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Identification of direct DAF-16 targets controlling longevity, metabolism and diapause by chromatin immunoprecipitation

Abstract

DAF-16, a forkhead transcription factor, is a key regulator of longevity, metabolism and dauer diapause in Caenorhabditis elegans. The precise mechanism by which DAF-16 regulates multiple functions, however, is poorly understood. Here, we used chromatin immunoprecipitation (ChIP) to identify direct targets of DAF-16. We cloned 103 target sequences containing consensus DAF-16 binding sites and selected 33 targets for further analysis. Expression of most of these genes is regulated in a DAF-16–dependent manner, and inactivation of more than half of these genes significantly altered DAF-16–dependent functions, including life span, fat storage and dauer formation. Our results show that the ChIP-based cloning strategy leads to greater enrichment for DAF-16 target genes than previous screening strategies. We also demonstrate that DAF-16 is recruited to multiple promoters to coordinate regulation of its downstream targets. The large number of target genes discovered provides insight into how DAF-16 controls diverse biological functions.

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Figure 1: Chromatin immunoprecipitation (ChIP) to identify DAF-16 targets.
Figure 2: ChIP cloning identified 103 targets of DAF-16 representing various biological functions.
Figure 3: Phenotypic analyses of DAF-16 target genes.

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Acknowledgements

We would like to thank M. Walhout, C. Mello, R. Davis, T. Duchaine, L. Maduira and M. Czech for their help and insights and members of the Tissenbaum lab and S. Evans for critical reading of the manuscript. Some of the strains were kindly provided by T. Stiernagle at the Caenorhabditis Genetics Center, which is funded by the US National Institutes of Health National Center for Research Resources. H.A.T. is a William Randolph Hearst Young Investigator. This project was funded in part by a Burroughs Wellcome Career Award in the Biomedical Sciences to H.A.T. and an endowment from the William Randolph Hearst Foundation and Worcester Foundation Scholar Award to H.A.T.

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Correspondence to Heidi A Tissenbaum.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Table 1

A list of 103 target genes identified by ChIP cloning. (PDF 35 kb)

Supplementary Table 2

A list of DAF-16 downstream target genes identified by ChIP cloning in common with previous studies. (PDF 12 kb)

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Wook Oh, S., Mukhopadhyay, A., Dixit, B. et al. Identification of direct DAF-16 targets controlling longevity, metabolism and diapause by chromatin immunoprecipitation. Nat Genet 38, 251–257 (2006). https://doi.org/10.1038/ng1723

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