Fig. 4

Proper localization of pausing is closely associated with the regulation of + 1 nucleosome by Ino80p. a Average profile shows median MNase-seq intensity in the auxin-untreated Ino80p-AID cells (GSM3304635) at P1 of no-shift and shift-to-5′ genes (left). The green line exhibits the median of 1000 bootstrap samples (Each sample containing the same number of genes to the original population and was obtained by resampling allowing replacement). Boxplot represents the distance from the + 1 dyad to the indicated pausing sites for shift-to-5′ genes (right). b Average profiles depict median MNase-seq intensity at P1 of shift-to-5′ genes in the auxin-untreated (Ctrl) or -treated (KD) data. GSM3304635 and GSM3304637 were used for the left panel, and GSM3177778 and GSM3177779 were used for the right panel (high MNase). For (a) and (b), the two dotted lines indicate the 10th (− 22 bp) and 90th (− 145 bp) percentiles of P2 relative to P1. c, d Average profiles display median PRO-seq intensity for the indicated samples around the + 1 dyad. The two dotted lines in profiles represent the expected position of the + 1 nucleosome (75 bp upstream and downstream of the + 1 dyad). e Genome browser view of PRO-seq signals for representative genes whose pausing sites were shifted in the 5′ direction in both Ino80p-KD and arp5Δ. All PRO-seq data were generated using combined biological replicates. Only genes with nucleosomes overlapped with H3K4me3 ChIP-seq enrichment (GSM2507874) were used in an effort to exclude false-positive nucleosomes (260 no-shift genes and 251 shift-to-5′ genes upon Ino80p-KD; 398 shifted to 5′ genes in arp5Δ). For average profiles, medians reflect the 10-bp bin. Asterisks represent statistically significant differences, as calculated using either Wilcoxon signed rank test or Mann-Whitney U test