Journal
SCIENCE
Volume 305, Issue 5691, Pages 1743-1746Publisher
AMER ASSOC ADVANCEMENT SCIENCE
DOI: 10.1126/science.1102216
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Funding
- NIGMS NIH HHS [R01 GM056264, R01 GM056264-08, R01 GM056264-07, R01 GM056264-08S1, R01-GM56264] Funding Source: Medline
- PHS HHS [2P303A42014] Funding Source: Medline
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Growth and development of the Caenorhabditis elegans foregut (pharynx) depends on coordinated gene expression, mediated by pharynx defective (PHA)-4/FoxA in combination with additional, largely unidentified transcription factors. Here, we used whole genome analysis to establish clusters of genes expressed in different pharyngeal cell types. We created an expectation maximization algorithm to identify cis-regulatory elements that activate expression within the pharyngeal gene clusters. One of these elements mediates the response to environmental conditions within pharyngeal muscles and is recognized by the nuclear hormone receptor (NHR) DAF-12. Our data suggest that PHA-4 and DAF-12 endow the pharynx with transcriptional plasticity to respond to diverse developmental and physiological cues. Our combination of bioinformatics and in vivo analysis has provided a powerful means for genome-wide investigation of transcriptional control.
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