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The 3C method uses formaldehyde cross-linking to covalently link interacting chromatin segments in intact cells. Cross-linked chromatin is then solubilized and digested with an appropriate restriction enzyme. This is followed by intramolecular ligation of cross-linked fragments. The resulting ‘3C template’ thus contains a large collection of ligation products. Each ligation product reflects an interaction between two genomic loci and can be detected by quantitative PCR using specific primers. The abundance of each ligation product is a measurement of the frequency with which the two loci interact. Thus, the 3C method can be used to capture and quantify physical interactions between genes and distant elements, both in cis and in trans.
(Dekker, 2006) The three 'C' s of chromosome conformation capture: controls, controls, controls. Nat Methods.