Promoter scanning during transcription initiation in Saccharomyces cerevisiae: Pol II in the “shooting gallery”

Transcription initiation by RNA Polymerase II is the first step of gene expression in eukaryotes. General transcription factors (GTFs) recruit Pol II to promoter DNA, facilitated by DNA sequence elements and any number of transcription regulators. Where and how efficiently Pol II initiates are determined by the biochemical properties of the transcription machinery and its interaction with promoter architectural features. For promoters examined In Saccharomyces cerevisiae, Pol II finds transcription start sites (TSSs) by a directional scanning mechanism, searching from upstream to downstream positions. As in higher eukaryotes, many TSSs may be used at any individual promoter. We aimed to understand the mechanisms by which TSSs are identified across promoter classes, and how TSS usage and overall efficiency are shaped by promoter architecture – promoter DNA sequence, the spatial relationship between promoter elements, and chromatin structure. We have used alteration of Pol II and GTF activities to perturb the initiation process and mapped changes to TSS usage genome wide. We find that alterations to Pol II, TFIIB, or TFIIF function widely alter the initiation landscape, supporting the hypothesis that Pol II promoter scanning operates at all yeast promoters. Furthermore, the relationship of TSS positions to promoter architecture is predictive of promoter-specific effects on TSS usage and promoter expression. We integrate our observations with previous data into a model for Pol II initiation in yeast – the “shooting gallery”. In this model, Pol II catalytic activity, and the rate and processivity of Pol II scanning determine the distribution of TSSs and their usage levels together with promoter sequence.