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 | |
HiChIP/PLAC-seq | Chromatin Immunoprecipitation (ChIP) to subset bound chromatin contacts | Reduce sequencing cost, focus on a subset of interactions | |
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] |