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Table 1 Different Hi-C-derived methods. Optimisations indicate their modification in their protocols compared to traditional Hi-C

From: Seeing the forest through the trees: prioritising potentially functional interactions from Hi-C

Hi-C flavours Optimisations Advantages compared to traditional Hi-C Reference
Traditional Hi-C [2]
In situ Hi-C Nuclear ligation; 4-based cutter Allow higher resolution data generation [3]
DNase Hi-C DNase I to digest cross-linked DNA Improve capture efficiency, reducing digestion bias but have A compartment bias [77]
Micro-C Crosslinking with DSG and micrococcal nuclease to digest cross-linked DNA Improve capture efficiency, reducing digestion bias but have A compartment bias [78]
BL-Hi-C HaeIII to digest cross-linked DNA, followed by a two-step ligation Improve capture efficiency in regulatory regions, reducing random ligation events [79]
DLO Hi-C No labelling and pull-down step Reduce experimental cost [80]
tag Hi-C Tn5-transposase tagmentation Focus on accessible chromatin, allow only hundreds of cells as input, reduce experimental cost [81]
Capture HiC RNA baits to subset specific chromatin contacts Reduce sequencing cost, focus on a subset of interactions [82]
Capture-C/NG Capture-C/Tiled-C Enrich the 3C library with biotinylated capture oligonucleotides Focus on the subset of interactions while retaining maximal library complexity [83,84,85]
HiChIP/PLAC-seq Chromatin Immunoprecipitation (ChIP) to subset bound chromatin contacts Reduce sequencing cost, focus on a subset of interactions [86, 87]
OCEAN-C Phenol–chloroform extraction step Focus on accessible chromatin [88]
HiCoP Column purified chromatin step Focus on accessible chromatin [89]
Methyl-HiC Bisulfite conversion Allow jointly profiling of DNA methylation and 3D genome structure [90]
Hi-C 2.0 Efficient unligated ends removal Largely reduce the dangling end DNA products [91]
Hi-C 3.0 Double cross-linking with FA and DSG and double digestion with DpnII and DdeI Improve the ability to identify A/B compartments and improve the enrichment of regulatory elements in loop detection [92]