title: Rpd3- and spt16-mediated nucleosome assembly and transcriptional regulation on yeast ribosomal DNA genes.
abstract: Ribosomal DNA (rDNA) genes in eukaryotes are organized into multicopy tandem arrays and transcribed by RNA polymerase I. During cell proliferation, ∼50% of these genes are active and have a relatively open chromatin structure characterized by elevated accessibility to psoralen cross-linking. In Saccharomyces cerevisiae, transcription of rDNA genes becomes repressed and chromatin structure closes when cells enter the diauxic shift and growth dramatically slows. In this study, we found that nucleosomes are massively depleted from the active rDNA genes during log phase and reassembled during the diauxic shift, largely accounting for the differences in psoralen accessibility between active and inactive genes. The Rpd3L histone deacetylase complex was required for diauxic shift-induced H4 and H2B deposition onto rDNA genes, suggesting involvement in assembly or stabilization of the entire nucleosome. The Spt16 subunit of FACT, however, was specifically required for H2B deposition, suggesting specificity for the H2A/H2B dimer. Miller chromatin spreads were used for electron microscopic visualization of rDNA genes in an spt16 mutant, which was found to be deficient in the assembly of normal nucleosomes on inactive genes and the disruption of nucleosomes on active genes, consistent with an inability to fully reactivate polymerase I (Pol I) transcription when cells exit stationary phase.
authors.affiliation: Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, Virginia, USA.
authors.forename: Joseph M
authors.initials: JM
authors.lastname: Johnson
authors.forename: Sarah L
authors.initials: SL
authors.lastname: French
authors.forename: Yvonne N
authors.initials: YN
authors.lastname: Osheim
authors.forename: Mingguang
authors.initials: M
authors.lastname: Li
authors.forename: Lindsey
authors.initials: L
authors.lastname: Hall
authors.forename: Ann L
authors.initials: AL
authors.lastname: Beyer
authors.forename: Jeffrey S
authors.initials: JS
authors.lastname: Smith
mesh_terms: D042002:Chromatin Assembly and Disassembly; D004256:DNA Polymerase I / Q000378:metabolism; D004271:DNA, Fungal / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics* / Q000378:metabolism; D044127:Epigenesis, Genetic; D015966:Gene Expression Regulation, Fungal; D005800:Genes, Fungal; D006609:High Mobility Group Proteins / Q000378:metabolism; D006655:Histone Deacetylases / Q000502:physiology*; D006657:Histones / Q000378:metabolism; D009707:Nucleosomes / Q000378:metabolism*; D011485:Protein Binding; D021122:Protein Subunits / Q000502:physiology; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism / Q000502:physiology*; D014158:Transcription, Genetic; D035602:Transcriptional Elongation Factors / Q000502:physiology*
chemical_list: D004271:DNA, Fungal; D004275:DNA, Ribosomal; C103154:HMO1 protein, S cerevisiae; D006609:High Mobility Group Proteins; D006657:Histones; D009707:Nucleosomes; D021122:Protein Subunits; C071238:SPT16 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D035602:Transcriptional Elongation Factors; D004256:DNA Polymerase I; C083536:POL1 protein, S cerevisiae; C071665:RPD3 protein, S cerevisiae; D006655:Histone Deacetylases