title: Uncoupling Promoter Opening from Start-Site Scanning.
abstract: Whereas RNA polymerase II (Pol II) transcription start sites (TSSs) occur about 30-35 bp downstream of the TATA box in metazoans, TSSs are located 40-120 bp downstream in S. cerevisiae. Promoter melting begins about 12 bp downstream in all eukaryotes, so Pol II is presumed to "scan" further downstream before starting transcription in yeast. Here we report that removal of the kinase complex TFIIK from TFIIH shifts the TSS in a yeast system upstream to the location observed in metazoans. Conversely, moving the normal TSS to an upstream location enables a high level of TFIIK-independent transcription in the yeast system. We distinguish two stages of the transcription initiation process: bubble formation by TFIIH, which fills the Pol II active center with single-stranded DNA, and subsequent scanning downstream, also driven by TFIIH, which requires displacement of the initial bubble. Omission of TFIIK uncouples the two stages of the process.
authors.affiliation: Department of Structural Biology, Stanford University, Stanford, CA 94305, USA.
authors.forename: Kenji
authors.initials: K
authors.lastname: Murakami
authors.affiliation: Department of Structural Biology, Stanford University, Stanford, CA 94305, USA.
authors.forename: Pierre-Jean
authors.initials: PJ
authors.lastname: Mattei
authors.affiliation: Department of Structural Biology, Stanford University, Stanford, CA 94305, USA.
authors.forename: Ralph E
authors.initials: RE
authors.lastname: Davis
authors.affiliation: Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA.
authors.forename: Huiyan
authors.initials: H
authors.lastname: Jin
authors.affiliation: Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA.
authors.forename: Craig D
authors.initials: CD
authors.lastname: Kaplan
authors.affiliation: Department of Structural Biology, Stanford University, Stanford, CA 94305, USA. Electronic address: kornberg@stanford.edu.
authors.forename: Roger D
authors.initials: RD
authors.lastname: Kornberg
mesh_terms: D001483:Base Sequence; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic; D012319:RNA Polymerase II / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000378:metabolism; D051758:Transcription Factor TFIIH / Q000235:genetics* / Q000378:metabolism; D024363:Transcription Initiation Site / Q000502:physiology*; D014158:Transcription, Genetic / Q000235:genetics
chemical_list: D029701:Saccharomyces cerevisiae Proteins; D051758:Transcription Factor TFIIH; D012319:RNA Polymerase II