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DNase Hi-C is a method to detect and quantify pairwise interactions between chromosome regions across the entire genome. DNase Hi-C was designed to overcome the limitations associated with restriction enzyme-based Hi-C approaches. Advances in molecular techniques led to the development of an improved version of this technique known as in situ DNase Hi-C that is dramatically simplified and easy to use.
The in situ DNase Hi-C protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. The cells are then permeabilized with their nuclei intact. Chromatin is then randomly fragmented by DNase I. The resulting chromatin fragments are end-repaired and dA-tailed, then marked with a biotinylated internal adaptor, and proximity ligation is carried out in the intact nucleus to favor ligation events between the cross-linked DNA fragments. The resulting DNA sample contains ligation products consisting of chimeric DNA fragments that were originally in close spatial proximity in the nucleus, marked with biotin at the junction. A whole-genome chromatin interaction library is constructed by shearing the DNA, selecting the biotin-containing fragments with streptavidin magnetic beads and PCR amplification. After high throughput sequencing, analysis of the resulting paired-end sequences produces a matrix that quantitatively characterizes the whole-genome chromatin contacts.
See Ramani et al 2016 for more details on in situ DNase Hi-C.
Image source: Ramani et. al. Nature Protocols 2016, Figure 1