Chip-chip approaches to understanding ER function
Jason Carroll, Shirley Liu, Wei Li, Cliff Meyer, Jun Song & Myles Brown
Estrogen Receptor (ER) regulation of target gene transcription is a significant factor in tumor development and progression. Previous work on ER-mediated transcription focused primarily on promoter regions of target genes, although recent work from our lab combining ER Chromatin Immunoprecipitation (ChIP) with tiled microarrays covering chromosomes 21 and 22, showed that distal enhancers appear to be the primary ER binding sites, and that these sites require the Forkhead protein FoxA1. We have extended on these ChIP-chip studies to map all the estrogen-induced ER and RNA PolII binding sites in the human genome. Furthermore, we have combined these data with expression microarrays after estrogen-treatment, to provide a complete network of receptor binding sites and the subsequent target genes of these binding events. We find approximately 3,600 ER binding sites, almost all of which are distal from promoter proximal regions and more than 3,600 RNA PolII sites, which exist almost exclusively at promoter regions. The binding profiles, in combination with the expression data reveal important details about the mechanisms by which ER regulates gene transcription. Furthermore, analysis of the sequence information contained within the binding sites reveals a complex network of transcription factors that are involved in regulating ER-mediated transcription.