Table 2.
Genomic technologies currently in use or in development in the 4DN network. UD = under development.
| Assay Name | Assay Abbreviation. | Key features |
|---|---|---|
| Chromosome Conformation Capture | All methods use proximity ligation to measure interacting genomic loci | |
| 3C 15,60 | Interactions between specific genomic loci, including genome-wide studies | |
| 4C 61 | Genome-wide interactions of a specific genomic locus | |
| 5C 62 | Many loci against many loci | |
| Hi-C 17 | Genome wide map of all interactions in the nucleus | |
| Single Cell Hi-C 36 | Hi-C variant that enables mapping contacts within single cells | |
| Combinatorial single-cell Hi-C 63 | Single cell Hi-C variant using split-pool barcoding to map single cells | |
| In situ Hi-C 63 | Hi-C variant that performs digestion and ligation in intact nuclei | |
| DNase Hi-C 64 | Hi-C variant that digests chromatin using DNase | |
| Micro-C 65, 66 | Hi-C variant that digests chromatin using micococcal nuclease | |
| Capture Hi-C 67,68 | Hi-C variant that incorporates selection of targeted genomic loci | |
| TCC 69 | A variant of Hi-C using bead-coupling of complexes | |
| Distance Hi-C UD | Variant of Hi-C using photo-activated crosslinkers to measure the distance between interacting DNA regions. | |
| COLA 70 | A variant of Hi-C using frequent restriction cutters to map >2 simultaneous DNA interactions | |
| Chromatin Interaction Analysis by paired-end-tag sequencing | ChIA-PET 6,71 | Genome-wide map of interactions bound to a specific protein. |
| Genome Architecture Mapping | GAM 37 | A cryosectioning method to map colocalized DNA regions in a ligation-independent manner. |
| Split-pool barcoding of RNA and DNA | SPRITE | A ligation-independent method to barcode interacting RNA and DNA. Enables mapping of higher-order contacts. |
| RNA interaction with chromatin by paired-end-tag sequencing | RICh-PET UD | Genome-wide mapping for all ncRNA-chromatin interactions. |
| Chromatin IP aided RICh-PET | ChIP RICh-PETUD | Genome-wide mapping for 3-way interactions involving ncRNA, DNA loci, and protein factors. |
| DNA Adenine Methyltrans-ferase Identification | DamID and Single-Cell DamID 72,8 | Genome-wide mapping of molecular contact frequency of DNA locus to a Dam methylase fusion protein: will be used to measure DNA proximity to different nuclear compartments |
| Tyramide Signal Amplification-Seq | TSA-Seq UD | Genome-wide mapping of estimated mean cytological distance (in microns) of DNA locus to a nuclear compartment. |
| Replication Labeling-Seq | Repli-Seq 73,74 | Genome-wide mapping of timing of DNA replication |
| Thousands of Reporters Integrated in Parallel | TRIP 50 | Genome-wide mapping of chromosome position effects on transcription and post-transcriptional processing |
| RNA Antisense Purification | RAP 48,49, 75,76 | Mapping of DNA regions, RNA species, and proteins that are in proximity to a specific noncoding RNA in the nucleus. |