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PMID: 15492775 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

Whole-genome analysis of temporal gene expression during foregut development.

PLoS biology ·Vol. 2 ·No. 11 ·2004-11-00 ·Pages e352

Gaudet J, Muttumu S, Horner M, Mango SE

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.

MeSH Terms
Animals Caenorhabditis elegans Caenorhabditis elegans Proteins/genetics,metabolism Chromosome Mapping Codon Computational Biology Gene Expression Regulation Gene Expression Regulation, Developmental Genes, Reporter Genome Green Fluorescent Proteins/metabolism Intestines/embryology Multigene Family Oligonucleotide Array Sequence Analysis Plasmids/metabolism Promoter Regions, Genetic Protein Binding Regulatory Elements, Transcriptional Time Factors Trans-Activators/genetics,metabolism Transgenes
Chemicals
Caenorhabditis elegans Proteins Codon Pha-4 protein, C elegans Trans-Activators Green Fluorescent Proteins
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Gaudet Jeb
Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA.
Muttumu Srikanth
Horner Michael
Mango Susan E
Conflict of Interest

The authors have declared that no conflicts of interest exist.

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Article Info
Journal
PLoS biology
Abbr.
PLoS Biol
ISSN
1545-7885
DOI
10.1371/journal.pbio.0020352
Published
2004-11-00
Epub
2004-00-19
Pages
e352
Language
English
Region
United States
NLM ID
101183755
PMCID
PMC523228
Subset
IM
Grants
NIGMS NIH HHS · R01 GM056264 · United States
NIGMS NIH HHS · R01 GM056264-08S1 · United States
NIGMS NIH HHS · R01 GM056264-08 · United States
NIGMS NIH HHS · R01 GM056264-07 · United States
NCI NIH HHS · 2P30CA42014 · United States
NCI NIH HHS · P30 CA042014 · United States
External Links
PubMed source DOI: 10.1371/journal.pbio.0020352 PMC Full Text View journal details
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