Table 3.

Summary of the techniques used to analyse chromatin conformation

Technique	Description	Type
3C [62]	First technique developed on which future techniques were based. The chromatin is first digested with enzymes and then re-ligated such that interacting regions are re-ligated together. The resulting products are analysed by quantitative polymerase chain reaction (qPCR) to quantify the frequency of interactions	One to one
4C [63]	Same as 3C, but resulting products are analysed by microarray to test the interactions originating from one region with the rest of the genome.	One to all
Hi-C [64]	Same as 3C, but the resulting products are fragmented and sequenced. This produces the most comprehensive analysis genome wide, but requires significant sequencing efforts to map all possible interactions across the whole genome.	All to all
Capture Hi-C [65]	Same as Hi-C, but the library is first enriched for specific regions to focus the sequencing efforts to regions of interest such as promoters or disease-associated loci.	Many to all
ChIA-PET and HiChIP [26, 27, 66, 67]	Same as Hi-C, but the library is enriched using a chromatin immunoprecipitation step; for example, markers of active regions of the genome. HiChIP is similar to ChIA-PET but provides significant improvements over it.	Many to many/all