Figure 6.
Cdc73 promotes expression of oncogenes but not DNA repair and OXPHOS genes through enhancers. (A) Venn diagram of differential H3K27ac (FDR < 0.05) in Rosa26CreERT2Cdc73f/f T-ALL cells (969 and 970) and control Rosa26CreERT2 T-ALL cells upon treatment with 6 nM OHT for 30 hours. (B-C) Volcano plots of significance vs log2(OHT/control) H3K27ac ChIP-seq signals of 969 (B) and control (C) cells in panel A. (D) Metagene plot of dynamic intergenic H3K27ac signals (defined as FDR < 0.05 in 969 and 970 cells but not in control cells) in 969 cells. (E-F) Venn diagram of differential eRNAs in Cdc73f/f T-ALL cells (969 and 970) that were repressed (E) or induced (F) upon treatment with 6 nM OHT for 30 hours. eRNAs were defined as intergenic BruUV-seq peaks or intragenic peaks that were antisense in direction relative to mRNAs. No differential eRNAs were identified after OHT treatment of control T-ALL cells. (G-J) BruUV-Seq log2(OHT/control) vs H3K27ac log2(OHT/Control) scatterplots of all overlapping intergenic peaks (G-H) or overlapping dynamic intergenic peaks (I-J) in control T-ALL cells (G,I) and Cdc73f/f T-ALL cells (969) (H,J). Overlapping dynamic peaks were defined as giving q < 0.05 and FDR < 0.05 in the same direction for the BruUV-Seq and H3K27ac comparisons respectively in both Cdc73f/f T-ALL cells but not in control T-ALL cells. (K) Spearman correlation coefficient analysis of eRNA and H3K27ac log2(OHT/control) from panel J and supplemental Figure 7G in 969 and 970 Cdc73f/f T-ALL cells. (L) Volcano plot of significance vs Bru-seq log2(OHT/control) of genes nearest overlapping OHT-downregulated dynamic intergenic BruUV-Seq and H3K27ac peaks in 969 Cdc73f/f T-ALL cells. (M-N) Display tracks of indicated ChIP-seq and assay for transposase-accessible chromatin (ATAC)-seq data sets at the Rasgrp1 locus in mouse 969 cells (M) or human THP-6 cells (N) showing nearest mouse-human homologous enhancers in red boxes that contain overlapping dynamic intergenic eRNA and H3K27ac peaks. Ets1 ChIP-seq (GSM461516); ATAC-seq (GSM2461649); DN3 Hi-C (GSE79422) analyzed in.50 (O-R) Metagene plots of H3K27ac signals at nonpromoter H2K27ac peaks nearest DNA repair (O,Q) and OXPHOS genes (P,R) from supplemental Table 1 in 969 cells (O-P) and 970 cells (Q-R). ∗∗∗FDR < 0.001; ∗∗∗∗FDR < 0.0001.

Cdc73 promotes expression of oncogenes but not DNA repair and OXPHOS genes through enhancers. (A) Venn diagram of differential H3K27ac (FDR < 0.05) in Rosa26CreERT2Cdc73f/f T-ALL cells (969 and 970) and control Rosa26CreERT2 T-ALL cells upon treatment with 6 nM OHT for 30 hours. (B-C) Volcano plots of significance vs log2(OHT/control) H3K27ac ChIP-seq signals of 969 (B) and control (C) cells in panel A. (D) Metagene plot of dynamic intergenic H3K27ac signals (defined as FDR < 0.05 in 969 and 970 cells but not in control cells) in 969 cells. (E-F) Venn diagram of differential eRNAs in Cdc73f/f T-ALL cells (969 and 970) that were repressed (E) or induced (F) upon treatment with 6 nM OHT for 30 hours. eRNAs were defined as intergenic BruUV-seq peaks or intragenic peaks that were antisense in direction relative to mRNAs. No differential eRNAs were identified after OHT treatment of control T-ALL cells. (G-J) BruUV-Seq log2(OHT/control) vs H3K27ac log2(OHT/Control) scatterplots of all overlapping intergenic peaks (G-H) or overlapping dynamic intergenic peaks (I-J) in control T-ALL cells (G,I) and Cdc73f/f T-ALL cells (969) (H,J). Overlapping dynamic peaks were defined as giving q < 0.05 and FDR < 0.05 in the same direction for the BruUV-Seq and H3K27ac comparisons respectively in both Cdc73f/f T-ALL cells but not in control T-ALL cells. (K) Spearman correlation coefficient analysis of eRNA and H3K27ac log2(OHT/control) from panel J and supplemental Figure 7G in 969 and 970 Cdc73f/f T-ALL cells. (L) Volcano plot of significance vs Bru-seq log2(OHT/control) of genes nearest overlapping OHT-downregulated dynamic intergenic BruUV-Seq and H3K27ac peaks in 969 Cdc73f/f T-ALL cells. (M-N) Display tracks of indicated ChIP-seq and assay for transposase-accessible chromatin (ATAC)-seq data sets at the Rasgrp1 locus in mouse 969 cells (M) or human THP-6 cells (N) showing nearest mouse-human homologous enhancers in red boxes that contain overlapping dynamic intergenic eRNA and H3K27ac peaks. Ets1 ChIP-seq (GSM461516); ATAC-seq (GSM2461649); DN3 Hi-C (GSE79422) analyzed in.50 (O-R) Metagene plots of H3K27ac signals at nonpromoter H2K27ac peaks nearest DNA repair (O,Q) and OXPHOS genes (P,R) from supplemental Table 1 in 969 cells (O-P) and 970 cells (Q-R). ∗∗∗FDR < 0.001; ∗∗∗∗FDR < 0.0001.

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