Table 1 Comparison between different chromatin conformation capturing techniques (adopted and modified from[23])

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