34Background 35 The majority of eukaryotic promoters utilize multiple transcription start sites (TSSs). How 36 multiple TSSs are specified at individual promoters across eukaryotes is not understood for 37 most species. In S. cerevisiae, a preinitiation complex comprised of Pol II and conserved 38 general transcription factors (GTFs) assembles and opens DNA upstream of TSSs. Evidence 39 from model promoters indicates that the PIC scans from upstream to downstream to identify 40TSSs. Prior results suggest that TSS distributions at promoters where scanning occurs shift in a 41 polar fashion upon alteration in Pol II catalytic activity or GTF function. 42Results 43 To determine extent of promoter scanning across promoter classes in S. cerevisiae, we 44perturbed Pol II catalytic activity and GTF function and analyzed their effects on TSS usage 45 genome-wide. We find that alterations to Pol II, TFIIB, or TFIIF function widely alter the initiation 46 landscape consistent with promoter scanning operating at all yeast promoters, regardless of 47 promoter class. Promoter architecture, however, can determine extent of promoter sensitivity to 48 altered Pol II activity in ways that are predicted by a scanning model. 49Conclusions 50Our observations coupled with previous data validate this scanning model for Pol II initiation in 51yeast -which we term the "shooting gallery". In this model, Pol II catalytic activity, and the rate 52 and processivity of Pol II scanning together with promoter sequence determine the distribution 53of TSSs and their usage. Comparison of TSS distributions and their relationship to promoter 54 sequence among other eukaryotes suggest some, but not all, share characteristics of S. 55 cerevisiae. 56 57 58 157

No abstract