Innate Antiviral Immunity

Yoon Jung Kim, Tae Hoon Kim, Kim, Yoon Jung, Kim, Tae Hoon

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.