Table 2.

The 3C family

Scale	Method	Main features	Refs.
Whole-genome	Hi-C	For mapping whole-genome chromatin interactions in a cell population; proximity ligation is carried out in a large volume	[58]
	TCC	Similar to Hi-C, except that proximity ligation is carried out on a solid phase-immobilized proteins	[59]
	Single-cell Hi-C	For mapping chromatin interactions at the single-cell level	[60]
	DNase Hi-C	Chromatin is fragmented with DNase I; proximity ligation is carried out in solid gel	[61]
	In situ Hi-C	Proximity ligation is carried out in the intact nucleus	[62]
	Micro-C	Chromatin is fragmented with micrococcal nuclease	[64]
	In situ DNase Hi-C	Chromatin is fragmented with DNase I; proximity ligation is carried out in the intact nucleus	[63]
Targeted	3C	The founding method of the 3C family of techniques; for detecting chromatin interactions between a pair of genomic loci	[57]
	ChIP-loop	Combines 3C with ChIP; for detecting chromatin interactions mediated by a particular protein between a pair of genomic loci	[65]
	4C	For detecting chromatin interactions between one locus and the rest of the genome	[66], [67]
	e4C	A more sensitive version of 4C by replacing inverse PCR with primer extension	[68]
	5C	For detecting chromatin interactions between multiple selected loci	[69]
	ChIA-PET	For detecting genome-wide chromatin interactions mediated by a particular protein	[70], [71]
	Capture-C	Combines 3C with a DNA capture technology; equivalent to a high-throughput version of 4C	[72]
	Capture-Hi-C	Combines Hi-C with a DNA capture technology; equivalent to a high-throughput version of 4C	[73]
	Targeted DNase Hi-C	Combines DNase or in situ DNase Hi-C with a DNA capture technology; equivalent to a high-throughput version of 4C	[61]

Note: 3C, chromosome conformation capture; TCC, tethered conformation capture; 4C, circularized chromosome conformation capture; e4C, enhanced 4C; 5C, carbon-copy chromosome conformation capture; ChIA-PET, chromatin interaction analysis by paired-end tag sequencing.