Figure 9. Simplified model of the cohesin and CTCF–mediated interactions in the human IGF2-H19 locus.

DNA elements are indicated as follows: CTCF AD (red bar); CCD (green bar), ICR (purple bar), and CTCF DS (Cerise bar), Enhancer is yellow oval. Pink and pale blue ovals represent the CTCF/cohesin complexes. CpG methylation is depicted as filled lollipops. (A) Linear representation of the IGF2-H19 locus. Elements above the bar represent the maternal allele with CTCF and cohesin binding the ICR and an active H19 gene. Elements below the bar represent the paternal allele with active IGF2 gene and methylated ICR. ChIP data indicate that cohesin and CTCF co-localise at the CCD, CTCF AD and CTCF DS on both alleles. 3C data indicate that these CTCF/cohesin sites interact strongly with each other; while the ICR and enhancer have limited allele specific interactions (long curved arrows indicate 3C interactions between 3C elements). Based on these data we propose the following model: (B) On the paternal allele, co-localisation of CTCF and cohesin at CTCF AD, CCD, and CTCF DS brings these regions together. The methylated ICR does not bind CTCF and is thus excluded from CTCF/cohesin interacting regions. The exclusion of the ICR may enable the IGF2 gene promoters and H19 enhancer region to interact, (shown by yellow oval close to IGF2 arrow) even though they are on different looping domains. (The H19 domain is shaded.) (C) On the maternal allele, CTCF/cohesin can bind to the unmethylated ICR which can then interact with other CTCF/cohesin sites. An interaction between CTCF AD/DMR0 and the ICR may be indirectly mediated through the interaction between CTCF AD/DMR0 and CTCF DS. A monoallelic interaction between the ICR and CTCF DS could redefine the H19 domain and constrain the enhancer to prevent interaction with IGF2 promoters on the maternal allele. Without cohesin, CTCF does not maintain stable loops and IGF2 promoters can access the enhancers and perhaps even other regulatory elements from neighbouring genes. Interactions between the various CTCF sites are likely to be dynamic and may occur sequentially.