Automated profiling of gene function during embryonic development

Cell. 2024 Jun 6;187(12):3141-3160.e23. doi: 10.1016/j.cell.2024.04.012. Epub 2024 May 16.


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.

Keywords: FACT complex; Integrator complex; automated analysis; cell fate specification; computer vision; de novo serine synthesis; embryonic development; energy generation; phenotypic profiling; tissue morphogenesis.

MeSH terms

  • Animals
  • Caenorhabditis elegans Proteins / genetics
  • Caenorhabditis elegans Proteins / metabolism
  • Caenorhabditis elegans* / embryology
  • Caenorhabditis elegans* / genetics
  • Caenorhabditis elegans* / metabolism
  • Embryo, Nonmammalian / metabolism
  • Embryonic Development*
  • Gene Expression Profiling / methods
  • Gene Expression Regulation, Developmental*
  • Gene Knockdown Techniques
  • Phenotype


  • Caenorhabditis elegans Proteins