Extended Data Fig. 2: E-P contact frequencies change only mildly upon activation (hemin treatment) or silencing of the GFP reporter gene. | Nature Structural & Molecular Biology

Extended Data Fig. 2: E-P contact frequencies change only mildly upon activation (hemin treatment) or silencing of the GFP reporter gene.

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

Extended Data Fig. 2

a. 4C-seq contact profile overlays comparing contacts of the integrated promoter (P) in the indicated E-lines (E0-11-47-100-407) cultured in the absence (green) or presence of Hemin (purple). Y-axis: 4C coverage normalized to 1 million cis-reads. Shared contacts are in light gray. Track below shows the differential contacts (DC) per 5 kb binned fragments. n= two technical replicates/clone. CTCF and SMC3 ChIP-seq signal tracks are shown for reference. Positions are in kb with respect to the integrated GFP reporter gene. b. 4C-seq contact profile overlays comparing the contacts of the integrated GFP reporter gene promoter in the expressing (green) and long-term silenced (red) E100 (top) and E407 (bottom) cell lines. c. 4C-seq contact profile overlays comparing the contacts of the integrated GFP reporter gene promoter in long-term silenced (red) E100 (top) and E407 (bottom) cell lines, versus its contacts in the noE cell line (lacking the enhancer). In b,c DC-tracks are plotted below each overlay. CTCF and SMC3 ChIP-seq signal tracks are shown for reference. Positions are in kb with respect to the integrated GFP reporter gene. GFP expression (FI) for the expressing (green), long-term silenced cell populations (red) or noE (darkgrey) are shown in the top right of each panel.

Back to article page