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

Yongbin Li, Siyu Chen, Weihong Liu, Di Zhao, Yimeng Gao, Shipeng Hu, Hanyu Liu, Yuanyuan Li, Lei Qu and Xiao Liu ()
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Yongbin Li: Capital Normal University
Siyu Chen: Tsinghua University
Weihong Liu: Tsinghua University
Di Zhao: Tsinghua University
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

Nature Communications, 2024, vol. 15, issue 1, 1-19

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-023-42677-6

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