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A proteomics landscape of circadian clock in mouse liver

Author

Listed:
  • Yunzhi Wang

    (Fudan University)

  • Lei Song

    (Tsinghua University)

  • Mingwei Liu

    (National Center for Protein Sciences)

  • Rui Ge

    (Fudan University)

  • Quan Zhou

    (National Center for Protein Sciences)

  • Wanlin Liu

    (National Center for Protein Sciences)

  • Ruiyang Li

    (Fudan University)

  • Jingbo Qie

    (Fudan University)

  • Bei Zhen

    (National Center for Protein Sciences)

  • Yi Wang

    (National Center for Protein Sciences
    Baylor College of Medicine)

  • Fuchu He

    (Fudan University
    Tsinghua University
    National Center for Protein Sciences)

  • Jun Qin

    (Fudan University
    National Center for Protein Sciences
    Baylor College of Medicine)

  • Chen Ding

    (Fudan University)

Abstract

As a circadian organ, liver executes diverse functions in different phase of the circadian clock. This process is believed to be driven by a transcription program. Here, we present a transcription factor (TF) DNA-binding activity-centered multi-dimensional proteomics landscape of the mouse liver, which includes DNA-binding profiles of different TFs, phosphorylation, and ubiquitylation patterns, the nuclear sub-proteome, the whole proteome as well as the transcriptome, to portray the hierarchical circadian clock network of this tissue. The TF DNA-binding activity indicates diurnal oscillation in four major pathways, namely the immune response, glucose metabolism, fatty acid metabolism, and the cell cycle. We also isolate the mouse liver Kupffer cells and measure their proteomes during the circadian cycle to reveal a cell-type resolved circadian clock. These comprehensive data sets provide a rich data resource for the understanding of mouse hepatic physiology around the circadian clock.

Suggested Citation

  • Yunzhi Wang & Lei Song & Mingwei Liu & Rui Ge & Quan Zhou & Wanlin Liu & Ruiyang Li & Jingbo Qie & Bei Zhen & Yi Wang & Fuchu He & Jun Qin & Chen Ding, 2018. "A proteomics landscape of circadian clock in mouse liver," Nature Communications, Nature, vol. 9(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-03898-2
    DOI: 10.1038/s41467-018-03898-2
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    Cited by:

    1. Jiyeon Lee & Julie M. Dimitry & Jong Hee Song & Minsoo Son & Patrick W. Sheehan & Melvin W. King & G. Travis Tabor & Young Ah Goo & Mitchell A. Lazar & Leonard Petrucelli & Erik S. Musiek, 2023. "Microglial REV-ERBĪ± regulates inflammation and lipid droplet formation to drive tauopathy in male mice," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    2. Hao A. Duong & Kenkichi Baba & Jason P. DeBruyne & Alec J. Davidson & Christopher Ehlen & Michael Powell & Gianluca Tosini, 2024. "Environmental circadian disruption re-writes liver circadian proteomes," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    3. Rongfeng Huang & Jianghui Chen & Meiyu Zhou & Haoran Xin & Sin Man Lam & Xiaoqing Jiang & Jie Li & Fang Deng & Guanghou Shui & Zhihui Zhang & Min-Dian Li, 2023. "Multi-omics profiling reveals rhythmic liver function shaped by meal timing," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    4. Ke Shui & Chenwei Wang & Xuedi Zhang & Shanshan Ma & Qinyu Li & Wanshan Ning & Weizhi Zhang & Miaomiao Chen & Di Peng & Hui Hu & Zheng Fang & Anyuan Guo & Guanjun Gao & Mingliang Ye & Luoying Zhang & , 2023. "Small-sample learning reveals propionylation in determining global protein homeostasis," Nature Communications, Nature, vol. 14(1), pages 1-23, December.

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