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Spatiotemporal transcriptomic atlas reveals the dynamic characteristics and key regulators of planarian regeneration

Author

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  • Guanshen Cui

    (Chinese Academy of Sciences
    China National Center for Bioinformation)

  • Kangning Dong

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Jia-Yi Zhou

    (Chinese Academy of Sciences
    China National Center for Bioinformation)

  • Shang Li

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Ying Wu

    (Chinese Academy of Sciences
    China National Center for Bioinformation)

  • Qinghua Han

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Bofei Yao

    (Chinese Academy of Sciences
    China National Center for Bioinformation)

  • Qunlun Shen

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Yong-Liang Zhao

    (Chinese Academy of Sciences
    China National Center for Bioinformation
    University of Chinese Academy of Sciences)

  • Ying Yang

    (Chinese Academy of Sciences
    China National Center for Bioinformation
    University of Chinese Academy of Sciences
    Chinese Academy of Sciences)

  • Jun Cai

    (Chinese Academy of Sciences
    China National Center for Bioinformation
    University of Chinese Academy of Sciences)

  • Shihua Zhang

    (Chinese Academy of Sciences
    University of Chinese Academy of Sciences
    Chinese Academy of Sciences
    University of Chinese Academy of Sciences)

  • Yun-Gui Yang

    (Chinese Academy of Sciences
    China National Center for Bioinformation
    University of Chinese Academy of Sciences
    Chinese Academy of Sciences)

Abstract

Whole-body regeneration of planarians is a natural wonder but how it occurs remains elusive. It requires coordinated responses from each cell in the remaining tissue with spatial awareness to regenerate new cells and missing body parts. While previous studies identified new genes essential to regeneration, a more efficient screening approach that can identify regeneration-associated genes in the spatial context is needed. Here, we present a comprehensive three-dimensional spatiotemporal transcriptomic landscape of planarian regeneration. We describe a pluripotent neoblast subtype, and show that depletion of its marker gene makes planarians more susceptible to sub-lethal radiation. Furthermore, we identified spatial gene expression modules essential for tissue development. Functional analysis of hub genes in spatial modules, such as plk1, shows their important roles in regeneration. Our three-dimensional transcriptomic atlas provides a powerful tool for deciphering regeneration and identifying homeostasis-related genes, and provides a publicly available online spatiotemporal analysis resource for planarian regeneration research.

Suggested Citation

  • Guanshen Cui & Kangning Dong & Jia-Yi Zhou & Shang Li & Ying Wu & Qinghua Han & Bofei Yao & Qunlun Shen & Yong-Liang Zhao & Ying Yang & Jun Cai & Shihua Zhang & Yun-Gui Yang, 2023. "Spatiotemporal transcriptomic atlas reveals the dynamic characteristics and key regulators of planarian regeneration," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-39016-0
    DOI: 10.1038/s41467-023-39016-0
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    References listed on IDEAS

    as
    1. M. Lucila Scimone & Lauren E. Cote & Peter W. Reddien, 2017. "Orthogonal muscle fibres have different instructive roles in planarian regeneration," Nature, Nature, vol. 551(7682), pages 623-628, November.
    2. Kangning Dong & Shihua Zhang, 2022. "Deciphering spatial domains from spatially resolved transcriptomics with an adaptive graph attention auto-encoder," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
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