1. Automated profiling of gene function during embryonic development.
- Author
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Green RA, Khaliullin RN, Zhao Z, Ochoa SD, Hendel JM, Chow TL, Moon H, Biggs RJ, Desai A, and Oegema K
- Subjects
- Animals, Caenorhabditis elegans Proteins metabolism, Caenorhabditis elegans Proteins genetics, Embryo, Nonmammalian metabolism, Gene Expression Profiling methods, Gene Knockdown Techniques, Phenotype, Caenorhabditis elegans embryology, Caenorhabditis elegans genetics, Caenorhabditis elegans metabolism, Embryonic Development, Gene Expression Regulation, Developmental
- Abstract
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., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 Elsevier Inc. All rights reserved.)
- Published
- 2024
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