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Fig. 1 | Genome Biology

Fig. 1

From: Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection

Fig. 1

CTCF sites as insulators in Pcdhα through directional chromatin looping. a Schematic of the three mouse Pcdh clusters. Genomic organizations of the Pcdh α and γ clusters are similar. Both contain variable exons, each of which is preceded by its own promoter and spliced to respective downstream constant exons. The Pcdhβ cluster contains only variable exons. Each of the variable exons (except αc2, β1, γc4, and γc5) carries one or two forward-oriented CTCF sites (indicated by tandem arrowheads). Two distal enhancers, HS7 (with no CBS) and HS5-1 (flanked by two reverse-oriented CBS elements of HS5-1a and HS5-1b), are located between the Pcdh α and β clusters. The super-enhancer of the Pcdh β and γ clusters, which contains a tandem array of reverse-oriented CBS elements, is located downstream of Pcdhγ. CBS, CTCF binding site; HS, hypersensitive site; SE, super-enhancer. b Single-cell expression patterns of the Pcdhα genes in mouse cortical cells. c CRISPR insertion of CBS elements by homologous recombination. d Schematic of the sequence motif (CTCF binding site contains four modules in the order of modules 1–4 for the forward orientation) and its mutation. e, f CTCF and Rad21 ChIP-seq of single-cell CRISPR clones with one or two forward-oriented CBS elements inserted into the location between the Pcdhα cluster and its downstream HS5-1 enhancer. gj QHR-4C interaction profiles of four CRISPR clones (F9 and F50 for one-CBS insertion; FF15 and FF56 for two-CBS insertion) as well as their CBS mutations (F4 and F25; FF19 and FF30) with HS5-1 (g, h) or α12 (i, j) as a viewpoint (VP), represented by arrowheads. kn Chromatin interaction profiles from an ensemble of 350,000 simulated conformations with HS5-1 (k, l) or α12 (m, n) as a viewpoint, corresponding to gj, respectively. Log2 ratios (insertion vs wild-type or mutation vs insertion) are shown under the 4C profiles

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