Extended Data Fig. 5: Features of active and repressive chromatin dynamics during hematopoiesis.

(a) Heatmap of log2 counts per million (CPM) of 50 kilobase bins across pseudobulks. Changing bins that are statistically significant are shown (deviance goodness-of-fit test from Poisson regression, Methods). The rows and columns are ordered by complete-linkage clustering. Above each heatmap is a dendrogram from clustering the columns, showing the relationship between cell types. (b) Distribution of log2 fold changes (FC) at statistically significant changing bins (null model: a bin has constant signal across all cell types, full model: a bin has signal that depends on cell type, deviance goodness-of-fit test) between pseudobulk of non-HSPCs versus HSPCs. Bimodal distribution highlights differences originate mainly between HSPCs and non-HSPCs. (c) GC content of dynamic 50 kb bins for the four histone marks. Number of dynamic bins depends on the mark. H3K4me1: n = 10518 bins; H3K4me3: n = 2225 bins; H3K27me3: n = 5494 bins; H3K9me3: n = 6085 bins. (d) Distance to nearest TSS measured from the center of each dynamic 50 kb bin. Dotted horizontal line represents 25 kb, meaning the bin would overlap with a TSS. Boxplots show 25th percentile, median and 75th percentile, with the whiskers spanning 97% of the data. (e) Gene ontology (GO) terms of HSPC-specific H3K9me3 (top) and H3K27me3 (bottom) regions. P-value and enrichment from Fisher’s exact test.