9. Genome-Wide Mapping of Protein–DNA Interactions by ChIP-Seq

  1. Dr. Matthias Harbers3,4 and
  2. Prof. Dr. Günter Kahl5,6,7
  1. Joshua W. K. Ho1,
  2. Artyom A. Alekseyenko1,
  3. Mitzi I. Kuroda1 and
  4. Peter J. Park2

Published Online: 23 JAN 2012

DOI: 10.1002/9783527644582.ch9

Tag-Based Next Generation Sequencing

Tag-Based Next Generation Sequencing

How to Cite

Ho, J. W. K., Alekseyenko, A. A., Kuroda, M. I. and Park, P. J. (2011) Genome-Wide Mapping of Protein–DNA Interactions by ChIP-Seq, in Tag-Based Next Generation Sequencing (eds M. Harbers and G. Kahl), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany. doi: 10.1002/9783527644582.ch9

Editor Information

  1. 3

    4-2-6 Nishihara, Kashiwa-Shi, Chiba 277-0885, Japan

  2. 4

    DNAFORM Inc., Leading Venture Plaza 2, 75-1 Ono-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0046, Japan

  3. 5

    Mohrmühlgasse 3, 63500 Seligenstadt, Germany

  4. 6

    University of Frankfurt am Main Biocenter, Max-von-Lauestraße 9, 60439 Frankfurt am Main, Germany

  5. 7

    Frankfurt Biotechnology Innovation Center (FIZ), GenXPro Ltd, Altenhöferallee 3, 60438 Frankfurt am Main, Germany

Author Information

  1. 1

    Brigham and Women's Hospital and Harvard Medical School, Division of Genetics, Department of Medicine, 77 Avenue Louis Pasteur, Boston, MA 02115, USA

  2. 2

    Harvard Medical School, Center for Biomedical Informatics, 10 Shattuck Street, Boston, MA 02115, USA

Publication History

  1. Published Online: 23 JAN 2012
  2. Published Print: 14 DEC 2011

ISBN Information

Print ISBN: 9783527328192

Online ISBN: 9783527644582



  • genome-wide mapping;
  • protein–DNA interactions;
  • ChIP-Seq;
  • methods;
  • applications


Chromatin immunoprecipitation (ChIP) followed by massively parallel sequencing (ChIP-seq) has enabled generation of genome-wide maps of various types of in vivo protein–DNA interaction at an unprecedented resolution. These maps have led to many important insights into the regulatory mechanisms of gene expression through transcription factor binding and epigenetic modifications. In this chapter, we present a common ChIP-seq experimental and analysis pipeline, and give examples of how ChIP-seq can be applied to tackle various biological questions.