GAGA Factor Maintains Nucleosome-Free Regions and Has a Role in RNA Polymerase II Recruitment to Promoters
Fig 2
GAF knock-down reduces promoter-proximal polymerase on many genes.
(A) 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) 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. (C) 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. (D) 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.