Genome-wide analysis of estrogen receptor binding sites

Jason S. Carroll; Clifford A. Meyer; Jun Song; Wei Li; Timothy R. Geistlinger; Jérôme 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

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, Jérôme 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

Research output: Contribution to journal › Article › peer-review

Abstract

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.

Original language	English (US)
Pages (from-to)	1289-1297
Number of pages	9
Journal	Nature Genetics
Volume	38
Issue number	11
DOIs	https://doi.org/10.1038/ng1901
State	Published - Nov 23 2006
Externally published	Yes

ASJC Scopus subject areas

Genetics

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10.1038/ng1901

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Carroll, J. S., Meyer, C. A., Song, J., Li, W., Geistlinger, T. R., Eeckhoute, J., Brodsky, A. S., Keeton, E. K., Fertuck, K. C., Hall, G. F., Wang, Q., Bekiranov, S., Sementchenko, V., Fox, E. A., Silver, P. A., Gingeras, T. R., Liu, X. S., & Brown, M. (2006). Genome-wide analysis of estrogen receptor binding sites. Nature Genetics, 38(11), 1289-1297. https://doi.org/10.1038/ng1901

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title = "Genome-wide analysis of estrogen receptor binding sites",

abstract = "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.",

author = "Carroll, {Jason S.} and Meyer, {Clifford A.} and Jun Song and Wei Li and Geistlinger, {Timothy R.} and J{\'e}r{\^o}me Eeckhoute and Brodsky, {Alexander S.} and Keeton, {Erika Krasnickas} and Fertuck, {Kirsten C.} and Hall, {Giles F.} and Qianben Wang and Stefan Bekiranov and Victor Sementchenko and Fox, {Edward A.} and Silver, {Pamela A.} and Gingeras, {Thomas R.} and Liu, {X. Shirley} and Myles Brown",

note = "Funding Information: The authors would like to thank D. Lynch, M. Lupien, M. Laza and O. J{\"a}nne for helpful discussions and review of the manuscript. This work was supported by grants from the US National Institute of Diabetes and Digestive and Kidney Diseases (DK074967) and the US National Cancer Institute–sponsored Dana-Farber/Harvard Cancer Center Breast Cancer SPORE Grant (CA089393); by the Claudia Adams Barr Program in Innovative Basic Cancer Research (M.B., P.A.S., X.S.L.); by US Department of Defense Breast Cancer Research Program Awards (M.B., J.S.C.) and by fellowships from the Fondation Recherche Medicale (J.E.), the Susan G. Komen Breast Cancer Foundation (E.K.K.) and the US National Institutes of Health (T.R.G. and C.A.M.).",

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AU - Geistlinger, Timothy R.

AU - Eeckhoute, Jérôme

AU - Brodsky, Alexander S.

AU - Keeton, Erika Krasnickas

AU - Fertuck, Kirsten C.

AU - Hall, Giles F.

AU - Wang, Qianben

AU - Bekiranov, Stefan

AU - Sementchenko, Victor

AU - Fox, Edward A.

AU - Silver, Pamela A.

AU - Gingeras, Thomas R.

AU - Liu, X. Shirley

AU - Brown, Myles

N1 - Funding Information: The authors would like to thank D. Lynch, M. Lupien, M. Laza and O. Jänne for helpful discussions and review of the manuscript. This work was supported by grants from the US National Institute of Diabetes and Digestive and Kidney Diseases (DK074967) and the US National Cancer Institute–sponsored Dana-Farber/Harvard Cancer Center Breast Cancer SPORE Grant (CA089393); by the Claudia Adams Barr Program in Innovative Basic Cancer Research (M.B., P.A.S., X.S.L.); by US Department of Defense Breast Cancer Research Program Awards (M.B., J.S.C.) and by fellowships from the Fondation Recherche Medicale (J.E.), the Susan G. Komen Breast Cancer Foundation (E.K.K.) and the US National Institutes of Health (T.R.G. and C.A.M.).

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Genome-wide analysis of estrogen receptor binding sites

Abstract

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