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Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci

Author

Listed:
  • Roland Jäger

    (The Institute of Cancer Research
    Present address: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, A-1090 Vienna, Austria)

  • Gabriele Migliorini

    (The Institute of Cancer Research)

  • Marc Henrion

    (The Institute of Cancer Research)

  • Radhika Kandaswamy

    (The Institute of Cancer Research)

  • Helen E. Speedy

    (The Institute of Cancer Research)

  • Andreas Heindl

    (The Institute of Cancer Research)

  • Nicola Whiffin

    (The Institute of Cancer Research)

  • Maria J. Carnicer

    (Haemato-Oncology Research Unit, The Institute of Cancer Research)

  • Laura Broome

    (Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research)

  • Nicola Dryden

    (Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research)

  • Takashi Nagano

    (Nuclear Dynamics Programme, The Babraham Institute)

  • Stefan Schoenfelder

    (Nuclear Dynamics Programme, The Babraham Institute)

  • Martin Enge

    (Science for Life Laboratory, Karolinska Institutet)

  • Yinyin Yuan

    (The Institute of Cancer Research)

  • Jussi Taipale

    (Science for Life Laboratory, Karolinska Institutet)

  • Peter Fraser

    (Nuclear Dynamics Programme, The Babraham Institute)

  • Olivia Fletcher

    (Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research)

  • Richard S. Houlston

    (The Institute of Cancer Research)

Abstract

Multiple regulatory elements distant from their targets on the linear genome can influence the expression of a single gene through chromatin looping. Chromosome conformation capture implemented in Hi-C allows for genome-wide agnostic characterization of chromatin contacts. However, detection of functional enhancer–promoter interactions is precluded by its effective resolution that is determined by both restriction fragmentation and sensitivity of the experiment. Here we develop a capture Hi-C (cHi-C) approach to allow an agnostic characterization of these physical interactions on a genome-wide scale. Single-nucleotide polymorphisms associated with complex diseases often reside within regulatory elements and exert effects through long-range regulation of gene expression. Applying this cHi-C approach to 14 colorectal cancer risk loci allows us to identify key long-range chromatin interactions in cis and trans involving these loci.

Suggested Citation

  • Roland Jäger & Gabriele Migliorini & Marc Henrion & Radhika Kandaswamy & Helen E. Speedy & Andreas Heindl & Nicola Whiffin & Maria J. Carnicer & Laura Broome & Nicola Dryden & Takashi Nagano & Stefan , 2015. "Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci," Nature Communications, Nature, vol. 6(1), pages 1-9, May.
    • Handle: RePEc:nat:natcom:v:6:y:2015:i:1:d:10.1038_ncomms7178
    DOI: 10.1038/ncomms7178
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    Cited by:

    1. Zhen Wah Tan & Enrico Guarnera & Igor N Berezovsky, 2018. "Exploring chromatin hierarchical organization via Markov State Modelling," PLOS Computational Biology, Public Library of Science, vol. 14(12), pages 1-35, December.
    2. M S Vijayabaskar & Debbie K Goode & Nadine Obier & Monika Lichtinger & Amber M L Emmett & Fatin N Zainul Abidin & Nisar Shar & Rebecca Hannah & Salam A Assi & Michael Lie-A-Ling & Berthold Gottgens & , 2019. "Identification of gene specific cis-regulatory elements during differentiation of mouse embryonic stem cells: An integrative approach using high-throughput datasets," PLOS Computational Biology, Public Library of Science, vol. 15(11), pages 1-29, November.

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