Multidimensional regulation of gene expression in the C. elegans embryo
- John Isaac Murray1,
- Thomas J Boyle2,
- Elicia Preston2,
- Dionne Vafeados2,
- Barbara Mericle2,
- Peter Weisdepp2,
- Zhongying Zhao2,
- Zhirong Bao3,
- Max E. Boeck2 and
- Robert Waterston2,4
- 1 University of Pennsylvania School of Medicine;
- 2 University of Washington;
- 3 Sloan-Kettering Institute
- ↵* Corresponding author; email: waterston{at}gs.washington.edu
Abstract
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; 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.
- Received September 13, 2011.
- Accepted April 5, 2012.
- Copyright © 2012, Cold Spring Harbor Laboratory Press
