Similarly, the translocation frequency of the Igh and Myc loci which are located on different chromosomes in mouse B lymphocytes directly correlates to their contact frequency in a 4C-seq experiment [ 34]. Furthermore, the actual observed intra-and inter-chromosomal translocation frequency has been shown to correlate with the contact probability in a Hi-C experiment in G1 arrested mouse BAY 80-6946 supplier pro-B cells [ 35••]. Within the fractal globule, chromatin is organized into discrete domains. A Hi-C analysis in mouse ES cells identified

2200 topological domains in which chromatin with a median size of 880 kb occupying about 91% of the genome interacts locally [36••]. These topological domains are enriched in housekeeping genes and SINE elements, and are separated by topological boundary regions with characteristics of insulator elements, such as CTCF-binding and a segregation of the heterochromatic H3K9me3 mark [36••]. This

organization of the topological domains is conserved between different human cell types, as well as between human and mouse [36••]. A follow up study by the same group using the ChIP-seq technique found a significant overlap of topological domains with cis-regulatory enhancer-promoter units in 19 embryonic and adult mouse tissues and cell types [37]. Similarly, a 4.5 Mb region encompassing Xist on the X chromosome in mouse ES cells was shown to partition into discrete topologically EX 527 manufacturer associating domains (TADs)

that are 200 kb to 1 Mb in size, and are present on both the active and inactive X chromosome in male and female ES cells [38••]. While they are enriched in, they do not require H3K27me3, H3K9me2 nor lamina-associated domains (LADs) for their maintenance [38••]. Within a TAD, genes are transcriptionally co-regulated, and while the TADs as a whole do not change, the internal TAD contacts rearrange upon ES cell differentiation supporting the link between chromatin structure and transcription [38••]. Similarly, a study of the active and inactive X-chromosome in human SATO3 lymphoblast cells revealed that transcription disrupts intrachromosomal interactions, leading to local chromatin decompaction Sodium butyrate at promoters [39]. A 5C study as part of the ENCODE project analyzed the interactions of transcriptional start sites (TSS) in 44 regions representing 1% of the genome in three human cell lines [40]. More than 1000 mostly asymmetric long-range interactions with distal elements resembling promoters and enhancers were identified within these regions [40]. However, in contrast to another study [37], ∼60% of the interactions were found in only one of the three cell lines analyzed indicating a cell-type specific chromatin folding [40]. Therefore, it remains to be determined how conserved these long-range interactions are between cell types or species.