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Environmentally Induced Foregut Remodeling by PHA-4/FoxA and DAF-12/NHR
Wanyuan Ao,1*Jeb Gaudet,1*W. James Kent,2Srikanth Muttumu,1Susan E. Mango1
Growth and development of the Caenorhabditis elegans foregut(pharynx) depends on coordinated gene expression, mediated bypharynx defective (PHA)-4/FoxA in combination with additional,largely unidentified transcription factors. Here, we used wholegenome analysis to establish clusters of genes expressed indifferent pharyngeal cell types. We created an expectation maximizationalgorithm to identify cis-regulatory elements that activateexpression within the pharyngeal gene clusters. One of theseelements mediates the response to environmental conditions withinpharyngeal muscles and is recognized by the nuclear hormonereceptor (NHR) DAF-12. Our data suggest that PHA-4 and DAF-12endow the pharynx with transcriptional plasticity to respondto diverse developmental and physiological cues. Our combinationof bioinformatics and in vivo analysis has provided a powerfulmeans 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.
Present address: Genes and Development Research Group, Universityof Calgary, Calgary, Alberta AB T2N 4N1, Canada.
To whom correspondence should be addresssed. E-mail: susan.mango{at}hci.utah.edu
MotifVoter: a novel ensemble method for fine-grained integration of generic motif finders.
E. Wijaya, S.-M. Yiu, N. T. Son, R. Kanagasabai, and W.-K. Sung (2008)
Bioinformatics
24, 2288-2295
|Abstract »|Full Text »|PDF »
The FLYWCH transcription factors FLH-1, FLH-2, and FLH-3 repress embryonic expression of microRNA genes in C. elegans.
M. C. Ow, N. J. Martinez, P. H. Olsen, H. S. Silverman, M. I. Barrasa, B. Conradt, A. J.M. Walhout, and V. Ambros (2008)
Genes & Dev.
22, 2520-2534
|Abstract »|Full Text »|PDF »
Computational identification and functional validation of regulatory motifs in cartilage-expressed genes.
S. R. Davies, L.-W. Chang, D. Patra, X. Xing, K. Posey, J. Hecht, G. D. Stormo, and L. J. Sandell (2007)
Genome Res.
17, 1438-1447
|Abstract »|Full Text »|PDF »
Genetic Suppressors of Caenorhabditis elegans pha-4/FoxA Identify the Predicted AAA Helicase ruvb-1/RuvB.
Present address: Genes and Development Research Group, University of Calgary, Calgary, Alberta AB T2N 4N1, Canada. 
To whom correspondence should be addresssed. E-mail: 
