Fig. 1.

PRO-seq reveals a non-uniform distribution at TSS genome-wide in S. cerevisiae. The gene set used in the previous study [28] was used (N = 3403) for analysis. a Scaled composite profile shows the median intensity of our Ctrl PRO-seq data generated in Ino80p-AID cells cultured without auxin treatment. Regions between 300 bp downstream from TSS and 300 bp upstream of TES were scaled to 60 bins. Outside of these regions were reflected as a 10-bp bin. b Heatmaps display previously published wt (w303a) PRO-seq data (GSM1974983) and our Ctrl PRO-seq data or wt (BY4741) PRO-seq data around TSS. Genes were sorted by the PR intensity of our Ctrl data. Signals reflect the 10-bp bin. c Scatterplots represent the correlation of PR and GB intensity and PI between the indicated data. d, e Average profiles show the median intensity of GSM1974983. Genes were grouped into quartiles based on PI of GSM1974983 (d) or Ctrl (e) data, where Q1 represents the highest PI. f Venn diagram indicates the overlap between paused and not paused genes defined based on GSM1974983 or Ctrl data. P value was calculated using the hypergeometric distribution. g, h Average profiles display the paused and not paused genes defined based on GSM1974983 (g; 177 paused genes and 2770 not paused genes) or Ctrl (h; 1815 paused genes and 980 not paused genes) data. The green line in the GSM1974983 plot (g) indicates 1655 genes defined as paused genes in only Ctrl data. The green line in the Ctrl plot (h) represents 160 genes defined as paused genes in both data. i Genome browser view of PRO-seq signal for representative genes among overlapped paused genes in both data. PRO-seq data were generated using combined biological replicates