Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.

Subscribe

Logo for

Science 305 (5691): 1743-1746

Copyright © 2004 by the American Association for the Advancement of Science

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}

Abstract: 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.

Back to Top

* 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


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
A general approach for discriminative de novo motif discovery from high-throughput data.
J. Grau, S. Posch, I. Grosse, and J. Keilwagen (2013)
Nucleic Acids Res. 41, e197
   Abstract »    Full Text »    PDF »
DNA motif elucidation using belief propagation.
K.-C. Wong, T.-M. Chan, C. Peng, Y. Li, and Z. Zhang (2013)
Nucleic Acids Res. 41, e153
   Abstract »    Full Text »    PDF »
Conserved Motifs and Prediction of Regulatory Modules in Caenorhabditis elegans.
G. Zhao, N. Ihuegbu, M. Lee, L. Schriefer, T. Wang, and G. D. Stormo (2012)
g3 2, 469-481
   Abstract »    Full Text »    PDF »
Host-finding behaviour in the nematode Pristionchus pacificus.
F. D. Brown, I. D'Anna, and R. J. Sommer (2011)
Proc R Soc B 278, 3260-3269
   Abstract »    Full Text »    PDF »
Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans.
W. Niu, Z. J. Lu, M. Zhong, M. Sarov, J. I. Murray, C. M. Brdlik, J. Janette, C. Chen, P. Alves, E. Preston, et al. (2011)
Genome Res. 21, 245-254
   Abstract »    Full Text »    PDF »
Scaffolding a Caenorhabditis nematode genome with RNA-seq.
A. Mortazavi, E. M. Schwarz, B. Williams, L. Schaeffer, I. Antoshechkin, B. J. Wold, and P. W. Sternberg (2010)
Genome Res. 20, 1740-1747
   Abstract »    Full Text »    PDF »
Identifying regulatory elements in eukaryotic genomes.
L. Narlikar and I. Ovcharenko (2009)
Briefings in Functional Genomics 8, 215-230
   Abstract »    Full Text »    PDF »
The polyadenylation site of Mimivirus transcripts obeys a stringent 'hairpin rule'.
D. Byrne, R. Grzela, A. Lartigue, S. Audic, S. Chenivesse, S. Encinas, J.-M. Claverie, and C. Abergel (2009)
Genome Res. 19, 1233-1242
   Abstract »    Full Text »    PDF »
The C. elegans Snail homolog CES-1 can activate gene expression in vivo and share targets with bHLH transcription factors.
J. S. Reece-Hoyes, B. Deplancke, M. I. Barrasa, J. Hatzold, R. B. Smit, H. E. Arda, P. A. Pope, J. Gaudet, B. Conradt, and A. J. M. Walhout (2009)
Nucleic Acids Res. 37, 3689-3698
   Abstract »    Full Text »    PDF »
Sam68 Regulates a Set of Alternatively Spliced Exons during Neurogenesis.
G. Chawla, C.-H. Lin, A. Han, L. Shiue, M. Ares Jr., and D. L. Black (2009)
Mol. Cell. Biol. 29, 201-213
   Abstract »    Full Text »    PDF »
Multigenome DNA sequence conservation identifies Hox cis-regulatory elements.
S. G. Kuntz, E. M. Schwarz, J. A. DeModena, T. De Buysscher, D. Trout, H. Shizuya, P. W. Sternberg, and B. J. Wold (2008)
Genome Res. 18, 1955-1968
   Abstract »    Full Text »    PDF »
Position-dependent motif characterization using non-negative matrix factorization.
L. N. Hutchins, S. M. Murphy, P. Singh, and J. H. Graber (2008)
Bioinformatics 24, 2684-2690
   Abstract »    Full Text »    PDF »
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.
D. L. Updike and S. E. Mango (2007)
Genetics 177, 819-833
   Abstract »    Full Text »    PDF »
Identification of muscle-specific regulatory modules in Caenorhabditis elegans.
G. Zhao, L. A. Schriefer, and G. D. Stormo (2007)
Genome Res. 17, 348-357
   Abstract »    Full Text »    PDF »
Repression of mesodermal fate by foxa, a key endoderm regulator of the sea urchin embryo.
P. Oliveri, K. D. Walton, E. H. Davidson, and D. R. McClay (2006)
Development 133, 4173-4181
   Abstract »    Full Text »    PDF »
Activation of nicotinic receptors uncouples a developmental timer from the molting timer in C. elegans.
A.-F. Ruaud and J.-L. Bessereau (2006)
Development 133, 2211-2222
   Abstract »    Full Text »    PDF »
A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles.
L.-W. Chang, R. Nagarajan, J. A. Magee, J. Milbrandt, and G. D. Stormo (2006)
Genome Res. 16, 405-413
   Abstract »    Full Text »    PDF »
Expression of Arabidopsis MIRNA Genes.
Z. Xie, E. Allen, N. Fahlgren, A. Calamar, S. A. Givan, and J. C. Carrington (2005)
Plant Physiology 138, 2145-2154
   Abstract »    Full Text »    PDF »
The circuitry of a master switch: Myod and the regulation of skeletal muscle gene transcription.
S. J. Tapscott (2005)
Development 132, 2685-2695
   Abstract »    Full Text »    PDF »
No Organ Left Behind: Tales of Gut Development and Evolution.
D. Y. R. Stainier (2005)
Science 307, 1902-1904
   Abstract »    Full Text »    PDF »

To Advertise     Find Products


Science Signaling. ISSN 1937-9145 (online), 1945-0877 (print). Pre-2008: Science's STKE. ISSN 1525-8882