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Detection of Allele-Specific 3D Chromatin Interactions Using High-Resolution In-Nucleus 4C-seq

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Spatial Genome Organization

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2532))

Abstract

Chromosome conformation capture techniques are a set of methods used to determine 3D genome organization through the capture and identification of physical contacts between pairs of genomic loci. Among them, 4C-seq (circular chromosome conformation capture coupled to high-throughput sequencing) allows for the identification and quantification of the sequences interacting with a preselected locus of interest. 4C-seq has been widely used in the literature, mainly to study chromatin loops between enhancers and promoters or between CTCF binding sites and to identify chromatin domain boundaries. As 3D-contacts may be established in an allele-specific manner, we describe an up-to-date allele-specific 4C-seq protocol, starting from the selection of allele-specific viewpoints to Illumina sequencing. This protocol has mainly been optimized for cultured mammalian cells, but can be adapted for other cell types with relatively minor changes in initial steps.

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Acknowledgments

We acknowledge funding from the Agence Nationale de la Recherche (project “IMP-REGULOME”—ANR-18-CE12-0022-02) to D. N.

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Authors and Affiliations

  1. Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France

    Mélanie Miranda, Daan Noordermeer & Benoit Moindrot

Authors
  1. Mélanie Miranda
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  2. Daan Noordermeer
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  3. Benoit Moindrot
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Corresponding authors

Correspondence to Daan Noordermeer or Benoit Moindrot .

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Editors and Affiliations

  1. Institut de génétique et de biologie moléculaire et cellulaire (IGBMC), Illkirch, France

    Tom Sexton

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Miranda, M., Noordermeer, D., Moindrot, B. (2022). Detection of Allele-Specific 3D Chromatin Interactions Using High-Resolution In-Nucleus 4C-seq. In: Sexton, T. (eds) Spatial Genome Organization. Methods in Molecular Biology, vol 2532. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2497-5_2

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  • DOI: https://doi.org/10.1007/978-1-0716-2497-5_2

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2496-8

  • Online ISBN: 978-1-0716-2497-5

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