Fig. 4 |. Characterization of chromatin state at distal candidate cis-regulatory elements across brain cell types.

a-c Heatmaps showing the modification levels of (a) active histone marks (H3K4me1, H3K4me3, H3K27ac), (b) repressive histone marks (H3K27me3, H3K9me3) and (c) chromatin accessibility of candidate CREs in each mouse brain cell type. The cCREs were grouped using K-means clustering based on histone modification signals (H3K27ac, H3K27me3 and H3K9me3) across different cell types. Cell types were indicated with colored dots below and the color of the dots are same as in Fig. 1d. d, Top enriched de novo motifs and GO terms for cCREs in different classes. e, Heatmap showing the enrichment of known transcription factor motifs for cCREs of each class in (a-c). cCREs in eIII-d group were further separated by their densities in each cell type, indicated by the colored dots left side. The color of the dots is the same as Fig. 1d. Each column represents a TF motif, colored by -Log₁₀(P-value) and ordered according to K-means clustering. f, Boxplots showing genomic coverage of chromHMM chromatin state. The boxes were drawn from lower quartile (Q1) to upper quartile (Q3) with the middle line denote the median, whiskers with maximum 1.5 IQR. n = 22 cell types. g, Representative genome browser view of chromHMM chromatin states on marker genes. Chromatin states were colored according to (f). h, Heatmap showing the fraction of variable bases in different chromatin states of FC L2/3 compared to the other 21 cell clusters.