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RESEARCH PAPER

Identification of C. elegans DAF-12-binding sites, response elements, and target genes

¹ Program in Biochemistry and Molecular Biology and ² Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94143-2280, USA; ³ Huffington Center on Aging, Baylor College of Medicine, Houston, Texas 77030, USA

Intracellular receptor DAF-12 regulates dauer formation and developmental age and affects Caenorhabditis elegans lifespan. Genetic analyses place DAF-12 at the convergence of several signal transduction pathways; however, the downstream effectors and the molecular basis for the receptor's multiple physiological outputs are unknown. Beginning with C. elegans genomic DNA, we devised a procedure for multiple rounds of selection and amplification that yielded fragments bearing DAF-12-binding sites. These genomic fragments mediated DAF-12-dependent transcriptional regulation both in Saccharomyces cerevisiae and in C. elegans; that is, they served as functional DAF-12 response elements. We determined that most of the genomic fragments that displayed DAF-12 response element activity in yeast were linked to genes that were regulated by DAF-12 in C. elegans; indeed, the response element-containing fragments typically resided within clusters of DAF-12-regulated genes. DAF-12 target gene regulation was developmental program and stage specific, potentially predicting a fit of these targets into regulatory networks governing aspects of C. elegans reproductive development and dauer formation.

[Keywords: DAF-12; In Vitro Genomic Selection; intracellular receptor; response element; target genes]

Received May 6, 2004; revised version accepted August 23, 2004.

Article and publication are at http://www.genesdev.org/cgi/doi/10.1101/gad.1218504.

⁴ Corresponding author. E-MAIL yamamoto{at}cgl.ucsf.edu; FAX (415) 476-6129.

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