Fig. 3

Ino80p knockdown causes the transition of RNAPII pausing at genes with the alternative pausing site. a Average profile indicates median PRO-seq intensity in Ino80p-AID cells under Ctrl and KD conditions for paused genes. b Boxplots represent the relative read ratio (log₁₀) at the significantly increasing peaks (red indicates the ratio of KD versus Ctrl and green indicates the ratio of Rescue versus Ctrl) at each replicate. To analyze the relative distance to P1 from each peak (x-axis), we first calculated the distance either from TSS to P1 or P1 to TSS + 250 bp, and divided each into 10 bins, and mapped the peak to the corresponding bins. Former and later bins were referred to as − 10 to − 1 and 1 to 10 depending on the distance from P1, respectively. To display the significantly enriched bins, bins with less than 5% of the total increasing peaks were excluded; in the end, 386 peaks for replicate 1 and 383 peaks for replicate 2 out of 618 peaks at 467 genes were used. c Average profiles exhibit median PRO-seq intensity at TSS of shift-to-5′ genes (left). The arrows and dotted lines represent the median of P1 (blue, 142 bp) and P2 (red, 56 bp). Boxplot shows the distance from TSS to the indicated pausing sites (right). d Average profiles represent median PRO-seq intensity for no-shift and shift-to-5′ genes in Ctrl data. The two dotted lines represent the 10th (− 22 bp) and 90th (− 144.8 bp) percentiles of P2 relative to P1 for shift-to-5′ genes. e Average profiles display median PRO-seq intensity (left), and boxplots depict the smoothed PRO-seq intensity (right) at the indicated pausing sites of shift-to-5′ genes. f Genome browser view of PRO-seq signal for representative shift-to-5′ genes. All data except for (a) were generated using combined biological replicates. For average profiles, medians reflect the 10-bp bin. Asterisks represent statistically significant differences based on Wilcoxon signed rank test