BACKGROUND: The majority of eukaryotic promoters utilize multiple transcription start sites (TSSs). How multiple TSSs are specified at individual promoters across eukaryotes is not understood for most species. In Saccharomyces cerevisiae, a pre-initiation complex (PIC) comprised of Pol II and conserved general transcription factors (GTFs) assembles and opens DNA upstream of TSSs. Evidence from model promoters indicates that the PIC scans from upstream to downstream to identify TSSs. Prior results suggest that TSS distributions at promoters where scanning occurs shift in a polar fashion upon alteration in Pol II catalytic activity or GTF function. RESULTS: To determine the extent of promoter scanning across promoter classes in S. cerevisiae, we perturb Pol II catalytic activity and GTF function and analyze their effects on TSS usage genome-wide. We find that alterations to Pol II, TFIIB, or TFIIF function widely alter the initiation landscape consistent with promoter scanning operating at all yeast promoters, regardless of promoter class. Promoter architecture, however, can determine the extent of promoter sensitivity to altered Pol II activity in ways that are predicted by a scanning model. CONCLUSIONS: Our observations coupled with previous data validate key predictions of the scanning model for Pol II initiation in yeast, which we term the shooting gallery. In this model, Pol II catalytic activity and the rate and processivity of Pol II scanning together with promoter sequence determine the distribution of TSSs and their usage.

Department of Biochemistry and Biophysics Texas A and M University College Station TX 77843 2128 USA

Department of Biochemistry and Molecular Biology Penn State University University Park PA 16802 USA

Department of Biological Sciences University of Pittsburgh Pittsburgh PA 15260 USA

Department of Computer Science and Engineering Texas A and M University College Station TX 77843 3127 USA

Department of Electrical and Computer Engineering Texas A and M University College Station TX 77843 3128 USA

Department of Genetics Rutgers University Piscataway NJ 08854 USA

Genomics and Bioinformatics Service Texas A and M AgriLife College Station TX 77845 USA

Present Address 1st Faculty of Medicine Charles University BIOCEV 252 42 Vestec Czech Republic

Present Address Department of Medicine Division of Translational Therapeutics Beth Israel Deaconess Medical Center Harvard Medical School Boston MA 02215 USA

Present Address Department of Molecular Biology and Genetics 458 Biotechnology Cornell University New York 14853 USA

Present Address Department of Neurology University of Michigan Ann Arbor MI 48109 USA

Present Address Whitaker Biomedical Engineering Institute Johns Hopkins University Baltimore MD 21218 USA

Waksman Institute of Microbiology Rutgers University Piscataway NJ 08854 USA

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