GSE36455
ERa and PolII ChIP seq from Mouse Uterus
To advance understanding of mechanisms leading to biological and transcriptional endpoints related to estrogen action in the mouse uterus, we have mapped ERa and RNA polymerase II binding sites using chromatin immunoprecipitation (ChIP) followed by sequencing of enriched chromatin fragments (ChIP-seq).   In the absence of hormone, 5184 ERa binding sites were apparent in the vehicle treated ovariectomized uterine chromatin, while 17240 were seen one hour after estrogen (E2) treatment, indicating that some sites are occupied by unliganded ERa, and that ERa binding is increased by E2.  Approximately 15% of the uterine ERa binding sites were adjacent to (<10 KB) annotated transcription start sites and many sites are found within genes or are found more than 100 KB distal from mapped genes; however, the density (sites per bp) of ERa binding sites is significantly greater adjacent to promoters.  An increase in quantity of sites but no significant positional differences were seen between vehicle and E2 treated samples in the overall locations of ERa binding sites either distal from, adjacent to or within genes.  Analysis of the PolII data revealed the presence of poised promoter proximal PolII on some highly upregulated genes. Additionally, co-recruitment of PolII and ERa to some distal enhancer regions was observed. A de novo motif analysis of sequences in the ERa bound chromatin confirmed that estrogen response elements (EREs) were significantly enriched. Interestingly, in areas of ERa binding without predicted ERE motifs, homeodomain transcription factor (Hox) binding motifs were significantly enriched. The integration of the ERa and PolII binding sites from our uterine ChIP-seq data with transcriptional responses revealed in our uterine microarrays has the potential to greatly enhance our understanding of mechanisms governing estrogen response in uterine and other estrogen target tissues. Overall design: one sample each, vehicle ER-alpha ChIP seq,1 hour estradiol ER-alpha ChIP seq, vehicle RNA polymerase II ChIP seq,1 hour estradiol RNA polymerase II ChIP seq, input DNA