Table 1.

Overview of the features of 3C-based methods

Method	Ease of use	Cost and time involved	Application
3C	Easy	Cheap, fast	For analysis of relatively small loci (up to 1–200 kb) and when the researcher has specific hypotheses regarding long-range interactions between known genomic elements
4C	Moderately challenging	Moderately expensive (array costs, additional data analysis, and data management)	For identification of all genomic regions that associate with a specific predefined gene or regulatory locus of interest
5C	Challenging, elaborate primer and microarray design	Expensive (costs of primers and microarrays, data analysis, and data management)	For mapping chromatin interaction networks between large sets of predefined elements; to discover networks of (novel) long-range interactions; to analyze long-range interactions involving many (up to thousands) genes or loci; to generate dense interaction matrices of defined genomic loci up to several megabases for gaining insight into 3D folding of chromatin
Chip-loop	Challenging	Moderately expensive because of the increased scale of experiment, especially when combined with 4C or 5C detection; good antibodies required	To establish whether a specific protein of interest is present when pairs of loci interact