Fig. 3: The human-specific CCD boundary at the PCDH locus confines PCDH-β promoter interaction with distal enhancers within the PCDH-γ region, reducing combinatorial diversification of PCDHs in human neuronal cells. | Nature Communications

Fig. 3: The human-specific CCD boundary at the PCDH locus confines PCDH-β promoter interaction with distal enhancers within the PCDH-γ region, reducing combinatorial diversification of PCDHs in human neuronal cells.

From: Evolutionary divergence in CTCF-mediated chromatin topology drives transcriptional innovation in humans

Fig. 3

a Track views illustrating CTCF loops within the PCDH-α, PCDH-β, and PCDH-γ loci in human and macaque neuronal cells. The red pentagon and dashed lines mark the human-specific (HS) boundary and its corresponding position in macaques. Transcription start sites (TSSs) for PCDH genes are shown. α1-14, PCDHA1 to PCDHA14; αC1 and αC2, PCDHAC1 and PCDHAC2; β1-16, PCDHB1 to PCDHB16; γA1-12, PCDHGA1 to PCDHGA12; γB1-7, PCDHGB1 to PCDHGB7; γC3-5, PCDHGC3 to PCDHGC5. b Volcano plot showing changes in CTCF binding intensity at the CTCF sites within the PCDH locus between human and macaque neuronal cells. The red dot represents the human-specific boundary. The x-axis denotes the log2 fold-change in binding intensity, and the y-axis indicates the FDR-adjusted p-values. c Box plot comparing CTCF-mediated chromatin interaction intensities between PCDH-β and PCDH-γ loci in human (n = 1287) and macaque (n = 1042) neuronal cells. The central line indicates the median, the box spans the interquartile range, and the whiskers extend to 1.5× the interquartile range. **** P < 0.0001 (one-tailed Wilcoxon test). d Contact maps depicting normalized CTCF-mediated chromatin interactions between PCDH-β and PCDH-γ loci in human (left) and macaque (right) neuronal cells at a 5-kb resolution. e Contact map showing different chromatin interaction patterns between the PCDH-β and PCDH-γ loci in human versus macaque neuronal cells. f RNAPII-mediated chromatin interactions at the PCDH-α, PCDH-β, and PCDH-γ loci in neuronal cells with enhancers (E1 to E5) were defined by H3K27ac peaks. g Heatmap of RNAPII-mediated chromatin interactions between PCDH promoters and enhancers (E1 to E5) in human and macaque neuronal cells. h Hierarchical clustering of combinatorial transcription of PCDH genes in individual human and macaque neuronal cells, grouped into nine clusters based on co-transcriptional profiles of PCDH genes. Species origin of each cell is indicated at the bottom. i Circos plots depicting the combinatorial transcription of PCDH genes in individual primary neuronal cells from humans (left) and macaques (right). The source data and exact P values for (b) and (c) are provided in the Source Data file.

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