Genes with reduced pausing in GAF-RNAi are enriched for GAF-bound promoters.

<p><b>(A)</b> Fraction of all genes or genes with significantly reduced promoter GRO-seq that are paused, have GAF-bound promoter, or high-confidence GAF peaks within their promoter. <b>(B)</b> The average GAF ChIP-seq reads from untreated (black and grey lines) or GAF-RNAi (maroon and red lines) cells between 500bp upstream to 500bp downstream for the TSS of paused genes with GAF-bound promoters separated into genes with significantly reduced promoter GRO-seq reads (Pause reduced) and all other paused genes with GAF-bound promoters (Paused unchanged).</p

GAF knock-down reduces promoter-proximal polymerase on many genes.

<p><b>(A)</b> The average GRO-seq reads (per million mapped reads) between 500bp upstream to 1000bp downstream for the TSS of all genes binned by 10bp. The reads from the sense strand are plotted above zero and the reads from the anti-sense strand are plotted below zero. <b>(B)</b> Promoter-proximal GRO-seq reads (100bp window with the most reads within 250bp of the TSS) of each gene for LacZ-RNAi and GAF-RNAi libraries plotted as the log₂ ratio of GAF-RNAi to LacZ-RNAi reads is plotted on the y-axis and log₂ of the average of LacZ-RNAi and GAF-RNAi reads on the x-axis. The regions with significant changes between the LacZ-RNAi and GAF-RNAi as determined by edgeR are colored red. <b>(C)</b> Gene body GRO-seq reads (500bp downstream of the TSS to the polyadenylation site) of each gene for LacZ-RNAi and GAF-RNAi libraries are plotted as in B. The regions with significant changes between the LacZ-RNAi and GAF-RNAi as determined by edgeR are colored orange. <b>(D)</b> The change in promoter-proximal and gene body reads represented as log₂ of the GAF-RNAi to LacZ-RNAi ratio. The promoter regions with significant changes between the LacZ-RNAi and GAF-RNAi as determined by edgeR are colored red.</p

Promoters with reduced pausing fill-in with nucleosomes.

<p><b>(A)</b> The average profile of LacZ-RNAi and GAF-RNAi MNase-seq reads 500bp upstream and downstream of the TSS of paused genes with GAF-bound promoters separated into genes with significantly reduced promoter GRO-seq reads (Pause reduced) and all other paused genes with GAF-bound promoters (Pause unchanged). <b>(B)</b> Heatmaps showing the LacZ-RNAi MNase-seq read level, GAF-RNAi MNase-seq read level, and the change in MNase-seq reads (GAF-RNAi subtracted from LacZ-RNAi) 500bp upstream and downstream from each TSS of paused genes with GAF-bound promoters arranged based on the significance of GRO-seq promoter read reduction in 10bp bins, as indicated by the left heatmap. The Pause reduced genes are indicated by the red bar at the bottom of the left heatmap. The p-values for increased MNase-seq reads from 100bp upstream to 50bp downstream of each TSS are indicated in the right heatmap. <b>(C)</b> The average profile of LacZ-RNAi and GAF-RNAi H2AvD reads 500bp upstream and downstream of the TSS of paused genes with GAF-bound promoters separated into Pause reduced genes and Pause unchanged genes. <b>(D)</b> The average profile of LacZ-RNAi and GAF-RNAi MNase-seq reads 500bp upstream and downstream of high confidence intergenic GAF peaks.</p

The number of paused and actively-transcribed genes for 9452 genes.

<p>The number of paused and actively-transcribed genes for 9452 genes.</p

Levels of insulator-associated factors and Motif-1-binding protein are highest on unaffected genes.

<p><b>(A)</b> The median intensity for the insulator protein BEAF32 (BEAF_70 ChIP-chip) 500bp upstream and downstream of the TSS of paused genes with GAF-bound promoters separated into genes with significantly reduced promoter GRO-seq reads (Pause reduced, red line) and all other paused genes with GAF-bound promoters (Pause unchanged, gray line). The shaded areas represent the 10% and 90% confidence intervals. <b>(B)</b> The same plot as in A for the chromodomain protein Chriz (Chro(Chriz)BR ChIP-chip). <b>(C)</b> The median ChIP-seq reads for the transcription factor Motif-1-binding protein ChIP-seq dataset, plotted the same as A. <b>(D)</b> Fraction of paused genes with GAF-bound promoters overlapping with regions of enrichment for BEAF32 in BEAF_70 ChIP-chip dataset within 500bp of their TSS. <b>(E)</b> The same plot as in D for Chriz in the Chro(Chriz)BR dataset. <b>(F)</b> The same plot as in D for Motif-1-binding protein ChIP-seq dataset on their promoter.</p

The number of paused and actively-transcribed genes for 1939 GAF-bound genes.

<p>The number of paused and actively-transcribed genes for 1939 GAF-bound genes.</p