Table 1 Advantages and disadvantages of current 3D genome technologies
From: From association to mechanism in complex disease genetics: the role of the 3D genome
Technique | Assay name/description | Target size | Assay platform | Cell input | Advantages | Disadvantages | References | |
|---|---|---|---|---|---|---|---|---|
Targeted | ||||||||
3C | Chromosome conformation capture | One target | Quantitative PCR | > 100 M | • Quantitative measurement of long-range interactions between two targeted loci • No sequencing required | • Low throughput • Large amount of input cells | ||
4C | Circular chromosome conformation capture or chromosome conformation capture-on-chip | Multiple targets | Microarray | > 100 M | • Identification of multiple DNA regions that interact with a target locus • Modified protocol: 4C-seq | • Relatively low throughput • Large amount of input cells | ||
5C | Chromosome conformation carbon copy | Multiple targets | Microarray or sequencing | > 100 M | • Multiplexed conformation capture • Higher efficiency and lower background compared to 3C | • Not all sites are compatible to 5C primer design • 5C cannot detect contacts larger than a few megabases | [41] | |
Capture-C | 3C with specific oligonucleotides capture | Multiple targets | Sequencing | 10-20 M | • Unbiased capture of all regions interacting with a specific target sequence • Reduced background signal compared to Hi-C • More informative contacts • Modified protocol: Capture Hi-C | • Interaction detection depends on the design of the target “bait” | [42] | |
Genome-wide | ||||||||
Non-protein-mediated | Hi-C | Chromosome conformation capture by high-throughput sequencing | All interactions | Sequencing | 20-25 M | • High throughput • Improved efficiency • First genome-wide assay • Modified protocol: in situ Hi-C; single cell Hi-C | • High background due to random ligations • Requires deep sequencing • Relatively low resolution | |
Protein-mediated | ChIA-PET | Chromatin interaction analysis by paired-end tag sequencing | All interactions | Sequencing | > 100 M | • Identify specific protein-mediated DNA loop structures • Reduced background noise in sequencing data | • Long processing time (> 6 days) • Requires high efficiency ChIP-grade antibodies | [49] |
HiChIP/ PLAC-seq | In situ Hi-C with protein-centric ChIP/proximity ligation-assisted ChIP-seq | All interactions | Sequencing | 1-10 M | • Faster protocol (2 days) • Higher efficiency than ChIA-PET • Less sequencing | • Requires high efficiency ChIP-grade antibodies | ||