Fig. 4
From: Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae
TSS usage mutants alter TSS usage efficiencies across TSS motifs consistent with promoter scanning initiation at all promoters. a Schematic indicating how normalized difference heat maps are generated (for visual purposes, differences scaled in this schematic to 1.5×). b In a directional scanning mechanism, TSS efficiency is defined as the usage at a given TSS divided by that usage and all downstream usage. This allows strength of TSS to be compared instead of absolute usage, which is determined by “first come, first served” priority effects as the probability of initiation reaches a limit of one. c Schematic illustrating that TSS usages/efficiencies across all promoters and positions form a matrix, and each of 64 motif TSSs represents only a subset of these values (for example A−8C−1A+ 1). Comparison of median or average values for usage/efficiency for each N−8N−1N+ 1 motif TSS subset across promoters at each promoter position allows for partial control of sequence and position variables in comparing how initiation mutants affect TSS usage. d Altered usage across TSS motifs in TSS usage-affecting mutants. Heat maps show difference in aggregate usage normalized to promoter number for different N−8Y−1R+ 1 TSS motifs. Strains are ordered on the x-axis from left to right from strongest downstream shifter to strongest upstream shifter, with class of Pol II mutant (fast or slow) indicated by green or blue color bars, respectively. Promoter positions from − 100 (upstream) to + 100 (downstream) flanking the median TSS position in WT are shown. Regardless or promoter class, TSS usage affecting mutants cause polar effects on distribution of TSS usage when examining motifs separately. e Motif efficiency was calculated as in b for a subset of N−8Y−1R+ 1 TSS motifs across promoters at each promoter position for all mutants. Heat maps are ordered as in d. Downstream-shifting mutants in d generally reduce TSS usage efficiencies across promoter positions. Upstream-shifting mutants in d generally shift TSS efficiencies upstream