Topological domains in mammalian genomes identified by analysis of chromatin interactions
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...We found that most peak loci encompass a unique DNA site containing a CTCF-binding motif, to which all three proteins (CTCF, SMC3, and RAD21) were bound (5-fold enrichment)....
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...On the other hand, the domains we observe are much smaller than the TADs (1 Mb) (Dixon et al., 2012) that have been reported in humans and mice on the basis of lower-resolution contact maps....
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...Our in situ Hi-C protocol involves crosslinking cells with formaldehyde, permeabilizing them with nuclei intact, digesting DNA with a suitable 4-cutter restriction enzyme (such as MboI), filling the 50-overhangs while incorporating a biotinylated nucleotide, ligating the resulting blunt-end fragments, shearing the DNA, capturing the biotinylated ligation junctions with streptavidin beads, and analyzing the resulting fragments with paired-end sequencing (Figure 1A)....
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...Because many of our loops demarcate domains, this observation is also consistent with studies suggesting that CTCF delimits structural and regulatory domains (Xie et al., 2007; Cuddapah et al., 2009; Dixon et al., 2012)....
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...(C) Percent of peak loci bound versus fold enrichment for 76 DNA-binding proteins....
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