Fig. 3
From: Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae
TSS motif usage and alterations in TSS usage affecting mutants. a Schematic of TSS distribution at an individual promoter defining primary TSS as most used followed by secondary and tertiary etc based on usage. b Preferred Y− 1R+ 1 motif usage observed in our TSS data as has been observed previously. S. cerevisiae selective enrichment for A at − 8 is apparent at the most highly used starts in promoters with higher expression (compare primary/top (1°) TSSs with secondary (2°) or tertiary TSSs from promoters within the top decile of expression). Promoters exhibiting very narrow TSS spreads (focused) show additional minor enrichments for bases near the TSS. c Schematic indicating how each TSS can be separated into one of 64 groups based on identity of nucleotides at positions − 8, − 1, and + 1 relative to the TSS (at + 1). d Overall TSS motif usage in WT and TSS usage affecting mutants. TSSs were separated by N− 8N−1N+ 1 identity (64 motifs) as the vast majority of TSS reads derive from N− 8Y−1R+ 1 sequences. This means each of 64 motifs encompasses TSSs for N−7N−6N−5N−4N− 3 N− 2 sequences. (Top) Percent motif usage determined for individual strains and displayed in heat map hierarchically clustered on the y-axis to group strains with similar motif usage distribution. (Bottom) Difference heat map illustrating relative changes in N−8Y−1R+ 1 motif usage in heat map hierarchically clustered on the y-axis to group strains with similar motif usage difference distribution. e Alteration in motif usage and apparent changes to reliance on an A−8 could arise from a number of possibilities. Alterations in TSS efficiencies in mutants could result in upstream or downstream shifts in TSS distribution if mutants have decreased or increased reliance, respectively, on a particular motif. Conversely, alteration in initiation efficiency in general (increase or decrease) could alter TSS motif usage if TSS motifs are unevenly distributed across yeast promoters (example distribution for hypothetical motif N). f TSS motifs are unevenly distributed across yeast promoters and differentially enriched correlating with steady state promoter expression levels. (Top) The apparent highest used A−8Y−1R+ 1 motif (A−8C−1A+ 1) and (bottom) the less preferred T−8T−1A+ 1 motif were compared for Taf1-enriched or Taf1-depleted promoters for promoters separated into overall expression decile (decile 1 contains highest expressed promoters, decile 10 the lowest)