Fig. 6: Tissue-specific enhancer recruits cohesin to create self-interacting domains and activate CTCF sites. | Nature Structural & Molecular Biology

Fig. 6: Tissue-specific enhancer recruits cohesin to create self-interacting domains and activate CTCF sites.

From: Building regulatory landscapes reveals that an enhancer can recruit cohesin to create contact domains, engage CTCF sites and activate distant genes

Fig. 6

a–e, The enhancer deposits cohesin (a–c) but not CTCF (d,e) at flanking CTCF sites and the gene promoter. ChIP–qPCR results showing relative enrichment of SMC1A protein bound to the integrated GFP reporter gene promoter (a), the left boundary site (b) and 3×-hCTCF binding sites (c), and of CTCF bound to 3×-hCTCF binding sites (d) and left boundary (e). Enrichment values on the y axis are relative to that measured at a strong SMC1A/CTCF binding site in K562 cells (see Methods). Data are presented as mean values ± s.d. n = 2 biological replicates per clone per position. f, The location of the enhancer dictates the domain contacted by the gene. Top: 4C-seq contact profile overlay showing the contacts of the integrated reporter gene promoter (P) gained (in blue) when located in the indicated CTCF binding landscape with an immediate proximal enhancer (E0). Bottom: 4C-seq contact profile overlay showing the contacts of the integrated reporter gene promoter (P) gained (in red) when located in the same CTCF binding landscape, but with the enhancer at position E100. In both plots, contacts are compared with that of the promoter in a cell line (no E) lacking integrated enhancers or CTCF sites. y axis: 4C coverage normalized per 1 million cis-reads. Differential contacts plotted per 5-kb genomic bins are shown below. n = 2 technical replicates/clone. n = 1 replicate per clone per position. g, The enhancer determines which CTCF sites are selected for cohesin deposition. ChIP–qPCR enrichment for SMC1A at the left boundary, promoter, proximally integrated 3×-mCTCF binding sites and distally integrated 3×-hCTCF binding sites, for a cell line without enhancer (no E, dark gray), a cell line with an enhancer and CTCF sites directly upstream of the promoter and additional CTCF sites 100kb upstream (EC0–C100, blue) and a cell line with CTCF sites directly upstream of the promoter and the enhancer and CTCF sites integrated 100kb upstream (C0–EC100, red).

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