Fig. 4

Endogenous CTCF sites as Pcdh insulators. a CTCF ChIP-seq of the Pcdhαc1 CBS deletion CRISPR HEC-1-B cell clones. b QHR-4C profiles of the long-range chromatin contacts with HS5-1 as a viewpoint in two single-cell CRISPR clones (D11, D16) with the deletion of the endogenous αc1 CBS. Log2 ratios (deletion vs wild-type) are also shown. c RNA-seq of the WT and αc1 CBS-deleted CRISPR clones. d–f Corresponding to a–c, respectively, but with α12 CBS deletion in two single-cell CRISPR clones (D32, D93). g 5C interaction profiles of the Pcdh α and β clusters in cortical tissues of the HS5-1b or HS5-1a CBS deletion mice. The log2 ratios of chromatin interactions of HS5-1 with Pcdhα or 5′ isoforms of β gene repertoire are highlighted by blue or black rectangles, respectively. Note the significant increase of chromatin interactions between HS5-1 with 5′ isoforms of the Pcdhβ cluster upon the HS5-1b deletion as indicated by enlargement of Insets A and B, compared with no alteration upon the HS5-1a deletion as indicated by enlargement of Insets A′ and B′.h, i QHR-4C confirmed the increased interactions with 5′ isoforms of the Pcdhβ cluster and the decreased interactions with the Pcdhα cluster. j, k RNA-seq revealed increased expression levels of the 5′ isoforms of the Pcdhβ cluster in the homozygous CBS HS5-1b deletion (j) mice in comparison with the HS5-1a deletion (k) mice as controls. Data as mean ± SD, *p < 0.05, **p < 0.01, ***p < 0.001. One-tailed Student’s t test