Fig. 5

Attributes of core promoter classes and PIC positioning in TSS usage-affecting mutants. a Enrichment by expression decile in WT of putative core promoter elements in Taf1-enriched and Taf1-depleted promoters. TATA consensus (TATAWAWR, W=A/T, R=A/G) is enriched in Taf1-depleted promoters while the GA-rich element (GAAAAA) is enriched in Taf1-enriched promoters. Yeast promoters are relatively AT-rich so there is a high probability of “TATA-like” elements differing from the TATA consensus by two mismatches. b Tested GAE or TATA-like elements do not greatly contribute to expression from promoters where tested. Expression by Northern blotting for promoters or classes of promoter mutant fused to a reporter gene. Promoter mutants were normalized to the respective WT version of each promoter. “Delete” mutants represent deletions of particular element types. “Mutant” elements represent elements where base composition has been altered. c GTF positioning by promoter classes determined by ChIP-exo for Sua7 (TFIIB) or Ssl2 (TFIIH). For each promoter, the median position of ChIP-exo reads on the top (TOP) or bottom (BOT) DNA strand was used to estimate GTF positioning. TOP and BOT strands are defined relative to promoter orientation in the genome and have the same upstream and downstream as a promoter. d Left graph shows histograms of GTF signal median positions for ChIP-exo read distributions at Taf1-enriched promoters while right graph shows histograms of GTF signal median positions for ChIP-exo read distributions at Taf1-depleted promoters. e Pol II mutant effects on GTF positioning as detected by ChIP-exo for Sua7 (TFIIB) or Ssl2 (TFIIH). Aggregate ChIP-exo signal for Taf1-enriched or Taf1-depleted promoters on top (TOP) or bottom (BOT) DNA strands in WT, rpb1 H1085Y, or rpb1 E1103G. Curves on graph indicate 2nd-order polynomial (10 neighbor) smoothing of promoter-normalized ChIP-exo reads averaged for the top 50% of promoters determined by ChIP-exo reads in WT cells. Biological replicate data are shown for each strain and replicates are essentially superimposable