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

From: Targeted Chromatin Capture (T2C): a novel high resolution high throughput method to detect genomic interactions and regulatory elements

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