UNIT 21.15 Chromatin Interaction Analysis Using Paired-End Tag Sequencing

  1. Melissa J. Fullwood,
  2. Yuyuan Han,
  3. Chia-Lin Wei,
  4. Xiaoan Ruan,
  5. Yijun Ruan

Published Online: 1 JAN 2010

DOI: 10.1002/0471142727.mb2115s89

Current Protocols in Molecular Biology

Current Protocols in Molecular Biology

How to Cite

Fullwood, M. J., Han, Y., Wei, C.-L., Ruan, X. and Ruan, Y. 2010. Chromatin Interaction Analysis Using Paired-End Tag Sequencing. Current Protocols in Molecular Biology. 89:21.15:21.15.1–21.15.25.

Author Information

  1. Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore

Publication History

  1. Published Online: 1 JAN 2010
  2. Published Print: JAN 2010


Chromatin Interaction Analysis using Paired-End Tag sequencing (ChIA-PET) is a technique developed for large-scale, de novo analysis of higher-order chromatin structures. Cells are treated with formaldehyde to cross-link chromatin interactions, DNA segments bound by protein factors are enriched by chromatin immunoprecipitation, and interacting DNA fragments are then captured by proximity ligation. The Paired-End Tag (PET) strategy is applied to the construction of ChIA-PET libraries, which are sequenced by high-throughput next-generation sequencing technologies. Finally, raw PET sequences are subjected to bioinformatics analysis, resulting in a genome-wide map of binding sites and chromatin interactions mediated by the protein factor under study. This unit describes ChIA-PET for genome-wide analysis of chromatin interactions in mammalian cells, with the application of Roche/454 and Illumina sequencing technologies. Curr. Protoc. Mol. Biol. 89:21.15.1-21.15.25. © 2010 by John Wiley & Sons, Inc.


  • PET;
  • paired-end;
  • mate-pair;
  • SAGE;
  • DNA sequencing;
  • ChIA-PET;
  • 454 sequencing;
  • Illumina sequencing;
  • transcription factor binding sites;
  • chromatin interactions;
  • chromosome conformation capture;
  • chromatin immunoprecipitation