Chromosome Conformation Capture for Research on Innate Antiviral Immunity

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.