Fig. 2
From: DOT1L inhibition reveals a distinct subset of enhancers dependent on H3K79 methylation
Loss of H3 lysine 79 methylation 2/3 (H3K79me2/3) at enhancers leads to a reduction in transcription at H3K79me2/3 Enhancer Element (KEE) genes. a Gene expression in wild-type SEM compared to ARID1B and CDK6 enhancer mutant clones, normalized to the housekeeping gene YWHAZ. Each point represents a biological replicate. Mann–Whitney U test, *p < 0.01, **p < 0.05 based upon nine biological replicates. Box plots show interquartile range; center line represents the median value. b Metaplot of H3K79me3 reference-normalized ChIP-seq (ChIP-rx) signal at all transcriptional start sites (TSSs) following DOT1Li (EPZ-5676) treatment (lilac) compared to control treatment (purple) in SEM cells. c MA plot of nascent RNA-seq data showing differential gene expression (up (red), down (orange), and insensitive (gray)) in SEM cells following DOT1Li. Differential expression = FDR (false discovery rate) < 0.05 from three biological replicates. d Proportion of differentially expressed genes and insensitive genes, which are directly marked with H3K79me2/3 in the gene body in SEM cells. e Proportion of KEE genes and non-KEE genes, which are upregulated (red), downregulated (orange), or insensitive (gray) following DOT1Li by nascent RNA sequencing (****p < 0.0001, Fisher’s exact test), n = 3. f Mean log FC of H3K79me2/3-marked genes associated with a KEE (purple) or non-KEE (gray) following DOT1Li, from nascent RNA-seq data (****p < 0.0001, Fisher’s exact test, n = 3). Error bars represent s.e.m. g Left: H3K79me3 ChIP-rx tracks showing control (−, purple) and DOT1Li (+, lilac) samples, and nascent RNA-seq tracks showing control (−, black) and DOT1Li (+ , orange) samples at ARID1B in SEM cells. Right: Bar chart displaying mean FPKM at ARID1B in control (−, black) and DOT1Li (+, orange) conditions. ****FDR < 0.0001, n = 3. Error bars represent s.e.m. Source data are provided as a source data file. See also Supplementary Fig. 2
