GSE108979
Identification of the ER-beta cistrome in ER-beta expressing MDA-MB-231 cells [ChIP-seq]
We have utilized ChIPseq to identify the ER-beta cistrome in ER-beta expressing MDA-MB-231 triple negative breast cancer cells.  ER-beta has been identified as a tumor suppressor in breast cancer and recent reports have demonstrated that ER-beta protein is detectable at moderate to high levels in approximately 30% of triple negative breast tumors.  Increased expression of ER-beta in triple negative breast cancer has also been reported to be associated with improved recurrence-free survival.  Treatment of ER-beta expressing triple negative breast cancer cells with estrogen, or the ER-beta selective agonist, LY500307, results in decreased cell proliferation, invasion and migration.  To begin to identify the molecular mechanisms by which ER-beta elicits tumor suppressive effects in triple negative breast cancer, we performed ChIPseq studies and identified the genome-wide binding sites for ER-beta following exposure to 1nM estrogen or 10nM LY500307 for 3 hours.  Over 28,000 and 10,000 unique ER-beta binding sites were identifed in response to these two ligands respectively.  The top transcription factor motifs identified under both treatment conditions were estrogen response elements and AP1 response elements.  The majority of ER-beta binding sites were found at enhancer regions located within introns or intergenic chromatin regions followed by gene promoters. Overall design: Examination of ER-beta binding sites in ER-beta expressing MDA-MB-231 cells.  ER-beta immunoprecipitations were carried out using a Flag-specific antibody (M2).  All treatment conditions were conducted in triplicate and data were normalized using input controls and compared to vehicle treated cells.