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Determination of High-Resolution 3D Chromatin Organization Using Circular Chromosome Conformation Capture (4C-seq)

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Book cover Polycomb Group Proteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1480))

Abstract

3D chromatin organization is essential for many aspects of transcriptional regulation. Circular Chromosome Conformation Capture followed by Illumina sequencing (4C-seq) is among the most powerful techniques to determine 3D chromatin organization. 4C-seq, like other modifications of the original 3C technique, uses the principle of “proximity ligation” to identify and quantify ten thousands of genomic interactions at a kilobase scale in a single experiment for predefined loci in the genome.

In this chapter we focus on the experimental steps in the 4C-seq protocol, providing detailed descriptions on the preparation of cells, the construction of the circularized 3C library and the generation of the Illumina high throughput sequencing library. This protocol is particularly suited for the use of mammalian tissue samples, but can be used with minimal changes on circulating cells and cell lines from other sources as well. In the final section of this chapter, we provide a brief overview of data analysis approaches, accompanied by links to publicly available analysis tools.

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Acknowledgements

We thank Céline Hernandez for comments on the manuscript. Work in the D.N. laboratory is supported by funds from the Fondation pour la Recherche Médicale (FRM—Amorçage de jeunes équipes 2014, grant AJE20140630069), the Biologie Intégrative des Génomes project funded by the Inititiative d’Excellence Paris-Saclay (ANR-11-IDEX-0003-02) and the Centre National de la Recherche Scientifique (CNRS).

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Authors and Affiliations

  1. Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris Sud, University Paris-Saclay, 1 Avenue de la terrasse, 91198, Gif sur Yvette, France

    Mélody Matelot & Daan Noordermeer

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  1. Mélody Matelot
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  2. Daan Noordermeer
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Correspondence to Daan Noordermeer .

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Editors and Affiliations

  1. IBCN-CNR, Institute of Cell Biology and Neurobiology and Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi”, Rome, Italy

    Chiara Lanzuolo

  2. Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan, Italy

    Beatrice Bodega

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Matelot, M., Noordermeer, D. (2016). Determination of High-Resolution 3D Chromatin Organization Using Circular Chromosome Conformation Capture (4C-seq). In: Lanzuolo, C., Bodega, B. (eds) Polycomb Group Proteins. Methods in Molecular Biology, vol 1480. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6380-5_20

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  • DOI: https://doi.org/10.1007/978-1-4939-6380-5_20

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6378-2

  • Online ISBN: 978-1-4939-6380-5

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