12. Chromatin Interaction Analysis Using Paired-End Tag Sequencing (ChIA-PET)

  1. Dr. Matthias Harbers2,3 and
  2. Prof. Dr. Günter Kahl4,5,6
  1. Xiaoan Ruan and
  2. Yijun Ruan

Published Online: 23 JAN 2012

DOI: 10.1002/9783527644582.ch12

Tag-Based Next Generation Sequencing

Tag-Based Next Generation Sequencing

How to Cite

Ruan, X. and Ruan, Y. (2011) Chromatin Interaction Analysis Using Paired-End Tag Sequencing (ChIA-PET), in Tag-Based Next Generation Sequencing (eds M. Harbers and G. Kahl), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany. doi: 10.1002/9783527644582.ch12

Editor Information

  1. 2

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

  2. 3

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

  3. 4

    Mohrmühlgasse 3, 63500 Seligenstadt, Germany

  4. 5

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

  5. 6

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

Author Information

  1. Genome Institute of Singapore, Genome Technology and Biology, 60 Biopolis Street, #02-01 Genome, Singapore 138672, Singapore

Publication History

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

ISBN Information

Print ISBN: 9783527328192

Online ISBN: 9783527644582



  • chromatin interaction analysis;
  • paired-end tag sequencing;
  • ChIA-PET;
  • methods;
  • timeline


Chromatin interaction analysis using paired-end tag sequencing (ChIA-PET) is a genome-wide, high-throughput, and unbiased approach for de novo detection of higher-order chromatin interactions. In a ChIA-PET analysis, cross-linked chromatin fibers are fragmented by sonication and enriched by chromatin immunoprecipitation (ChIP) with a specific antibody of interest. In the enriched chromatin complexes, tethered DNA fragments are joined together by specifically designed DNA linkers through proximity ligation and PETs are extracted for high-throughput sequencing analysis. Mapping PET sequences to a reference genome can reveal genome-wide binding sites and chromatin interactions associated with the protein factor(s) under study. The entire ChIA-PET protocol comprises three major parts: ChIP sample preparation, ChIA-PET library construction, and PET sequencing and mapping. The detailed procedures described here mainly focus on the first two parts, which can be completed in approximately 4 weeks.