Table 2: Genomic technologies currently in use or in development in the 4DN Network

From: The 4D nucleome project

Assay NameAssay AbbreviationKey features
Chromosome Conformation Capture3C15,61Interactions between specific genomic loci, including genome-wide studies
 4C62Genome-wide interactions of a specific genomic locus
 5C63Many loci against many loci
 Hi-C17Genome-wide map of all interactions in the nucleus
 Single-cell Hi-C36Hi-C variant that enables mapping contacts within single cells
 Combinatorial single-cell Hi-C64Single-cell Hi-C variant using split-pool barcoding to map single cells
 In situ Hi-C64Hi-C variant that performs digestion and ligation in intact nuclei
 DNase Hi-C65Hi-C variant that digests chromatin using DNase
 Micro-C66,67Hi-C variant that digests chromatin using micrococcal nuclease
 Capture Hi-C68,69Hi-C variant that incorporates selection of targeted genomic loci
 TCC70A 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.
 COLA71A variant of Hi-C using frequent restriction cutters to map >2 simultaneous DNA interactions
Chromatin-interaction analysis by paired-end-tag sequencingChIA-PET6,72Genome-wide map of interactions bound to a specific protein
Genome architecture mappingGAM37A cryosectioning method to map colocalized DNA regions in a ligation-independent manner
Split-pool barcoding of RNA and DNASPRITEA ligation-independent method to barcode interacting RNA and DNA that enables mapping of higher-order contacts
RNA interaction with chromatin by paired-end-tag sequencingRICh-PET (UD)Genome-wide mapping for all ncRNA-chromatin interactions
Chromatin-immunoprecipitation aided RICh-PETChIP RICh-PET, UDGenome-wide mapping for three-way interactions involving ncRNA, DNA loci and protein factors
DNA adenine methyltransferase identificationDamID and Single-Cell DamID8,73Genome-wide mapping of molecular contact frequency of DNA loci to a Dam-methylase fusion protein: will be used to measure DNA proximity to different nuclear compartments
Tyramide signal amplification–sequencingTSA–seq (UD)Genome-wide mapping of estimated mean cytological distance (in μm) of a DNA locus in a nuclear compartment
Replicated DNA sequencingRepli–seq74,75Genome-wide mapping of the timing of DNA replication
Thousands of reporters integrated in parallelTRIP51Genome-wide mapping of chromosome position effects on transcription and post-transcriptional processing
RNA antisense purificationRAP49,50,76,77Mapping of DNA regions, RNA species and proteins that are in proximity to a specific ncRNA in the nucleus
  1. UD, under development; SPRITE, split pool recognition of interactions by tag extension