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Discovery of estrogen receptor α target genes and response elements in breast tumor cells

Chin-Yo Lin1*, Anders Ström2, Vinsensius Berlian Vega1, Say Li Kong1, Ai Li Yeo1, Jane S Thomsen2, Wan Ching Chan1, Balraj Doray1, Dhinoth K Bangarusamy1, Adaikalavan Ramasamy1, Liza A Vergara1, Suisheng Tang3, Allen Chong3, Vladimir B Bajic3, Lance D Miller1, Jan-Åke Gustafsson24 and Edison T Liu1*

Author Affiliations

1 Genome Institute of Singapore, Singapore 117528

2 Center for Biotechnology, Karolinska Institute, Novum, S-141 57 Huddinge, Sweden

3 Knowledge Extraction Lab, Institute for Infocomm Research, Singapore 119613

4 Department of Medical Nutrition, Karolinska Institute, Novum, S-141 86 Huddinge, Sweden

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Genome Biology 2004, 5:R66  doi:10.1186/gb-2004-5-9-r66

Published: 12 August 2004

Abstract

Background

Estrogens and their receptors are important in human development, physiology and disease. In this study, we utilized an integrated genome-wide molecular and computational approach to characterize the interaction between the activated estrogen receptor (ER) and the regulatory elements of candidate target genes.

Results

Of around 19,000 genes surveyed in this study, we observed 137 ER-regulated genes in T-47D cells, of which only 89 were direct target genes. Meta-analysis of heterogeneous in vitro and in vivo datasets showed that the expression profiles in T-47D and MCF-7 cells are remarkably similar and overlap with genes differentially expressed between ER-positive and ER-negative tumors. Computational analysis revealed a significant enrichment of putative estrogen response elements (EREs) in the cis-regulatory regions of direct target genes. Chromatin immunoprecipitation confirmed ligand-dependent ER binding at the computationally predicted EREs in our highest ranked ER direct target genes, NRIP1, GREB1 and ABCA3. Wider examination of the cis-regulatory regions flanking the transcriptional start sites showed species conservation in mouse-human comparisons in only 6% of predicted EREs.

Conclusions

Only a small core set of human genes, validated across experimental systems and closely associated with ER status in breast tumors, appear to be sufficient to induce ER effects in breast cancer cells. That cis-regulatory regions of these core ER target genes are poorly conserved suggests that different evolutionary mechanisms are operative at transcriptional control elements than at coding regions. These results predict that certain biological effects of estrogen signaling will differ between mouse and human to a larger extent than previously thought.