Inferring chromatin organization. Inferring chromatin organization. The original 3C method is outlined from top to bottom on the left. Formaldehyde cross-linking captures interactions between DNA segments (blue and green lines) mediated by protein complexes (colored shapes). The chromatin is next digested with a restriction enzyme, and the free DNA ends are joined by proximity ligation before reverse cross-linking and purification. The genome-wide ChIA-PET and Hi-C techniques are related to 3C, and key steps are shown from left to right. The Y-shaped molecule represents antibodies. Biotinylated nucleotides are shown as red dots. Streptavidin beads are shown in brown. The genome-scale 4C and 5C methods indicated at the bottom require the production of 3C libraries, and specific key steps are outlined from left to right. Green arrows represent PCR primers specific to the bait region. 5C primers used during the ligation-mediated amplification step are illustrated with green and blue lines, where the light and dark gray moieties represent universal primer sequences. James Fraser et al. Microbiol. Mol. Biol. Rev. 2015; doi:10.1128/MMBR.00006-15