title: Mapping Protein-DNA Interactions Using ChIP-exo and Illumina-Based Sequencing.
abstract: Chromatin immunoprecipitation (ChIP) provides a means of enriching DNA associated with transcription factors, histone modifications, and indeed any other proteins for which suitably characterized antibodies are available. Over the years, sequence detection has progressed from quantitative real-time PCR and Southern blotting to microarrays (ChIP-chip) and now high-throughput sequencing (ChIP-seq). This progression has vastly increased the sequence coverage and data volumes generated. This in turn has enabled informaticians to predict the identity of multi-protein complexes on DNA based on the overrepresentation of sequence motifs in DNA enriched by ChIP with a single antibody against a single protein. In the course of the development of high-throughput sequencing, little has changed in the ChIP methodology until recently. In the last three years, a number of modifications have been made to the ChIP protocol with the goal of enhancing the sensitivity of the method and further reducing the levels of nonspecific background sequences in ChIPped samples. In this chapter, we provide a brief commentary on these methodological changes and describe a detailed ChIP-exo method able to generate narrower peaks and greater peak coverage from ChIPped material.
authors.affiliation: Prostate Cancer Research Group, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership University of Oslo and Oslo University Hospital, Oslo, Norway. stefan.barfeld@ncmm.uio.no.
authors.forename: Stefan J
authors.initials: SJ
authors.lastname: Barfeld
authors.affiliation: Prostate Cancer Research Group, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership University of Oslo and Oslo University Hospital, Oslo, Norway. ian.mills@ncmm.uio.no.|Molecular Oncology, Institute of Cancer Research and Oslo University Hospital, Oslo, Norway. ian.mills@ncmm.uio.no.|Prostate Cancer Research Group, Centre for Cancer Research and Cell Biology (CCRCB), Queen's University of Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK. ian.mills@ncmm.uio.no.
authors.forename: Ian G
authors.initials: IG
authors.lastname: Mills
mesh_terms: D047369:Chromatin Immunoprecipitation / Q000379:methods*; D004273:DNA, Neoplasm / Q000378:metabolism*; D005092:Exonucleases / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008297:Male; D011471:Prostatic Neoplasms / Q000235:genetics / Q000378:metabolism*; D025941:Protein Interaction Mapping / Q000379:methods*; D011944:Receptors, Androgen / Q000378:metabolism*; D017422:Sequence Analysis, DNA / Q000379:methods*; D014407:Tumor Cells, Cultured
chemical_list: C410798:AR protein, human; D004273:DNA, Neoplasm; D011944:Receptors, Androgen; D005092:Exonucleases
keywords: Androgen receptor; Cancer; Chromatin immunoprecipitation; Exonuclease; Prostate