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

Background: The Estrogen Receptor alpha (ER alpha) 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 ER alpha, which are a direct consequence of the receptors binding preference at specific sites on the chromatin. The identification of ER alpha 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 ER alpha 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.