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Chromatin pp 301–320Cite as

Circular Chromosome Conformation Capture Sequencing (4C-Seq ) in Primary Adherent Cells

Part of the Methods in Molecular Biology book series (MIMB,volume 2458)


The three-dimensional structure of the genome is highly organized and is an important aspect of gene regulation. Chromatin interactions can be identified using chromosome conformation capture-based techniques, which rely on proximity ligation. Of these techniques, circular chromosome conformation capture sequencing (4C-seq) is used to identify all chromatin interactions occurring with a single chromosomal location (one versus all). Here we describe a 4C-seq protocol that has been optimized for primary adherent cells, for which the first digestion step is inefficient using standard 4C-seq protocols. It can, however, also be applied to other cell or tissue types. This protocol utilizes a standard DNA library preparation method using a commercial kit, and includes a description of the data processing steps.

Key words

  • 4C-seq
  • Chromosome conformation capture
  • Genome organization
  • Chromatin architecture
  • Next-generation sequencing

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  • DOI: 10.1007/978-1-0716-2140-0_16
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The authors were supported in this work by grants from the Heart Foundation of New Zealand (post-doctoral research fellowship [1691] and small project grant [1804]), the Dunedin School of Medicine Dean’s Bequest fund, and Health Research Council of New Zealand Grants [14-155, 17-402].

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Correspondence to Judith Marsman .

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Marsman, J., Day, R.C., Gimenez, G. (2022). Circular Chromosome Conformation Capture Sequencing (4C-Seq ) in Primary Adherent Cells. In: Horsfield, J., Marsman, J. (eds) Chromatin. Methods in Molecular Biology, vol 2458. Humana, New York, NY.

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2139-4

  • Online ISBN: 978-1-0716-2140-0

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