Fig. 4

Reduction of paused RNA-Pol in Gaf mutants. a Distribution of RNA-Pol and GAF in the 83B-C region. RNA-Pol and GAF reads at each nucleotide were normalized with the total reads of each sample. The cumulative reads of RNA-Pol and GAF in the section from 1,525,747 to 1,660,521 of the third chromosome are shown with the gene map below. Genes with significant reduction of promoter-proximal RNA-Pol in mutants are indicated by arrows. Note that input reads are significantly higher than background reads in ChIP samples, potentially reducing the number of enriched peaks. The average read for the input sample is 70. Red dash lines marking this value in GAF ChIP and input are shown in GAF panel. b–g Correlation between RNA-Pol and GAF. RNA-Pol density in the promoter-proximal region (b, e; from −100 to +150) and gene body (c, f; from +500 to the end) in WT (b, c) or mutants (e, f) is separately plotted against the WT level of GAF occupancy according to the enrichment score of each promoter. PIs calculated from the ratio of RNA-Pol densities in the promoter-proximal region over the gene body are similarly plotted for WT (d) and mutants (g). Three hundred and sixty-five genes were included in this analysis. Statistical values for Spearman’s rank correlation coefficient (ρ) and p value (p) are shown. h GAF distribution in different ranks of targets. Three hundred and sixty-five GAF targets are divided into four ranks based on the overall GAF enrichment score from −500 to TSS. Ranks I to IV range from lowest to highest GAF scores. GAF distribution from −500 to +500 is shown for each rank. The normalized reads of both GAF peaks and input are shown in y-axis. i Dosage-dependent relationship between RNA-Pol pausing and GAF occupancy. The PIs of each rank of genes in WT and mutants are represented by box plots. The whiskers represent 5 and 95 % of each rank. The statistical significance of differences calculated by Mann–Whitney U test is indicated for ranks III (p = 0.03, *) and IV (p = 6.04 × 10⁻⁵, ***)