Fig. 2. Enhancer–promoter interactions in NeuN+ and NeuN− cells.

a (Left) cell-type-specific regulatory networks were built by linking genes to NeuN+ and NeuN− specific H3K27ac peaks via Hi–C interactions in NeuN+ and NeuN− cells, respectively. (Right) The number of cell-type-specific peaks and their assigned genes in NeuN+ and NeuN− cells is described. A neuronal gene, HOMER1, is engaged with NeuN+ specific H3K27ac peaks via loops in NeuN+ cells (b), while an oligodendrocyte gene, SOX10, is engaged with NeuN− specific H3K27ac peaks via loops in NeuN− cells (c). The regions that interact with the gene promoter (gray) are highlighted in green (NeuN+) and purple (NeuN−), respectively. Boxplots in the right show expression levels of HOMER1 (FDR = 7.26e−32) and SOX10 (FDR = 1.88e−49) in NeuN+ (n = 4) and NeuN− (n = 4) cells, respectively. FPKM Fragments Per Kilobase of transcript per Million mapped reads. Center, median; box = Q1–Q3; minima, Q1 − 1.5 × IQR; maxima, Q3 + 1.5 × IQR. *FDR < 0.05 calculated by DESeq2 (two-sided Wald test). Source data are provided as a Source Data file. d Genes assigned to NeuN+ specific peaks are enriched for synaptic co-expression modules, while genes assigned to NeuN− specific peaks are enriched for co-expression modules involved in transcriptional regulation and immune response during neurodevelopment. Significant enrichment (Sig.), FDR < 0.05. Fisher’s exact test was used for statistics analysis. OR, odds ratio. e Genes assigned to NeuN+ specific peaks are more highly enriched for synaptic functions such as exocytosis, intracellular signal transduction, protein cluster and structural plasticity than genes assigned to NeuN− specific peaks. Sig., FDR < 0.05. Fisher’s exact test was used for statistics analysis. f Genes assigned to NeuN+ specific peaks are highly expressed in neurons, while genes assigned to NeuN− specific peaks are highly expressed in oligodendrocytes and astrocytes. Astro astrocytes, Micro microglia, Endo Endothelial, Oligo oligodendrocytes.