Fig 2: CA disproportionately increases transcription of SE-associated genes(a-b) GSEA plots show that genes upregulated upon 3h CA treatment of MOLM-14 cells are significantly enriched in (a) MOLM-14 SE-associated genes (SE genes) and (b) genes downregulated by IBET-151 =2-fold in MOLM-13 cells. Red bars in b indicate H3K27ac SE genes in MOLM-14 cells in GSEA leading edge (22 genes, Fisher's exact test, p = 1.2 × 10-3). (c) Scatterplot of false discovery rate (FDR-q) versus normalized enrichment score (NES) for indicated gene sets evaluated by GSEA (n = 3,867), including C2 of MSigDB. (d) Cumulative distribution plots of RNA pol II TR. (e) Change in mRNA copy number/cell of selected SE genes after 3 h treatment (red and blue bars) or after 6 h I-BET151 treatment with CA treatment for the final 3 h (green bar) (mean ± s.e.m., n=3 biological replicates, one of two experiments shown). (f) Effect of change in expression of selected SE genes on MOLM-14 cell growth (mean ± s.e.m., with n=3 biological replicates for siETV6 and siFOSL2 and 6 for other siRNA knockdowns, 24 for FLAG-CEBPA and 12 for other inducible expressions, one of 2-6 experiments shown). (g) GSEA of SE genes in CA-treated cells. Regions of CDK8 and H3K27Ac co-enrichment identify SE genes in each cell line.

Fig 3: CDK8 is asymmetrically loaded at SEs in MOLM-14 cells(a) Clustering of total ChIP-seq signal of CDK8, MED1, BRD4, H3K27ac, RNA pol II, and H3K4me1 on CDK8 positive regions. Each respective cluster is ordered by CDK8 signal. The red bar indicates the cluster most highly enriched for the factors listed above. (b) Overlap between SEs independently identified by ChIP-seq signal for CDK8, MED1 and BRD4 based on the collapsed superset of regions identified by any one factor. (c) ChIP-seq binding profiles at the CEBPA locus.