ArticlePLoS biology2004
Whole-genome analysis of temporal gene expression during foregut development.
Article in PLoS biology, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed.
- PHA-4/FoxA controls the function of pharyngeal and extrapharyngeal enteric neurons inGenes & development · 2026Article
- PHA-4/FoxA controls the function of pharyngeal and extrapharyngeal enteric neurons ofbioRxiv : the preprint server for biology · 2025Article
- Unconventional Myosins fromBiomolecules · 2022Review
- The emergent role of mitochondrial surveillance in cellular health.Aging cell · 2022Review
- Feedforward regulatory logic controls the specification-to-differentiation transition and terminal cell fate during Caenorhabditis elegans endoderm development.Development (Cambridge, England) · 2022Article
- Evolutionary Dynamics of the SKN-1 → MED → END-1,3 Regulatory Gene Cascade inG3 (Bethesda, Md.) · 2020Article
- Reduction of mRNA export unmasks different tissue sensitivities to low mRNA levels during Caenorhabditis elegans development.PLoS genetics · 2019Article
- Genome-wide discovery of active regulatory elements and transcription factor footprints inGenome research · 2017Article
- Temporal regulation of epithelium formation mediated by FoxA, MKLP1, MgcRacGAP, and PAR-6.Molecular biology of the cell · 2017Article
- A conserved mitochondrial surveillance pathway is required for defense against Pseudomonas aeruginosa.PLoS genetics · 2017Article
- Tissue enrichment analysis for C. elegans genomics.BMC bioinformatics · 2016Article
- Overlapping cell population expression profiling and regulatory inference in C. elegans.BMC genomics · 2016Article
- TGF-β signaling can act from multiple tissues to regulate C. elegans body size.BMC developmental biology · 2014Article
- Distinct DNA binding sites contribute to the TCF transcriptional switch in C. elegans and Drosophila.PLoS genetics · 2014Article
- Cell interactions and patterned intercalations shape and link epithelial tubes in C. elegans.PLoS genetics · 2013Article
- Conserved Motifs and Prediction of Regulatory Modules in Caenorhabditis elegans.G3 (Bethesda, Md.) · 2012Article
- Contribution of transcription factor binding site motif variants to condition-specific gene expression patterns in budding yeast.PloS one · 2012Article
- Trachealess (Trh) regulates all tracheal genes during Drosophila embryogenesis.Developmental biology · 2011Article
- Seeing elegance in gene regulatory networks of the worm.Current opinion in genetics & development · 2011Review
- Temporal coordination of gene networks by Zelda in the early Drosophila embryo.PLoS genetics · 2011Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
We have investigated the cis-regulatory network that mediates temporal gene expression during organogenesis. Previous studies demonstrated that the organ selector gene pha-4/FoxA is critical to establish the onset of transcription of Caenorhabditis elegans foregut (pharynx) genes. Here, we discover additional cis-regulatory elements that function in combination with PHA-4. We use a computational approach to identify candidate cis-regulatory sites for genes activated either early or late during pharyngeal development. Analysis of natural or synthetic promoters reveals that six of these sites function in vivo. The newly discovered temporal elements, together with predicted PHA-4 sites, account for the onset of expression of roughly half of the pharyngeal genes examined. Moreover, combinations of temporal elements and PHA-4 sites can be used in genome-wide searches to predict pharyngeal genes, with more than 85% accuracy for their onset of expression. These findings suggest a regulatory code for temporal gene expression during foregut development and provide a means to predict gene expression patterns based solely on genomic sequence.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.