Fig. 6: Transcription kinetics changes correlate with gene expression changes in Dot1l^−/− cells.

a Stacked bar plots per H3K79me3 quintile showing number of genes with significant changes in nascent transcription, as measured by TT-seq in Dot1l^−/− CH12F3 compared to WT cells. b Correlation between TT-seq and RNA-seq log₂ fold changes (Dot1l^−/− over WT) in CH12F3 cells. Each dot represents a gene with colors-coded expression changes in Dot1l^−/− versus WT cells by RNA-seq. Spearman correlation coefficient shown. c Metagene plots showing 5% trimmed means ChIP-seq coverage of H3K79me3, TT-seq, RNAPII, S2P-RNAPII and S5P-RNAPII signals in WT and Dot1l^−/− CH12F3 cells for genes categorized by their gene expression change. d Metaplots showing average elongation velocities for genes categorized as in (c). e Quantification for average elongation velocities at indicated gene segments downstream from the TSS for genes categorized as in (c). f Inferred RNAPII promoter-proximal pause duration for genes categorized as in (c). e, f In box and whisker plots, line inside box represents median; top and bottom edges of the box indicate 25th and 75th percentiles; and whiskers extend the largest value up to 1.5 times the inter-quartile range. P values by Kruskal–Wallis test with paired two-sided Wilcoxon rank sum test for multiple comparisons.