Multidimensional regulation of gene expression in the C. elegans embryo

John Isaac Murray, Thomas J. Boyle, Elicia Preston, Dionne Vafeados, Barbara Mericle, Peter Weisdepp, Zhongying ZHAO, Zhirong Bao, Max Boeck, Robert H. Waterston*

*Corresponding author for this work

Research output: Contribution to journalJournal articlepeer-review

106 Citations (Scopus)


How cells adopt different expression patterns is a fundamental question of developmental biology. We quantitativelymeasured 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 correlatedwith 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.

Original languageEnglish
Pages (from-to)1282-1294
Number of pages13
JournalGenome Research
Issue number7
Publication statusPublished - Jul 2012

Scopus Subject Areas

  • Genetics
  • Genetics(clinical)


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