Fig. 5: Tissue-specific enhancer requires cohesin to create self-interacting domains and activate CTCF sites.

a, SMC1A depletion causes loss of enhancer-induced contacts. 4C-seq contact profile overlays comparing contacts of the integrated promoter (P) in two cell lines, E100 (top) and EC100 (bottom), following CRISPRi knockdown (KD) of SMC1A (pink) versus contacts measured in cells treated with control single guide RNA (sgRNA) (blue). Shared contacts are in gray. y axis: 4C coverage normalized per 1 million cis-reads. Differential contacts plotted per 5-kb genomic bins are shown below. b,c, 4C-seq differential-contacts tracks showing, for cell lines E100 (b) and EC100 (c), in green the gained contacts of the gene promoter in control cells, SMC1A-depleted cells and RAD21-depleted cells, as compared with its contacts in the cell line lacking the enhancer. Similarly, in orange and yellow, respectively, are shown the gained contacts by the enhancer and the 3×-hCTCF sites in control cells, SMC1A-depleted cells and RAD21-depleted cells, as compared with the contacts of their corresponding endogenous chromosomal position in the cell line lacking the enhancer (no E). Note that in all instances, the enhancer-stimulated contacts seen in control cells are (partially) lost again upon cohesin depletion. d, SMC1A depletion causes loss of enhancer-induced contacts in E407. 4C-seq contact profile overlays comparing contacts of the integrated promoter (P, top) and enhancer (E, bottom) in E407 cells following CRISPRi depletion of SMC1A (pink), versus those measured in E407 cells treated with control sgRNA (blue). y axis, 4C coverage normalized per 1 million cis-reads. Differential contacts (DC) plotted per 5-kb genomic bins are shown below.