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A full-body transcription factor expression atlas with completely resolved cell identities in C. elegans

Author

Listed:
  • Yongbin Li

    (Capital Normal University)

  • Siyu Chen

    (Tsinghua University)

  • Weihong Liu

    (Tsinghua University
    Hanwang Technology Co., Ltd)

  • Di Zhao

    (Tsinghua University
    Tianjin University of Sport)

  • Yimeng Gao

    (Capital Normal University)

  • Shipeng Hu

    (Capital Normal University)

  • Hanyu Liu

    (Capital Normal University)

  • Yuanyuan Li

    (Anhui University)

  • Lei Qu

    (Anhui University)

  • Xiao Liu

    (Capital Normal University)

Abstract

Invariant cell lineage in C. elegans enables spatiotemporal resolution of transcriptional regulatory mechanisms controlling the fate of each cell. Here, we develop RAPCAT (Robust-point-matching- And Piecewise-affine-based Cell Annotation Tool) to automate cell identity assignment in three-dimensional image stacks of L1 larvae and profile reporter expression of 620 transcription factors in every cell. Transcription factor profile-based clustering analysis defines 80 cell types distinct from conventional phenotypic cell types and identifies three general phenotypic modalities related to these classifications. First, transcription factors are broadly downregulated in quiescent stage Hermaphrodite Specific Neurons, suggesting stage- and cell type-specific variation in transcriptome size. Second, transcription factor expression is more closely associated with morphology than other phenotypic modalities in different pre- and post-differentiation developmental stages. Finally, embryonic cell lineages can be associated with specific transcription factor expression patterns and functions that persist throughout postembryonic life. This study presents a comprehensive transcription factor atlas for investigation of intra-cell type heterogeneity.

Suggested Citation

  • Yongbin Li & Siyu Chen & Weihong Liu & Di Zhao & Yimeng Gao & Shipeng Hu & Hanyu Liu & Yuanyuan Li & Lei Qu & Xiao Liu, 2024. "A full-body transcription factor expression atlas with completely resolved cell identities in C. elegans," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-023-42677-6
    DOI: 10.1038/s41467-023-42677-6
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    References listed on IDEAS

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