Table 1.

Comparison between different chromatin conformation capturing techniques (adopted and modified from [23])

Method	Applications	Advantages	Limitations
3C-qPCR	One-to-one	Simple analysis	Laborious, requires knowledge of the locus and proper controls
3C-seq/4C-seq	One-to-all	Good resolution, good signal-to-noise ratio	Restricted to single viewpoint per experiment when multiplexing several viewpoints, analysis requires extra bioinformatics expertise, not an all-to-all genome-wide method
3C-on-chip (4C)	One-to-all	Relatively simple data analysis	Poor signal-to-noise ratio, difficult to obtain genome-wide coverage
5C	Many-to-many	Identifies interactions between many individual fragments	Very laborious, no genome-wide coverage, primer design can be challenging. Analysis requires advanced bioinformatics expertise
Hi-C	All-to-all	Explores the genome-wide interactions between all individual fragments	Very expensive, requires a large sequence effort to obtain sufficient coverage, approximately 10 to 40 kbp resolution, requires advanced bioinformatics expertise
T2C	Many-to-all	Explores the interactome of a selected region in cis but also in trans, high (restriction fragment) resolution, cheaper than Hi-C and 5C, requiring only half a lane of Illumina HiSeq2000	Is restricted to the selected regions of the genome, requires advanced bioinformatics expertise