Nature Genetics
- 38, 1289 - 1297 (2006)
Published online: 1 October 2006; Corrected online: 20 October 2006 | doi:10.1038/ng1901
Genome-wide analysis of estrogen receptor binding sitesJason S Carroll1, Clifford A Meyer2, 3, Jun Song2, 3, Wei Li2, 3, Timothy R Geistlinger1, Jérôme Eeckhoute1, Alexander S Brodsky4, Erika Krasnickas Keeton1, Kirsten C Fertuck1, Giles F Hall5, Qianben Wang1, Stefan Bekiranov6, 8, Victor Sementchenko6, Edward A Fox5, Pamela A Silver5, 7, Thomas R Gingeras6, X Shirley Liu2, 3 & Myles Brown11
Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 44 Binney St., Boston, Massachusetts 02115, USA. 2
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard Medical School, 44 Binney St., Boston, Massachusetts 02115, USA. 3
Harvard School of Public Health, 677 Huntington Avenue, Boston, Massachusetts 02115, USA. 4
Brown University, Laboratories for Molecular Medicine, Center for Genomics and Proteomics, Providence, Rhode Island 02903, USA. 5
Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, 44 Binney St., Boston, Massachusetts 02115, USA. 6
Affymetrix, 3380 Central Expressway, Santa Clara, California 95051, USA. 7
Department of Systems Biology, Harvard Medical School, 200 Longwood Ave., Boston, Massachusetts 02115, USA. 8
Current address: Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA.
Correspondence should be addressed to Myles Brown myles_brown@dfci.harvard.edu or X Shirley Liu xsliu@jimmy.harvard.edu 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.
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