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Human Molecular Genetics Advance Access published online on October 12, 2005
Human Molecular Genetics, doi:10.1093/hmg/ddi378
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© The Author 2005. Published by Oxford University Press. All rights reserved
Received July 4, 2005
Revised August 19, 2005
Accepted September 28, 2005

Article

Binding sites for metabolic disease related transcription factors inferred at base pair resolution by chromatin immunoprecipitation and genomic microarrays

Alvaro Rada-Iglesias 1, Ola Wallerman 1, Christoph Koch 2, Adam Ameur 3, Stefan Enroth 3, Gayle Clelland 2, Kenneth Wester 1, Sarah Wilcox 2, Oliver M. Dovey 2, Peter D. Ellis 2, Vicki L. Wraight 2, Keith James 2, Rob Andrews 2, Cordelia Langford 2, Pawandeep Dhami 2, Nigel Carter 2, David Vetrie 2, Fredrik Pontén 1, Jan Komorowski 3, Ian Dunham 2, and Claes Wadelius 4*

1 Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
2 Wellcome Trust Sanger Institute, Cambridge, UK
3 Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden
4 Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-75185 Uppsala, Sweden

* To whom correspondence should be addressed.
Claes Wadelius, E-mail: Claes.Wadelius{at}genpat.uu.se


  Abstract

We present a detailed in vivo characterization of hepatocyte transcriptional regulation in HepG2 cells, using chromatin immunoprecipitation and detection on PCR fragment based genomic tiling path arrays covering the Encyclopedia of DNA elements (ENCODE) regions. Our data suggest that HNF-4{alpha} and HNF-3{beta}, which were commonly bound to distal regulatory elements, may cooperate in the regulation of a large fraction of the liver transcriptome, and that both HNF-4{alpha} and USF1 may promote H3 acetylation to many of their targets. Importantly, bioinformatic analysis of the sequences bound by each TF shows an overrepresentation of motifs highly similar to the in vitro established consensus sequences. Based on these data we have inferred tentative binding sites at bp resolution. Some of these sites have previously been found by in vitro analysis and some were verified in vitro in this study. Our data suggests that a similar approach could be used for the in vivo characterization of all predicted/uncharacterized TF and that the analysis could be scaled to the whole genome.


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