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Mapping Protein–DNA Interactions Using ChIP-exo and Illumina-Based Sequencing

  • Stefan J. BarfeldEmail author
  • Ian G. MillsEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1443)

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.

Key words

Chromatin immunoprecipitation Exonuclease Cancer Androgen receptor Prostate 

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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.Prostate Cancer Research Group, Centre for Molecular Medicine Norway (NCMM)Nordic EMBL Partnership University of Oslo and Oslo University HospitalOsloNorway
  2. 2.Molecular OncologyInstitute of Cancer Research and Oslo University HospitalOsloNorway
  3. 3.Prostate Cancer Research Group, Centre for Cancer Research and Cell Biology (CCRCB)Queen’s University of BelfastBelfastUK

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