Fig. 4: DOT1L inactivation results in local epigenetic changes and upregulation of Polycomb repressed genes in NPC48h.

a Log2 fold-changes of global scaling factors estimated via RELACS in EPZ-treated cells with respect to DMSO levels, for the seven histone modifications included in this study for mESC (left) and NPC48h (right). b Promoter-associated active marks change consistently with EPZ-induced transcriptional dynamics. Upper panel: empirical cumulative density function (ECDF) of log2 fold-change of H3K27ac (top) and H3K4me3 (bottom) peaks overlapping promoter (TSS−1000 bp, +500 bp) of differentially expressed genes (EPZ vs DMSO, adjusted p-value < 0.05) in mESC (left) and NPC48h (right). The red line shows the ECDF of log2 fold-change of peaks overlapping promoters of upregulated genes upon EPZ treatment, while the blue and black line depicts the same information for downregulated genes and all annotated genes respectively. Transcriptionally affected genes upon EPZ treatment show a corresponding gain/loss of H3K27ac and H3K4me3 on their promoters. The epigenetic response is evident in NPC48h, while is almost absent in mESC. c Dimensionality reduction (tSNE) of the chromatin state signature of protein-coding genes for mESC (left) and NPC48h (right). Genes are represented as dots. For each cell type, color-code is based on the most abundant chromatin state present in the promoter region on the left map. On the right map, color-code is a gradient mapping the expression level of each gene. A 2D kernel density plot was over-imposed to show the distribution of differentially expressed genes (adjusted p-value < 0.05) on the tSNE map. d Promoter chromatin state is weakly associated with transcriptional deregulation. For mESC (left) and NPC48h (right), heatmap summarizing the emission probability of the hidden Markov model, next to a histogram showing the proportion of differentially expressed genes (adjusted p-value < 0.05) classified according to the the most abundant promoter chromatin state. Next, a plot showing the expected log2 fold-change posterior distribution (95% credible interval) of each group of genes sharing the same most represented chromatin state in the promoter. Log2 fold-change distributions of states not associated with promoters are shaded. For each group, the expected mean expression log2 fold-changes is close to 0, suggesting that a small fraction of genes in each group is transcriptionally affected.