Genome-wide identification of estrogen receptor α-binding sites in mouse liver

We report the genome-wide identification of estrogen receptor alpha (ER alpha)-binding regions in mouse liver using a combination of chromatin immunoprecipitation and tiled microarrays that cover all non-repetitive sequences in the mouse genome. This analysis identified 5568 ER alpha-binding regions. In agreement with what has previously been reported for human cell lines, many ER alpha-binding regions are located far away from transcription start sites; approximately 40% of ER alpha-binding regions are located within 10 kb of annotated transcription start sites. Almost 50% of ER alpha-binding regions overlap genes. The majority of ER alpha-binding regions lie in regions that are evolutionarily conserved between human and mouse. Motif-finding algorithms identified the estrogen response element, and variants thereof, together with binding sites for activator protein 1, basic-helix-loop-helix proteins, ETS proteins, and Forkhead proteins as the most common motifs present in identified ER alpha-binding regions. To correlate ER alpha 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, 4, and 6 h after treatment with ER alpha-selective agonist propyl pyrazole triol. Five of these eight selected genes, Shp, Stat3, Pdgds, Pck1, and Pdk4, all responded to propyl pyrazole triol 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 alpha to DNA in intact chromatin.