Table 1 Characteristics and application of 3D genomics technology

3C

Chromosome conformation capture

Formaldehyde crosslinking, fragment DNA, adjacent ligation, DNA purification, forward PCR

The C-series, which is the basis of all C technologies, identifies known interactions between DNA with minimal throughput, whereas 3C can verify only one interaction

One to one

[5, 134]

4C

Chromosome conformation capture-on-chip

Formaldehyde crosslinking, fragmented DNA, nearby connection, DNA purification, reverse PCR, ChiP analysis or sequencing by adding adapter

Identification of a known interesting fragment and the interaction of multiple genes, high throughput, but there is a random positive connection caused by false positive

One to many

[5, 135]

5C

Chromosome conformation capture carbon copy

Formaldehyde crosslinking, fragment DNA, universal connector linking, adjacent linking, DNA purification, forward PCR

All interactions in a region can be detected, but that region is generally < 1 Mb. Coverage issues also make the technique unsuitable for whole genome sequencing

Many to many

[5, 7]

ChIA-PET

Chromatin interaction analysis by paired-end tag

Formaldehyde/EGS crosslinking, cell lysis, ChIP, linker nearby connection, tagmentation, PCR, sequencing

Capturing genome-wide interaction of target proteins in the nucleus. Compared with Hi-C, which has the advantage of high resolution, it is possible to reconstruct the genome three-dimensional structure together with Hi-C

Many to many + protein specific

[28, 136]

Capture-C

Chromosome conformation capture coupled with oligonucleotide capture technology

Formaldehyde crosslinking, Fragmented DNA, Nearby connection, Purified circular DNA, Probe hybridization, Sequencing

By hybridization of biotin DNA probes, identification or searching for multiple purposes of known multiple segments intercropping, enrichment sequencing to improve fluence, but there is a random positive connection caused by false positive

Many to all

[15]

Capture-HiC

Hi-C coupled with oligonucleotide capture technology

Specific probe labeling, Formaldehyde crosslinking, Enzymes fragment DNA, End biotin labeling, Dilute the solution, Nearby connection, Purified circular DNA, Sonication, Immunomagnetic beads precipitation, Sequencing

Specific probes were used to study only the target region to capture chromatin interactions in the region where the probe was located (e.g. the promoter region)

Many to all

[66]

PLAC-seq

Proximity ligation-assisted ChIP-seq

Formaldehyde crosslinking, fragment DNA, biotin labeling, ligating, cell lysis, ultrasound, ChIP, DNA purification, immunomagnetic bead precipitation, sequencing

Capture genome-wide interactions of target proteins in the nucleus

Many versus all + antibody to recapture

[137]

HiChIP

Protein-centric chromatin conformation assay

Formaldehyde crosslinking, fragment DNA, biotin labeling, ligating, cell lysis, ultrasound, ChIP, DNA purification, immunomagnetic bead precipitation, sequencing

Capture genome-wide interactions of target proteins in the nucleus

Many versus all + antibody to recapture

[27]

Hi-C

High throughput chromosome conformation capture

Formaldehyde crosslinking, enzymes fragment DNA, end biotin labeling, dilute the solution, nearby connection, purified circular DNA, sonication, immunomagnetic beads precipitation, sequencing

Capturing genome-wide interactions within the nucleus, the resolution is low at present, and there are random connections and background noise

All to all

[12, 138]

In situ Hi-C

In situ chromosome conformation capture

Formaldehyde crosslinking, enzymes fragment DNA, end biotin labeling, dilute the solution, nearby connection, purified circular DNA, sonication, immunomagnetic bead precipitation, sequencing

Capture genome-wide interactions of target proteins in the nucleus

All to all

[13]

ATAC-seq

Assay for transposase-accessible chromatin with high-throughput sequencing

Nucleoplasmic separation, chromatin fragmentation, joint labeling, DNA purification, PCR amplification, double-terminal sequencing

Transposase splices open sections of nuclear chromatin in a specific spatiotemporal context to access the regulatory sequences of all active transcription in the genome

Genome-wide

[139]

ATAC-see

Assay of transposase-accessible chromatin with visualization

Nucleoplasmic separation, chromatin fragmentation, fluorescence labeled splice, DNA purification, PCR amplification, double-terminal sequencing

Transposase can obtain the regulatory sequences of all active transcription in the genome in a specific space and time by slicing open chromatin regions in a specific space and time, and three-dimensional immobile nuclei can be visualized by slicing open chromatin regions in a specific space and time

Genome-wide

[140]

Single-cell ATAC-seq

Single cell assay for transposase accessible chromatin with high-throughput sequencing

Nucleoplasmic separation, chromatin fragmentation, joint labeling, DNA purification, PCR amplification, double-terminal sequencing

Transposase splice open portions of nuclear chromatin in a specific temporal and spatial context to obtain regulatory sequences of all active transcription in the genome within a single cell

Genome-wide

[18, 141, 142]