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A pig BodyMap transcriptome reveals diverse tissue physiologies and evolutionary dynamics of transcription

Author

Listed:
  • Long Jin

    (Sichuan Agricultural University)

  • Qianzi Tang

    (Sichuan Agricultural University)

  • Silu Hu

    (Sichuan Agricultural University)

  • Zhongxu Chen

    (Tcuni Inc.)

  • Xuming Zhou

    (Chinese Academy of Sciences)

  • Bo Zeng

    (Sichuan Agricultural University)

  • Yuhao Wang

    (Sichuan Agricultural University)

  • Mengnan He

    (Sichuan Agricultural University)

  • Yan Li

    (Sichuan Agricultural University)

  • Lixuan Gui

    (Tcuni Inc.)

  • Linyuan Shen

    (Sichuan Agricultural University)

  • Keren Long

    (Sichuan Agricultural University)

  • Jideng Ma

    (Sichuan Agricultural University)

  • Xun Wang

    (Sichuan Agricultural University)

  • Zhengli Chen

    (Sichuan Agricultural University)

  • Yanzhi Jiang

    (Sichuan Agricultural University)

  • Guoqing Tang

    (Sichuan Agricultural University)

  • Li Zhu

    (Sichuan Agricultural University)

  • Fei Liu

    (Sichuan Agricultural University)

  • Bo Zhang

    (Ya’an Digital Economy Operation Company)

  • Zhiqing Huang

    (Sichuan Agricultural University)

  • Guisen Li

    (Sichuan Provincial People’s Hospital)

  • Diyan Li

    (Sichuan Agricultural University)

  • Vadim N. Gladyshev

    (Brigham and Women’s Hospital)

  • Jingdong Yin

    (China Agricultural University)

  • Yiren Gu

    (Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy)

  • Xuewei Li

    (Sichuan Agricultural University)

  • Mingzhou Li

    (Sichuan Agricultural University)

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.

Suggested Citation

  • Long Jin & Qianzi Tang & Silu Hu & Zhongxu Chen & Xuming Zhou & Bo Zeng & Yuhao Wang & Mengnan He & Yan Li & Lixuan Gui & Linyuan Shen & Keren Long & Jideng Ma & Xun Wang & Zhengli Chen & Yanzhi Jiang, 2021. "A pig BodyMap transcriptome reveals diverse tissue physiologies and evolutionary dynamics of transcription," Nature Communications, Nature, vol. 12(1), pages 1-17, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-23560-8
    DOI: 10.1038/s41467-021-23560-8
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    Cited by:

    1. Long Jin & Danyang Wang & Jiaman Zhang & Pengliang Liu & Yujie Wang & Yu Lin & Can Liu & Ziyin Han & Keren Long & Diyan Li & Yu Jiang & Guisen Li & Yu Zhang & Jingyi Bai & Xiaokai Li & Jing Li & Lu Lu, 2023. "Dynamic chromatin architecture of the porcine adipose tissues with weight gain and loss," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    2. Fei Wang & Peiwen Ding & Xue Liang & Xiangning Ding & Camilla Blunk Brandt & Evelina Sjöstedt & Jiacheng Zhu & Saga Bolund & Lijing Zhang & Laura P. M. H. Rooij & Lihua Luo & Yanan Wei & Wandong Zhao , 2022. "Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level," Nature Communications, Nature, vol. 13(1), pages 1-18, December.

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