title: A carrier-assisted ChIP-seq method for estrogen receptor-chromatin interactions from breast cancer core needle biopsy samples.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, UK. Jason.Carroll@cruk.cam.ac.uk
authors.forename: Wilbert
authors.initials: W
authors.lastname: Zwart
authors.forename: Rutger
authors.initials: R
authors.lastname: Koornstra
authors.forename: Jelle
authors.initials: J
authors.lastname: Wesseling
authors.forename: Emiel
authors.initials: E
authors.lastname: Rutgers
authors.forename: Sabine
authors.initials: S
authors.lastname: Linn
authors.forename: Jason S
authors.initials: JS
authors.lastname: Carroll
mesh_terms: D062005:Biopsy, Large-Core Needle; D001943:Breast Neoplasms / Q000473:pathology*; D002843:Chromatin / Q000378:metabolism*; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D047628:Estrogen Receptor alpha / Q000378:metabolism*; D006801:Humans; D061986:MCF-7 Cells; D011485:Protein Binding; D017421:Sequence Analysis / Q000379:methods*
chemical_list: D002843:Chromatin; D047628:Estrogen Receptor alpha
references.citation: Nature. 2012 Jan 04;481(7381):389-93
references.pmid: 22217937
references.citation: Nat Methods. 2011 Jun 05;8(7):565-7
references.pmid: 21642965
references.citation: Nat Genet. 2011 Jan;43(1):27-33
references.pmid: 21151129
references.citation: Nat Methods. 2010 Aug;7(8):615-8
references.pmid: 20622861
references.citation: Nat Genet. 2010 Apr;42(4):343-7
references.pmid: 20208536
references.citation: Clin Cancer Res. 2009 Mar 15;15(6):2098-106
references.pmid: 19276281
references.citation: Genome Biol. 2008;9(9):R137
references.pmid: 18798982
references.citation: J Natl Cancer Inst. 2006 May 17;98(10):671-80
references.pmid: 16705121
references.citation: Methods. 2009 Jul;48(3):240-8
references.pmid: 19275939
references.citation: Nature. 2009 Nov 5;462(7269):58-64
references.pmid: 19890323
references.citation: Nat Protoc. 2011 Sep 29;6(10):1656-68
references.pmid: 21959244
references.citation: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W551-4
references.pmid: 16845068
references.citation: BMJ. 2002 Sep 21;325(7365):648-51
references.pmid: 12242180
references.citation: Nat Genet. 2006 Jul;38(7):835-41
references.pmid: 16767102
references.citation: Nature. 2000 Aug 17;406(6797):747-52
references.pmid: 10963602
references.citation: Nat Genet. 2006 Nov;38(11):1289-97
references.pmid: 17013392
references.citation: Cancer Res. 2001 Jun 15;61(12):4744-9
references.pmid: 11406546
references.citation: Genes Dev. 2010 Oct 1;24(19):2219-27
references.pmid: 20889718
references.citation: EMBO J. 2011 Oct 14;30(23):4764-76
references.pmid: 22002538
references.citation: J Natl Cancer Inst. 2003 Mar 5;95(5):353-61
references.pmid: 12618500
references.citation: Breast Cancer Res Treat. 2010 Oct;123(3):725-31
references.pmid: 20020197
references.citation: Int J Cancer. 2010 Dec 15;127(12):2893-917
references.pmid: 21351269
references.citation: J Natl Cancer Inst. 2004 Jun 16;96(12):926-35
references.pmid: 15199112
references.citation: Cancer Cell. 2004 Jun;5(6):597-605
references.pmid: 15193262