Gene expression is influenced by the 3D organisation of the genome.
We think of DNA as a long sequence of bases, but to fit in a nucleus, that long sequence has to be folded in on itself many times. This may mean that certain sequences far apart in the sequence are actually in close proximity to each other in 3D space. This 3D arrangement can lead to interactions of DNA sequences far apart in the genome that may regulate the expression of different genes. To investigate this, DNA can be exposed to a kind of molecular superglue that sticks any neighbouring strands together. Endonucleases then chop up the DNA until all that is left are the intersections between tangled strands. These can then be sequenced to work out which long distance sequences are actually neighbours.
Based on the research of Eileen Furlong.