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Submitted on March 5, 2007
Accepted on September 20, 2007
binding sites in mouse liver
Department of Biosciences and Nutrition, Karolinska Institutet, Novum, S141 57, Huddinge, Sweden, The Bioinformatics Centre, Department of Molecular Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 København N, Denmark
* To whom correspondence should be addressed. E-mail: hui.gao{at}biosci.ki.se.
We report the genome-wide identification of estrogen receptor 
(ER) binding regions in mouse liver using a combination of chromatin immunoprecipitation (ChIP) and tiled microarrays that cover all non-repetitive sequences in the mouse genome. This analysis identified 5568 ER binding regions. In agreement with what has previously been reported for human cell lines, many ER binding regions are located far away from transcription start sites; approximately 40% of ER binding regions are located within 10kb of annotated transcription start sites. Almost 50% of ER binding regions overlap genes. The majority of ER binding regions lie in regions that are evolutionary conserved between human and mouse. Motif-finding algorithms identified the estrogen response element (ERE), and variants thereof, together with binding sites for activator protein 1 (AP1), basic-helix-loop-helix (bHLH) proteins, ETS proteins and Forkhead proteins as the most common motifs present in identified ER binding regions. To correlate ER binding to the promoter of specific genes, with changes in expression levels of the corresponding mRNAs, expression levels of selected mRNAs were assayed in livers 2 h, 4 h and 6 h after treatment with ER selective agonist propyl pyrazole triol (PPT). Five of these 8 selected genes, Shp, Stat3, Pdgds, Pck1 and Pdk4 all responded to PPT after 4 h treatment. These results extend our previous studies using gene expression profiling to characterize estrogen signaling in mouse liver, by characterizing the first step in this signaling cascade, the binding of ER to DNA in intact chromatin.
•
ChIP-on-chip •
mouse liver
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