Fig. 8: Human-specific CTCF loops regulate the function of excitatory neuronal cells in human forebrain organoids.

a Diagram showing primers for the quantitative chromosome conformation capture (3C-qPCR) assays to assess interactions between human-specific enhancers (HSE1, HSE2) and promoters of TGIF1, DLGAP1-206, and DLGAP1-201 in WT and KO organoids. b Comparison of relative interaction intensity between anchor points, as described in (a), and promoters of TGIF1, DLGAP1-206, and DLGAP1-201 in WT and KO organoids. The data are presented as mean ± standard deviation, n = 3 or 4 for each condition. P values are provided (one-tailed Student’s t-test). c Bar plots showing fold change in DLGAP1-201 and DLGAP1-206 transcript levels between WT and KO organoids. Data are shown as mean ± standard deviation, with three organoids used as replicates for each time point. d Comparison of the isoform ratio (DLGAP1−206:DLGAP1−201) in WT and KO organoids. The P value was calculated using one-tailed Student’s t-test. e Representative action potential traces in neurons from WT and KO organoids at day 60. f Traces of miniature excitatory postsynaptic currents (mEPSCs) in excitatory neurons from WT and KO organoids at day 60, with CNQX used to inhibit receptor activity. Dot plots showing reduced amplitude (g) and frequency (h) of mEPSCs in KO organoid excitatory neurons at day 60 compared to WT. Each point represents an individual neuron, with black lines indicate the median. Data from two independent organoid batches (biological replicates). P values are provided (one-tailed Student’s t-test). i Diagram summarizing the pleiotropic effects of human-specific CTCF loops in human forebrain organoid development and function. HSEs human-specific enhancers, Es enhancers. The source data for (b, d, g, h) are provided in the Source Data file.