Genome-Wide Identification of Estrogen Receptor α-Binding Sites in Mouse Liver

Abstract

We report the genome-wide identification of estrogen receptor alpha (ERalpha)-binding regions in mouse liver using a combination of chromatin immunoprecipitation and tiled microarrays that cover all nonrepetitive sequences in the mouse genome. This analysis identified 5568 ERalpha-binding regions. In agreement with what has previously been reported for human cell lines, many ERalpha-binding regions are located far away from transcription start sites; approximately 40% of ERalpha-binding regions are located within 10 kb of annotated transcription start sites. Almost 50% of ERalpha-binding regions overlap genes. The majority of ERalpha-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 ERalpha-binding regions. To correlate ERalpha 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 ERalpha-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 ERalpha to DNA in intact chromatin.

Genome-wide profiling of PPARγ:RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis

“…Notably, 50% of all target sites are located within genes. A similar high percentage of intragenic binding sites was shown recently for ER␣ in MCF-7 cells and in mouse liver (Carroll et al 2006;Gao et al 2008). Another noticeable feature is that numerous genes have several adjacent PPAR␥: RXR-binding sites.…”

Expanded methyl-sensitive cut counting reveals hypomethylation as an epigenetic state that highlights functional sequences of the genome

“…The Foxa 2 gene codes for the forkhead box protein A2, which is a transcriptional activator for liver-specific genes (25), and the Esr1 gene codes for the nuclear estrogen receptor α. This is the major estrogen receptor expressed in the liver, where it regulates glucose homeostasis as well as lipid metabolism (26). Among the remaining 2% of regulatory elements, we also found tissuerelated transcription-binding sites (i.e., Hnf4A).…”

The genome landscape of ERα- and ERβ-binding DNA regions

“…Recently, chromatin immunoprecipitation (ChIP) has been used in combination with genomic DNA microarrays (chip) (ChIP-on-chip) and DNA sequencing (ChIP-PETs) to pursue whole genome identification of ER␣-binding DNA regions in intact chromatin of cultured cell lines and tissue samples (10)(11)(12). However, no large scale identification of ER␤-binding DNA regions has been reported.…”