title: The Rpd3 core complex is a chromatin stabilization module.
abstract: The S. cerevisiae Rpd3 large (Rpd3L) and small (Rpd3S) histone deacetylase (HDAC) complexes are prototypes for understanding transcriptional repression in eukaryotes [1]. The current view is that they function by deacetylating chromatin, thereby limiting accessibility of transcriptional factors to the underlying DNA. However, an Rpd3 catalytic mutant retains substantial repression capability when targeted to a promoter as a LexA fusion protein [2]. We investigated the HDAC-independent properties of the Rpd3 complexes biochemically and discovered a chaperone function, which promotes histone deposition onto DNA, and a novel activity, which prevents nucleosome eviction but not remodeling mediated by the ATP-dependent RSC complex. These HDAC-independent activities inhibit Pol II transcription on a nucleosomal template. The functions of the endogenous Rpd3 complexes can be recapitulated with recombinant Rpd3 core complex comprising Sin3, Rpd3, and Ume1. To test the hypothesis that Rpd3 contributes to chromatin stabilization in vivo, we measured histone H3 density genomewide and found that it was reduced at promoters in an Rpd3 deletion mutant but partially restored in a catalytic mutant. Importantly, the effects on H3 density are most apparent on RSC-enriched genes [3]. Our data suggest that the Rpd3 core complex could contribute to repression via a novel nucleosome stabilization function.
authors.affiliation: Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1737, USA.
authors.forename: Xiao-Fen
authors.initials: XF
authors.lastname: Chen
authors.forename: Benjamin
authors.initials: B
authors.lastname: Kuryan
authors.forename: Tasuku
authors.initials: T
authors.lastname: Kitada
authors.forename: Nancy
authors.initials: N
authors.lastname: Tran
authors.forename: Jing-Yu
authors.initials: JY
authors.lastname: Li
authors.forename: Siavash
authors.initials: S
authors.lastname: Kurdistani
authors.forename: Michael
authors.initials: M
authors.lastname: Grunstein
authors.forename: Bing
authors.initials: B
authors.lastname: Li
authors.forename: Michael
authors.initials: M
authors.lastname: Carey
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism; D002843:Chromatin / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D016681:Genome, Fungal; D006655:Histone Deacetylases / Q000235:genetics / Q000378:metabolism*; D006657:Histones / Q000235:genetics / Q000378:metabolism; D018832:Molecular Chaperones / Q000378:metabolism; D009707:Nucleosomes / Q000378:metabolism*; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D002843:Chromatin; D004268:DNA-Binding Proteins; D006657:Histones; D018832:Molecular Chaperones; D009707:Nucleosomes; C103337:RSC complex, S cerevisiae; D012097:Repressor Proteins; C071731:SIN3 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; C462439:UME1 protein, S cerevisiae; D000255:Adenosine Triphosphate; C071665:RPD3 protein, S cerevisiae; D006655:Histone Deacetylases