Hi-C |
High interaction frequency with shared gene loci |
3D topology of TADs or whole chromosomes and relation to nuclear structures |
18,39
|
4C-seq |
High interaction frequency |
Frequency of long-range gene interaction between >2 genes/structures |
|
|
Loss of interaction upon NB disassembly |
|
15,21 |
hiFISH |
Known direct interaction with NBs or genes |
Frequency of long-range gene interaction between >2 genes/structures |
21,29,40
|
NB-centric deep sequencing assays (e.g. Immuno-TRAP) |
Specific co-localization with structure |
Higher-order gene interaction with target nuclear structure |
19,20
|
ChIP-seq / DamID |
Shared NB/compartment marker protein or transcription factor binding sites |
Gene position within CTs or relative to NBs/transcription factories |
33,41
|