Fig. 2

Tandem CTCF sites balance the usage of Pcdh β and γ promoters. a, b Single-cell RNA-seq of cortical neurons of the WT (a) and CBS b-e (b) deletion mice. Note that the absence of Pcdhβ expression in single cortical neurons of the CTCF sites b-e deletion mice. c QHR-4C profiles with a repertoire of the Pcdhβ promoters as a viewpoint show that they form spatial chromatin contacts with the distal CTCF sites d-f, but not proximal CTCF sites a-c, within the super-enhancer in the mouse cortical tissues. Inset in the upper right corner, ChIP-seq with a specific antibody against CTCF or Rad21. d QHR-4C profiles with a repertoire of the Pcdhγ promoters as a viewpoint show that, in addition to distal CTCF sites, they form gradually increased spatial chromatin contacts with the proximal CTCF sites a-c in the super-enhancer in the mouse cortical tissues. e QHR-4C interaction profiles with a repertoire of increasingly distal CTCF sites in the super-enhancer as a viewpoint show increased spatial chromatin contacts with the Pcdhβ cluster. f Schematic of the deletions of individual CTCF sites or their combinations in the Pcdh β and γ super-enhancer in mice. SE, super-enhancer; del, deletion