Fig. 1: Cell-type specific subcompartment architectures in adult mouse cerebral cortex.

a (Left) Workflow. Fluorescence activated nuclei sorting (FANS) was performed on dissected adult mouse cortical tissue (n = 4, 2 F/2 M), followed by in situ Hi-C on intact NeuN+ and NeuN− nuclei. Genome alignment (HiC-Pro (v2.9)) was facilitated by split-mapping at the known chimeric ligation junctions to generate genome-wide pairwise contact maps. Hi-C read counts for NeuN+ and NeuN− (observed/expected) were then independently piped into a k-means clustering algorithm, ultimately generating four clusters representative of chromatin subcompartments in each population. b Correspondence of the NeuN+ and NeuN− determined subcompartments; genome extents of each subcompartment as indicated. Percent overlap of coordinates from each NeuN− subcompartment with each of the NeuN+ subcompartments are represented on the indicated color scale of white (0%) to red (100%). c Heatmap of mean Hi–C (observed/expected) read counts for NeuN + (left) and NeuN− (right) between loci comprising the designated subcompartments; 250 kb resolution. d Heatmap summarizing the characterization of determined clusters as ‘A’ (active) or ‘B’ (inactive) with lamin-associated domains (LADs), enhancer coordinates, and mENCODE ChIP-Seq data for RNAPolII, CTCF, several histone modifications, and mENCODE blacklisted sequences in NeuN+ (left) and NeuN− (right), as indicated. The fraction of 250 kb bins comprising the cluster overlapping these genome tracks is indicated on a scale of 0 (blue) to 1 (red). e Enrichment heatmap of differential NeuN+ and NeuN− H3K79me2 (n = 2), H3K27ac (n = 3), and H3K9me3 (n = 4) tagged sequences with loci comprising each of the four subcompartments (Fisher’s 2 × 2 exact testing, one-sided) (Left) NeuN+ histone modification enrichment, diffReps (p < 0.001). (Right) NeuN− histone modification enrichment, diffReps (p < 0.001). f Representative NeuN+ long-range contact patterns (250 kb resolution) for multiple genomic intervals comprising each chromatin subcompartment. Normalized NeuN+ and NeuN− histone modification profiles tracks of NeuN+ and NeuN− H3K79me2 (n = 2), H3K27ac (n = 3), and H3K9me3 (n = 4) are included. g (Left) Individual Circos plots from four biological replicates for NeuN + (left) and NeuN− (right) trans-chromosomal contacts (1 Mb resolution, HOMER (v4.8), threshold for significant interactions displayed (binomial testing): p < 10⁻⁵⁰; see Methods section). NeuN+ and NeuN− Circos plots aligned horizontally originate from the same brain tissue. Zoom-in window bottom right show 50 Mb portion of chr4; notice sharply different trans profiles for NeuN+ and NeuN−. (Right) Pearson’s correlation heatmap of loci involved in trans- interactions in NeuN+ and NeuN− across replicates (n = 4,4). Scale as shown (r = 0 (blue), r = 0.5 (white), r = 1 (red)); 1 Mb resolution. h (Left) Hi–C trans contact maps for NeuN+ (green) and NeuN− (orange) across 50 Mb windows from six chromosomes, as indicated. NeuN + (n = 4) mean trans interactions in black, SEM in green; NeuN− (n = 4) mean trans interactions in gray, SEM in orange. Subcompartment designations in NeuN + (top) and NeuN− (bottom) included. Y-axis shows number of significant trans contacts (HOMER, threshold: p < 10⁻⁵⁰) (green) for NeuN+ and (yellow) NeuN− nuclei. Source data are provided as a Source Data file.