ,03 medical and health sciences ,Phylogenetics ,Animals ,Cell Lineage ,RNA, Messenger ,Muscle, Skeletal ,Evolutionary dynamics ,Enhancer ,Gene ,Cell Nucleus ,Spatial Analysis ,Gene Expression Profiling ,Robustness (evolution) ,RNA, Circular ,General Chemistry ,Gene expression profiling ,Alternative Splicing ,MicroRNAs ,030104 developmental biology ,Long non-coding RNAs ,Gene expression ,030217 neurology & neurosurgery - Abstract
A comprehensive transcriptomic survey of pigs can provide a mechanistic understanding of tissue specialization processes underlying economically valuable traits and accelerate their use as a biomedical model. Here we characterize four transcript types (lncRNAs, TUCPs, miRNAs, and circRNAs) and protein-coding genes in 31 adult pig tissues and two cell lines. We uncover the transcriptomic variability among 47 skeletal muscles, and six adipose depots linked to their different origins, metabolism, cell composition, physical activity, and mitochondrial pathways. We perform comparative analysis of the transcriptomes of seven tissues from pigs and nine other vertebrates to reveal that evolutionary divergence in transcription potentially contributes to lineage-specific biology. Long-range promoter–enhancer interaction analysis in subcutaneous adipose tissues across species suggests evolutionarily stable transcription patterns likely attributable to redundant enhancers buffering gene expression patterns against perturbations, thereby conferring robustness during speciation. This study can facilitate adoption of the pig as a biomedical model for human biology and disease and uncovers the molecular bases of valuable traits., A comprehensive transcriptomic survey of the pig could enable mechanistic understanding of tissue specialization and accelerate its use as a biomedical model. Here the authors characterize four distinct transcript types in 31 adult pig tissues to dissect their distinct structural and transcriptional features and uncover transcriptomic variability related to tissue physiology.
- Published
- 2021