Figure 3.

The chromatin conformation capture (3C) assay. The 3C assay is used to measure chromatin loops that define promoter–enhancer interactions. Promoter–enhancer interactions are cross-linked, chromatin is then digested with a restriction enzyme, and the resulting restriction fragments are ligated under dilute conditions to favor the ligation of DNA fragments that are in close proximity due to being held together by cross-links. The resulting ligation products are then purified, subjected to quantitative PCR, or high-throughput sequencing (Hi-C).