Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae

Chenxi Qiu, Chenxi Qiu, Huiyan Jin, Irina Vvedenskaya, Irina Vvedenskaya, Jordi Abante Llenas, Jordi Abante Llenas, Tingting Zhao, Indranil Malik, Indranil Malik, Alex M. Visbisky, Scott L. Schwartz, Ping Cui, Pavel Čabart, Pavel Čabart, Kang Hoo Han, William K.M. Lai, William K.M. Lai, Richard P. Metz, Charles D. JohnsonSing Hoi Sze, Sing Hoi Sze, B. Franklin Pugh, B. Franklin Pugh, Bryce E. Nickels, Bryce E. Nickels, Craig D. Kaplan

Research output: Contribution to journalArticlepeer-review

27 Scopus citations


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.

Original languageEnglish (US)
Article number132
JournalGenome biology
Issue number1
StatePublished - Jun 2 2020

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology


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