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Innate Antiviral Immunity pp 195–208Cite as

Chromosome Conformation Capture for Research on Innate Antiviral Immunity

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1656))

Abstract

Chromosome conformation capture (3C) technology has revolutionized our knowledge on chromatin folding and nuclear organization. This cis-loop detection approach can be used to identify candidate regulatory elements interacting with target gene of interest. This chapter introduces the application of 3C technique to investigate a dynamic alteration in the chromosome folding structure or genomic architecture resulting from interaction changes between the enhancer and its target gene. Innate antiviral immunity is one of the well-known gene induction systems, involving rapid first-line response to virus or pathogen to trigger gene expression changes in order to protect cells and to limit further infection. Thus, the 3C technique can be a powerful tool for exploring how enhancers control expression of immunity genes during virus infection. 3C assay consists of four major steps: Cross-linking with formaldehyde, restriction enzyme digestion, ligation of cross-linked DNA fragments, and quantitative data analysis. Here, we discuss in detail the design, application, and data analysis of a 3C experiment.

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Authors and Affiliations

  1. Department of Biological Science and Center for Systems Biology, The University of Texas at Dallas, 800 Campbell Rd., Richardson, TX, 75080, USA

    Yoon Jung Kim & Tae Hoon Kim

Authors
  1. Yoon Jung Kim
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  2. Tae Hoon Kim
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Correspondence to Tae Hoon Kim .

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Editors and Affiliations

  1. Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada

    Karen Mossman

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Kim, Y.J., Kim, T.H. (2017). Chromosome Conformation Capture for Research on Innate Antiviral Immunity. In: Mossman, K. (eds) Innate Antiviral Immunity. Methods in Molecular Biology, vol 1656. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7237-1_13

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  • DOI: https://doi.org/10.1007/978-1-4939-7237-1_13

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7236-4

  • Online ISBN: 978-1-4939-7237-1

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