The three-dimensional folding of chromosomes compartmentalizes the genome and 
and can bring distant functional elements, such as promoters and enhancers, into 
close spatial proximity (2-6). Deciphering the relationship between chromosome 
organization and genome activity will aid in understanding genomic processes, 
like transcription and replication. However, little is known about how 
chromosomes fold. Microscopy is unable to distinguish large numbers of loci 
simultaneously or at high resolution. To date, the detection of chromosomal 
interactions using chromosome conformation capture (3C) and its subsequent 
adaptations required the choice of a set of target loci, making genome-wide 
studies impossible (7-10). We developed Hi-C, an extension of 3C that is capable 
of identifying long range interactions in an unbiased, genome-wide fashion. In 
Hi-C, cells are fixed with formaldehyde, causing interacting loci to be bound to 
one another by means of covalent DNA-protein cross-links. When the DNA is 
subsequently fragmented with a restriction enzyme, these loci remain linked. A 
biotinylated residue is incorporated as the 5' overhangs are filled in. Next, 
blunt-end ligation is performed under dilute conditions that favor ligation 
events between cross-linked DNA fragments. This results in a genome-wide library 
of ligation products, corresponding to pairs of fragments that were originally 
in close proximity to each other in the nucleus. Each ligation product is marked 
with biotin at the site of the junction. The library is sheared, and the 
junctions are pulled-down with streptavidin beads. The purified junctions can 
subsequently be analyzed using a high-throughput sequencer, resulting in a 
catalog of interacting fragments. Direct analysis of the resulting contact 
matrix reveals numerous features of genomic organization, such as the presence 
of chromosome territories and the preferential association of small gene-rich 
chromosomes. Correlation analysis can be applied to the contact matrix, 
demonstrating that the human genome is segregated into two compartments: a less 
densely packed compartment containing open, accessible, and active chromatin and 
a more dense compartment containing closed, inaccessible, and inactive chromatin 
regions. Finally, ensemble analysis of the contact matrix, coupled with 
theoretical derivations and computational simulations, revealed that at the 
megabase scale Hi-C reveals features consistent with a fractal globule 
conformation.