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Human Molecular Genetics Advance Access originally published online on October 12, 2005
Human Molecular Genetics 2005 14(22):3435-3447; doi:10.1093/hmg/ddi378
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

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

Alvaro Rada-Iglesias1, Ola Wallerman1, Christoph Koch3, Adam Ameur2, Stefan Enroth2, Gayle Clelland3, Kenneth Wester1, Sarah Wilcox3, Oliver M. Dovey3, Peter D. Ellis3, Vicki L. Wraight3, Keith James3, Rob Andrews3, Cordelia Langford3, Pawandeep Dhami3, Nigel Carter3, David Vetrie3, Fredrik Pontén1, Jan Komorowski2, Ian Dunham3 and Claes Wadelius1,*

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

* To whom correspondence should be addressed. Tel: +46 184714076; Fax: +46 184714808; Email: claes.wadelius{at}genpat.uu.se

Received July 4, 2005; Revised August 19, 2005; Accepted September 28, 2005

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 element (ENCODE) regions. Our data suggest that HNF-4{alpha} and HNF-3ß, 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 transcription factor (TF) shows an over-representation of motifs highly similar to the in vitro established consensus sequences. On the basis of these data, we have inferred tentative binding sites at base pair resolution. Some of these sites have been previously 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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