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Open Access Highly Accessed Methodology article

A carrier-assisted ChIP-seq method for estrogen receptor-chromatin interactions from breast cancer core needle biopsy samples

Wilbert Zwart15, Rutger Koornstra1, Jelle Wesseling12, Emiel Rutgers3, Sabine Linn14 and Jason S Carroll56*

Author Affiliations

1 Department of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands

2 Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands

3 Department of Surgical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands

4 Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands

5 Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK

6 Department of Oncology, University of Cambridge, Cambridge CB2 OXY, UK

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BMC Genomics 2013, 14:232  doi:10.1186/1471-2164-14-232

Published: 8 April 2013

Abstract

Background

The Estrogen Receptor alpha (ERα) is the key transcriptional regulator in luminal breast cancer and is therefore the main target for adjuvant treatment of this subtype. Luminal gene signatures are dictated by the transcriptional capacities of ERα, which are a direct consequence of the receptors binding preference at specific sites on the chromatin. The identification of ERα binding signatures on a genome-wide level has greatly enhanced our understanding of Estrogen Receptor biology in cell lines and tumours, but the technique has its limitations with respect to its applicability in limited amounts of tumour tissue.

Results

Here, we present a refinement of the ChIP-seq procedures to enable transcription factor mapping on limited amounts of tissue culture cells as well as from a limited amount of tumor tissue derived from core needle biopsies. Our approach uses a carrier that can be removed prior to DNA amplification and sequencing.

Conclusion

We illustrate the applicability of this refined technology by mapping the ERα genome-wide chromatin binding landscape in core needle biopsy material from primary breast tumours. With this, our refined technology permits for a high-resolution transcription factor mapping even from clinical samples.