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

• Published in: Nature communications 2024-01, Vol.15 (1), p.358-19, Article 358
• Main Authors: Li, Yongbin, Chen, Siyu, Liu, Weihong, Zhao, Di, Gao, Yimeng, Hu, Shipeng, Liu, Hanyu, Li, Yuanyuan, Qu, Lei, Liu, Xiao
• Format: Article
• Language: English
• Subjects: 13/89; 14/19; 38/35; 42/44; 49/39; 631/136/142; 631/1647/245; 631/208/191; 631/208/200; 631/337/2019; 64/11; Animals; Annotations; Ascomycota; Automation; Caenorhabditis elegans - genetics; Cell differentiation; Cell Differentiation - genetics; Cell lineage; Cluster analysis; Clustering; Developmental stages; Gene Expression Regulation; Hermaphrodites; Heterogeneity; Humanities and Social Sciences; Invariants; Larvae; multidisciplinary; Regulatory mechanisms (biology); Science; Science (multidisciplinary); Transcription factors; Transcription Factors - genetics; Transcriptomes
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-023-42677-6

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. Invariant cell lineage in C. elegans enables the analysis of transcriptional regulatory mechanisms controlling the fate of each cell at spatiotemporal resolution. Here, the authors develop a tool automating C. elegans cell identification and create an expression atlas of 620 transcription factors.