title: Properties of an intergenic terminator and start site switch that regulate IMD2 transcription in yeast.
abstract: The IMD2 gene in Saccharomyces cerevisiae is regulated by intracellular guanine nucleotides. Regulation is exerted through the choice of alternative transcription start sites that results in synthesis of either an unstable short transcript terminating upstream of the start codon or a full-length productive IMD2 mRNA. Start site selection is dictated by the intracellular guanine nucleotide levels. Here we have mapped the polyadenylation sites of the upstream, unstable short transcripts that form a heterogeneous family of RNAs of approximately 200 nucleotides. The switch from the upstream to downstream start sites required the Rpb9 subunit of RNA polymerase II. The enzyme's ability to locate the downstream initiation site decreased exponentially as the start was moved downstream from the TATA box. This suggests that RNA polymerase II's pincer grip is important as it slides on DNA in search of a start site. Exosome degradation of the upstream transcripts was highly dependent upon the distance between the terminator and promoter. Similarly, termination was dependent upon the Sen1 helicase when close to the promoter. These findings extend the emerging concept that distinct modes of termination by RNA polymerase II exist and that the distance of the terminator from the promoter, as well as its sequence, is important for the pathway chosen.
authors.affiliation: Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA.
authors.forename: M Harley
authors.initials: MH
authors.lastname: Jenks
authors.forename: Thomas W
authors.initials: TW
authors.lastname: O'Rourke
authors.forename: Daniel
authors.initials: D
authors.lastname: Reines
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry; D004271:DNA, Fungal / Q000235:genetics; D015966:Gene Expression Regulation, Fungal; D007168:IMP Dehydrogenase / Q000235:genetics* / Q000502:physiology*; D008954:Models, Biological; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009154:Mutation; D016366:Open Reading Frames; D011401:Promoter Regions, Genetic; D012319:RNA Polymerase II / Q000378:metabolism; D022661:RNA, Untranslated; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000502:physiology*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000502:physiology*; D013728:Terminator Regions, Genetic
chemical_list: D004271:DNA, Fungal; D022661:RNA, Untranslated; D029701:Saccharomyces cerevisiae Proteins; D004247:DNA; C477283:IMD2 protein, S cerevisiae; D007168:IMP Dehydrogenase; D012319:RNA Polymerase II