Table 1.
Single-cell Hi-C techniques and characteristics.
| Methods | Full Name | Procedure | Characteristics |
|---|---|---|---|
| Hi-C [11] (in situ Hi-C) [12] |
Chromosome conformation capture by high-throughput sequencing | Crosslinking, restriction enzyme digestion, end filling with biotinylated dNTP and proximity ligation (ligation performed in intact nuclei in an in situ Hi-C), reverse crosslinking, sonication and streptavidin enrichment, and sequencing. | Widely used genome-wide method |
| Single-cell Hi-C [17,18] |
Single-cell Hi-C | Similar to in situ Hi-C, individual nuclei selected using microscopy after proximity ligation. Remaining steps done in single cells separately. Sonication replaced with a second restriction enzyme to fragment ligation products. | The first single-cell chromatin structure method, relatively low throughput |
| Sci-Hi-C [19,20] | Single-cell combinatorial indexed Hi-C | Crosslinking, restriction digestion, distributed to 96 wells and barcoded bridge-adaptor ligation, nuclei pooled and proximity ligation, redistribution to 96 wells and barcoded sequencing-adaptor ligation, sequencing. | A larger number of single cells with fewer interactions per cell |
| Single-cell Hi-C [21] | Single-cell Hi-C | Crosslinking, single nuclei sorting with FACS, nuclei imaging, overlaid nuclei with low melting agarose. Remaining steps similar to in situ Hi-C but done in single cells. | Combination of imaging with determination of genome structure |
| Sn Hi-C [22] | Single-nucleus Hi-C | Similar to in situ Hi-C but omitting biotin incorporation. Single nuclei sorted by FACS after proximity ligation and then whole genome amplification was done to single nuclei. | More contacts per single cell |
| Improved multiplexed single-cell Hi-C [23] | Improved multiplexed single-cell Hi-C | Improved from [17], with flow cytometry sorting, Tn5 transposase library preparation, and an automation scheme. | Moderate contacts per single cell |
| Dip-C [24] | Single-cell Hi-C of diploid cells | Similar to Sn Hi-C [22]. Whole-genome amplification done with multiplex end-tagging amplification. | Distinguishes two haplotypes of each chromosome |