20 months ago
Czech Republic, Brno, CEITEC
First, I would recommend to go through "xC" (chromosomal conformation capture) technologies: http://www.ncbi.nlm.nih.gov/pubmed/19588093. Actually in early times people were doing FISH analysis and counting the number of cells that have two marked regions in close proximity to see if given chromosomal regions are in contact.
HiC basically gives you a map of contacts between all pairs of genomic loci. Todays resolution allows you to split the genome into 0.5-1Mb regions and to get an estimate of contact frequency between a pair of regions on the same/different chromosomes.
HiC is most useful in fundamental research and can help to link epigenetics with physical chromatin interactions and positioning in the nucleus. It can also be used to see how the DNA is folded during various cell cycle stages, etc. This approach could also be used to probe if spatial positioning matters when dealing with "fragile" (frequently mutated) DNA regions, therefore it is important in cancer research.