2024-05-23 カリフォルニア大学サンディエゴ校(UCSD)
<関連情報>
- https://today.ucsd.edu/story/new-atlas-provides-unprecedented-insights-on-how-genes-function-in-early-embryo-development
- https://www.cell.com/cell/abstract/S0092-8674(24)00407-0
胚発生過程における遺伝子機能の自動プロファイリング Automated profiling of gene function during embryonic development
Rebecca A. Green,Renat N. Khaliullin,Zhiling Zhao,…,Ronald J. Biggs
Cell Published:May 16, 2024
DOI:https://doi.org/10.1016/j.cell.2024.04.012
Highlights
- 4D imaging of C. elegans embryogenesis documents the effects of 500 gene knockdowns
- Parameterization of temporal feature curves generates numerical signatures for knockdowns
- Comparing knockdown signatures generates ranked lists of genes with similar functions
- Movies, feature curve sets, ranked gene lists, and UMAPs are available in PhenoBank
Summary
Systematic functional profiling of the gene set that directs embryonic development is an important challenge. To tackle this challenge, we used 4D imaging of C. elegans embryogenesis to capture the effects of 500 gene knockdowns and developed an automated approach to compare developmental phenotypes. The automated approach quantifies features—including germ layer cell numbers, tissue position, and tissue shape—to generate temporal curves whose parameterization yields numerical phenotypic signatures. In conjunction with a new similarity metric that operates across phenotypic space, these signatures enabled the generation of ranked lists of genes predicted to have similar functions, accessible in the PhenoBank web portal, for ∼25% of essential development genes. The approach identified new gene and pathway relationships in cell fate specification and morphogenesis and highlighted the utilization of specialized energy generation pathways during embryogenesis. Collectively, the effort establishes the foundation for comprehensive analysis of the gene set that builds a multicellular organism.
Graphical abstract
