title: DNA Topoisomerases maintain promoters in a state competent for transcriptional activation in Saccharomyces cerevisiae.
abstract: To investigate the role of DNA topoisomerases in transcription, we have studied global gene expression in Saccharomyces cerevisiae cells deficient for topoisomerases I and II and performed single-gene analyses to support our findings. The genome-wide studies show a general transcriptional down-regulation upon lack of the enzymes, which correlates with gene activity but not gene length. Furthermore, our data reveal a distinct subclass of genes with a strong requirement for topoisomerases. These genes are characterized by high transcriptional plasticity, chromatin regulation, TATA box presence, and enrichment of a nucleosome at a critical position in the promoter region, in line with a repressible/inducible mode of regulation. Single-gene studies with a range of genes belonging to this group demonstrate that topoisomerases play an important role during activation of these genes. Subsequent in-depth analysis of the inducible PHO5 gene reveals that topoisomerases are essential for binding of the Pho4p transcription factor to the PHO5 promoter, which is required for promoter nucleosome removal during activation. In contrast, topoisomerases are dispensable for constitutive transcription initiation and elongation of PHO5, as well as the nuclear entrance of Pho4p. Finally, we provide evidence that topoisomerases are required to maintain the PHO5 promoter in a superhelical state, which is competent for proper activation. In conclusion, our results reveal a hitherto unknown function of topoisomerases during transcriptional activation of genes with a repressible/inducible mode of regulation.
authors.affiliation: Laboratory of Genome Research, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
authors.forename: Jakob Madsen
authors.initials: JM
authors.lastname: Pedersen
authors.forename: Jacob
authors.initials: J
authors.lastname: Fredsoe
authors.forename: Morten
authors.initials: M
authors.lastname: Roedgaard
authors.forename: Lotte
authors.initials: L
authors.lastname: Andreasen
authors.forename: Kamilla
authors.initials: K
authors.lastname: Mundbjerg
authors.forename: Mogens
authors.initials: M
authors.lastname: Kruhøffer
authors.forename: Marie
authors.initials: M
authors.lastname: Brinch
authors.forename: Mikkel Heide
authors.initials: MH
authors.lastname: Schierup
authors.forename: Lotte
authors.initials: L
authors.lastname: Bjergbaek
authors.forename: Anni Hangaard
authors.initials: AH
authors.lastname: Andersen
mesh_terms: D000135:Acid Phosphatase / Q000235:genetics / Q000378:metabolism; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D026942:DNA Topoisomerases / Q000235:genetics* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D009707:Nucleosomes / Q000378:metabolism; D011401:Promoter Regions, Genetic; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism; D016385:TATA Box / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D015533:Transcriptional Activation / Q000235:genetics*
chemical_list: D002843:Chromatin; D004268:DNA-Binding Proteins; D009707:Nucleosomes; C060292:PHO4 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; D000135:Acid Phosphatase; C488916:PHO5 protein, S cerevisiae; D026942:DNA Topoisomerases