Fig. 3
Chromatin-state transitions reflect mDA development. a RNA-seq: Volcano plot showing differential gene expression between NPC and mDA neurons. Differentially expressed genes with an adjusted p-value < 0.05 obtained by Wald test are shown. b Volcano plot as in a where differentially expressed and H3K27me3 and/or H3K9me3-marked genes are colored according to: marked in mDA – pink, marked in NPC – green, and marked in both mDA and NPC – gray. c ChIP-seq heatmaps showing the abundance of H3K27me3, H3K4me3, and H3K9me3 as RPKMs ± 10 kb around TSS of genes that were upregulated in mDA and associated with a chromatin state containing H3K27me3 and/or H3K9me3 and d genes that were downregulated in mDA and associated with a chromatin state containing H3K27me3 and/or H3K9me3, respectively. The arrow indicates H3K27me3+ genes that gain H3K9me3 in mDA. e Chromatin-state transitions between NPC and mDA neurons for upregulated genes in mDA. Colored squares indicate transitions that occurred significantly more often than expected (odds ratio, orange = more than expected, blue = less than expected, p < 0.05 according to Fisher’s exact test and adjusted for multiple testing). f Heatmaps of average H3K27me3, H3K4me3, and H3K9me3 RPKMs ± 10 kb around TSS of genes upregulated from NPC to mDA and K4 in NPC and K4 in mDA. g Gene ontology (GO) of the top (−log10 (adj p-value), Fisher’s exact test) biological processes for upregulated genes in mDA that were K4 in NPC and K4 in mDA. h Heatmaps as in f of genes upregulated in mDA and K4/K27 in NPC and K4 in mDA. i GO of the top biological processes for upregulated genes in mDA that were K4/K27 in NPC and K4 in mDA. j Chromatin-state transitions between NPC and mDA neurons for downregulated genes in mDA (e). k Heatmaps as in f of genes downregulated in mDA and K4 in NPC and K4/K27 in mDA. l GO of the top biological processes for downregulated genes in mDA that were K4 in NPC and K4/K27 in mDA. m Heatmaps as in f of genes downregulated in mDA, and categorized as K4/K27 in NPC and K4/K27 in mDA. n GO of the top biological processes for downregulated genes in mDA that were K4/K27 in NPC and K4/K27 in mDA
