Multidimensional regulation of gene expression in the C. elegans embryo

Genome Res. 2012 Jul;22(7):1282-94. doi: 10.1101/gr.131920.111. Epub 2012 Apr 16.


How cells adopt different expression patterns is a fundamental question of developmental biology. We quantitatively measured reporter expression of 127 genes, primarily transcription factors, in every cell and with high temporal resolution in C. elegans embryos. Embryonic cells are highly distinct in their gene expression; expression of the 127 genes studied here can distinguish nearly all pairs of cells, even between cells of the same tissue type. We observed recurrent lineage-regulated expression patterns for many genes in diverse contexts. These patterns are regulated in part by the TCF-LEF transcription factor POP-1. Other genes' reporters exhibited patterns correlated with tissue, position, and left-right asymmetry. Sequential patterns both within tissues and series of sublineages suggest regulatory pathways. Expression patterns often differ between embryonic and larval stages for the same genes, emphasizing the importance of profiling expression in different stages. This work greatly expands the number of genes in each of these categories and provides the first large-scale, digitally based, cellular resolution compendium of gene expression dynamics in live animals. The resulting data sets will be a useful resource for future research.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Body Patterning
  • Caenorhabditis elegans / embryology*
  • Caenorhabditis elegans / genetics*
  • Caenorhabditis elegans / metabolism
  • Caenorhabditis elegans Proteins / genetics
  • Caenorhabditis elegans Proteins / metabolism
  • Cell Division
  • Cell Lineage
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • Embryonic Development
  • Gene Expression Profiling
  • Gene Expression Regulation, Developmental*
  • Genes, Reporter*
  • High Mobility Group Proteins / genetics
  • High Mobility Group Proteins / metabolism
  • Organ Specificity
  • Promoter Regions, Genetic
  • Regulatory Elements, Transcriptional
  • Transcription Factors / genetics
  • Transcription Factors / metabolism


  • Caenorhabditis elegans Proteins
  • DNA-Binding Proteins
  • High Mobility Group Proteins
  • Transcription Factors
  • pop-1 protein, C elegans