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Nature Genetics 38, 1289–1297 (1 November 2006) | doi:10.1038/ng1901

Genome-wide analysis of estrogen receptor binding sites

Jason S Carroll , Clifford A Meyer , Jun Song , Wei Li , Timothy R Geistlinger , J|[eacute]|r|[ocirc]|me Eeckhoute , Alexander S Brodsky , Erika Krasnickas Keeton , Kirsten C Fertuck , Giles F Hall , Qianben Wang , Stefan Bekiranov , Victor Sementchenko , Edward A Fox , Pamela A Silver , Thomas R Gingeras , X Shirley Liu & Myles Brown

The estrogen receptor is the master transcriptional regulator of breast cancer phenotype and the archetype of a molecular therapeutic target. We mapped all estrogen receptor and RNA polymerase II binding sites on a genome-wide scale, identifying the authentic cis binding sites and target genes, in breast cancer cells. Combining this unique resource with gene expression data demonstrates distinct temporal mechanisms of estrogen-mediated gene regulation, particularly in the case of estrogen-suppressed genes. Furthermore, this resource has allowed the identification of cis-regulatory sites in previously unexplored regions of the genome and the cooperating transcription factors underlying estrogen signaling in breast cancer.