Fig. 2

Features of the non-uniform distribution of transcription elongation in S. cerevisiae. a Average profile shows median PRO-seq intensity around TSS (left). In total, 2599 paused and 1990 not paused genes were classified among 5697 total filtered protein-coding genes (right). b Genome browser view of PRO-seq signals for representative paused (top) or not paused genes (bottom). c Average profile indicates median MNase-seq (GSM3304635) intensity centered on TSS of paused and not paused genes. d Boxplots exhibit the relationship of PRO-seq PR density (left) and PI (right) to the bottom (0–20%), middle (40–60%), and top (80–100%) pentiles of gene activity. Only paused genes were considered. Asterisks represent statistically significant differences based on Mann-Whitney U test. e Cumulative curve analyzes the distance from TSS to P1 at paused genes. The red dotted lines represent the 25th (76 bp) and 75th (156 bp) percentiles. f Average profiles show median MNase-seq intensity (GSM3304635) at TSS (left) and median PRO-seq intensity at the + 1 dyad (right). The + 1 dyad was defined by the improved nucleosome-positioning algorithm (iNPS) using existing MNase-seq data (GSM3304635) [57]. The two dotted red lines represent the 25th (Q1; 76 bp) and 75th (Q3; 156 bp) percentiles of P1 (left), and the two dotted black lines represent the expected position of the + 1 nucleosome (right; 75 bp upstream and downstream of + 1 dyad). All PRO-seq data represent the Ctrl data that were generated in auxin-untreated Ino80p-AID cells and combined biological replicates were used. For average profiles, medians reflect the 10-bp bin