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Fig. 4 | BMC Genomics

Fig. 4

From: CTCF-mediated chromatin loops enclose inducible gene regulatory domains

Fig. 4

Models of CTCF loop formation and genomic organization. a Model of CTCF loop-enclosed genomic domain. CTCF loops enclose domains of enhancer-regulated stimulus-responsive genes, separating them from domains of constitutively expressed housekeeping genes. b The strong preference shown by CTCF binding sites for interacting with partner sites on their 3′ side that have an opposite orientation cannot be explained by a spatial diffusion model in which partner sites encounter each other through diffusion in three-dimensional nuclear space. Such a mechanism would not be able to distinguish between the three depicted scenarios (upstream vs downstream location of partner sites and parallel vs anti-parallel orientation of partner sites). The strong observed preference for scenario (iii) implies chromatin template-mediated contact between the partner sites. c Mechanistic model for the formation of interactions between CTCF-bound genomic sites. Relatively stationary RNAP2 molecules in transcription factories reel in the chromatin template, bringing distal CTCF binding sites towards the factory. Bound CTCF molecules presenting their C-terminus to the RNAP2 polymerase interact with and are efficiently dislodged by the polymerase. Those presenting their N-terminus stall the polymerase, giving them time to interact with other factory-tethered CTCF molecules

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