Fig. 5: BRD4 controls transcription elongation at genes and enhancers. | Nature Communications

Fig. 5: BRD4 controls transcription elongation at genes and enhancers.

From: High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription

Fig. 5: BRD4 controls transcription elongation at genes and enhancers.The alternative text for this image may have been generated using AI.

a Target gene example with two associated FANTOM5 enhancers in K562 cells. All FANTOM5 enhancers of MYC are detected as putative enhancers by HiS-NET-seq and show significant Pol II occupancy reductions after 2 h of BRD4 degradation (padj <7.8e−07). HiS-NET-seq profiles are shown from two merged biological replicate measurements. b Quantification of Pol II occupancy changes (log2) at gene-body regions of putative target genes. The Boxplot quantification distinguishes between the number of responsive enhancers (significant reduction in Pol II occupancy after 2 h dTAG7 treatment, padj <0.05) connected to the corresponding target gene (one-sided Wilcoxon rank sum test; *p = 0.048; ***p = 2.1e−04). See Fig. 4h legend for boxplot definition. c Pol II occupancy changes (log2) between 2 h of dTAG7 treatment and the DMSO control. The significance reports the padj values from the Wald test calculated by DEseq2 as described in the Method section. The red and blue data points mark significant (padj <0.05) changes. Data is RLE normalized (see Methods) to spike-in controls from mouse NIH/3T3 cells. Analyzed are promoter-proximal regions (n = 7324) and gene-body regions (n = 9730) of non-overlapping active genes. d Pausing matrices depict Pol II occupancy changes (log2) upon 40 min and 2 h of dTAG7 treatment in distal (x-axis) and proximal regions (y-axis) of active genes (40 min: n = 7090 and 2 h: n = 7324) and putative enhancer regions (40 min: n = 1017 and 2 h: n = 5422). Red arrows that are representatively shown in the first panel mark the figure quadrant associated with increased Pol II proximal pausing and decreased elongation at genes. e, f BRD4 ChIP-Rx occupancy changes (log2) at different regions. The significance reports the padj values from the Wald test calculated by DiffBind as described in the Method section. e Heatmaps show significant (blue, padj <0.05) and non-significant (gray, padj >0.05) BRD4 occupancy changes at promoter, extragenic-, and intragenic enhancer regions after 2 h of dTAG7 treatment. f BRD4 occupancy changes at all detected BRD4 peaks after 40 min and 2 h of dTAG7 treatment (n = 16,233). The blue and red data points mark significant changes (padj <0.05). a–f Data were obtained for human K562 dTAG-BRD4 cells.

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