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Science 17 September 2004:
Vol. 305. no. 5691, pp. 1743 - 1746
DOI: 10.1126/science.1102216
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Research Articles

Environmentally Induced Foregut Remodeling by PHA-4/FoxA and DAF-12/NHR

Wanyuan Ao,1* Jeb Gaudet,1*{dagger} W. James Kent,2 Srikanth Muttumu,1 Susan E. Mango1{ddagger}

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.

1 Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT 84112, USA.
2 Genome Bioinformatics Group, University of California, Santa Cruz, CA 95064, USA.



* These authors contributed equally to this work.

{dagger} Present address: Genes and Development Research Group, University of Calgary, Calgary, Alberta AB T2N 4N1, Canada.

{ddagger} To whom correspondence should be addresssed. E-mail: susan.mango{at}hci.utah.edu

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