Fig. 6: Human-specific CTCF loops define distinct DLGAP1 isoform usage in neuronal cells between humans and macaques.

a CTCF loops at the DLGAP1 locus in human and macaque neuronal cells. Human-specific loops, originating from a human-specific CTCF site (Fig. S9b), are shown with interaction intensities. Two loops, encompassing the DLGAP1−206 promoter, are highlighted in yellow. Dashed red lines indicate the human-specific CTCF site in humans and its corresponding position in macaques. b 5-kb resolution contact maps depicting CTCF-mediated chromatin interactions at the DLGAP1 locus in human (left) and macaque (right) neuronal cells. Zoomed-in views show interactions centered on the DLGAP1−206 promoter, with red circles marking significant differences (P < 0.05, as determined by DEseq2, see “Methods”) between species, corresponding to the human-specific CTCF loops shown in (a). c Paternally inherited variants at the human-specific CTCF site shown in (a) were detected in families with autism spectrum disorder. In family SF0171486, a 10-nucleotide deletion is observed in the patient’s sibling, whereas in family 12997, both the patient and the sibling both carry a C > A single nucleotide variant (SNV). d RNAPII loops connect eight human-specific enhancers to the DLGAP1−206 TSS, all within the human-specific CTCF loops in human neuronal cells. e Uniform Manifold Approximation and Projection (UMAP) visualization of single-cell DLGAP1 transcript levels in human (left) and macaque (right) neuronal cells, with annotations for NPC (neural progenitor cells), IPC (intermediate progenitor cells), and EN (excitatory neurons). f Frequency distribution of the predominant DLGAP1 isoforms, DLGAP1-201 and DLGAP1−206, in neuronal cells derived from humans (top) or macaques (bottom), as determined by single-cell isoform sequencing. A macaque-specific exon (MSE) is highlighted. g Heatmap of chromatin accessibility at the human-specific (HS) CTCF site, enhancers, and the DLGAP1−206 TSS during neural differentiation in the human fetal prefrontal cortex. h Diagram illustrating that human-specific CTCF loops act in a concordant yet constrained manner to restrict distinctive human enhancers to interact with specific isoform promoters through RNAPII looping, resulting in divergent isoform usage between species.