Extended Data Fig. 8: SBS polymer model and rescue experiments using dCas9-CTCF.
From: Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation
a, Genome browser snapshots of the Vcan locus. Arcs show changes of chromatin contacts anchored on the Vcan promoter, distal enhancer, and CBSs identified s between wild type NPCs and NPCs in which promoter-proximal CTCF motif sequences were deleted. The colors of arcs represent degrees of interaction change upon the deletion of CTCF motif sequences (blue to red, -/+log10(p-value)). The promoter region and interacting enhancer region are shown in green and yellow shadows, respectively. CTCF, H3K27ac, H3K4me1, H3K4me3, and H3K27me3 ChIP-seq, and TAD boundaries in wild type NPCs are also shown. b, Schematic representation of the dCas9-CTCF rescue experiments. c, Western blot of cells lysates expressing dCas9-CTCF or dCas9 control plasmids. Uncropped images are available as source data online. d, Snapshots of heatmaps around Vcan showing mapped reads of PLAC-seq in dCas9-CTCF (top and bottom strand) and dCas9 control cell lines. Peaks of chromatin contacts between theVcan gene promoter and the downstream distal element are shown in zoom-in. e, SBS model showing triplet interactions between the Vcan promoter (black), distal enhancer (blue) and CBSsthat weaken upon CTCF depletion (white arrows). Heatmaps from each viewpoint in control and CTCF-depleted NPCs are shown. CTCFs (+) (browns) and CTCFs (-) (reds) are convergently oriented. f, Hi-C contact maps (left) of the Vcan locus in control and auxin treated NPCs and the SBS polymer model (right) (HiCRep stratum adjusted correlation SCC=0.76 and SCC=0.62 respectively). Genomic positions of Vcan promoter (black), distal enhancer (blue) and relevant motif-oriented CBSs (brown and red) are shown by colored triangles. g, SBS derived 3D structures of the Vcan locus in control and CTCF-depleted NPCs, with relevant elements indicated by colored beads (color as in (b)).
