Extended Data Fig. 6: Cell type- and region-specific chromatin modification peaks.

a, Schematic of the human brain colored by brain region (left) and force directed-layout of the main regional branches, colored by annotated brain region and developmental stage (right). b, Heatmap of peak enrichment (tf-idf-normalized fragment counts) of lineage-specific peaks showing co-occurrence of H3K27me3 and H3K4me3 marks in the neuroepithelium and switch to activator (H3K4me3) or repressor (H3K4me3) in a regional branch. Expression of the closest gene is shown in the right panel (min-max scaled log(transcript counts per 10k + 1)). c, Overlaid genomic tracks showing enrichment of bivalent peaks close to lineage-specific genes in the neuroepithelium that switch to activation or repression in the regional branches (overlaid blue-H3K27me3, magenta-H3K4me3). d, Scatter plot showing transcription factor motif enrichment in the H3K27me3 and H3K4me3 co-marked peaks plotted against their expression fold change in the respective regions (see Methods ‘Transcription factor motif enrichment’). Colored dots indicate a motif enrichment Fisher exact test FDR < 0.01. e, Scatter plot showing transcription factor motif enrichment in the H3K27me3 and H3K27ac switching peaks plotted against their expression fold change in the respective regions. Colored dots indicate a motif enrichment Fisher exact test FDR < 0.01.