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MRNA profiling of glucose-repressed 14-3-3 and hdac yeast mutants

ABSTRACT: Previous results suggest that Bmh might inhibit the activity of the transcription factor Adr1 after binding to Adr1-dependent promoters. In a strain lacking the two major histone deacetylases, Hda1 and Rpd3 (hdac?), Adr1 is bound to its target promoters recruiting what appears to be an inactive RNA ploymerase II preinitiation complex (PIC). To determine whether Bmh activity inhibits this inactive PIC and the generality of this effect on glucose-repressed gene expression, the mRNA profiles of wild type, bmh mutant, hdac mutant, and bmh hdac mutant cells grown in high glucose medium were compared. Total RNAs were purified from triplicate cultures of W303-1A (wild type), YLL1087 (bmh1-ts bmh2?), CTY-TY44 (hda1? rpd3?) and KBY3 (bmh1-ts bmh2? hda1? rpd3?) cells exponentially growing in YP broth containing 5% glucose and then profiled using Affymetrix Yeast 2.0 arrays.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Kenneth Dombek

PROVIDER: E-GEOD-40116 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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mRNA profiling of glucose-repressed 14-3-3 and hdac yeast mutants

Project description:Previous results suggest that Bmh might inhibit the activity of the transcription factor Adr1 after binding to Adr1-dependent promoters. In a strain lacking the two major histone deacetylases, Hda1 and Rpd3 (hdac∆), Adr1 is bound to its target promoters recruiting what appears to be an inactive RNA ploymerase II preinitiation complex (PIC). To determine whether Bmh activity inhibits this inactive PIC and the generality of this effect on glucose-repressed gene expression, the mRNA profiles of wild type, bmh mutant, hdac mutant, and bmh hdac mutant cells grown in high glucose medium were compared.

2013-01-15 | GSE40116 | GEO

The Rpd3 Core Complex is a Chromatin Stabilization Module

Project description: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. H3 were ChIP'd from yeast strains and normalized to input.

2012-01-01 | E-GEOD-33829 | biostudies-arrayexpress

Role of histone modifications in pervasive transcription and antisense-mediated silencing in yeast

Project description:Whole transcriptome analyses of various histone modification mutants in a Drrp6 strain using high-density tiling arrays. To assess the importance of histone modifications in antisense-mediated repression genome-wide, we performed high-density tiling arrays on cells lacking Rrp6 alone or combined with loss of the HMT Set1 or the HDACs Hda1 and Rpd3. Expression profiles are also provided in a searchable web-database: http://steinmetzlab.embl.de//cgi- bin/viewStutzLabArray.pl?showSamples=stutzLabArray&type=heatmap&gene=rrp6. Normalized file, created using protocol P-MTAB-27905, provided as an additional archive.

2013-03-01 | E-MTAB-1316 | biostudies-arrayexpress

Expression analysis of various fungi grown in glucose or xylose

Project description:This SuperSeries is composed of the following subset Series: GSE24853: Expression analysis of Spathaspora passalidarum NRRL Y-27907 grown in glucose or xylose GSE24854: Expression analysis of Pichia stipitis CBS 6054 grown in glucose or xylose GSE24855: Expression analysis of Lodderomyces elongisporus NRRL YB-4239 grown in glucose or xylose GSE24856: Expression analysis of Candida tenuis NRRL Y-1498 grown in glucose or xylose GSE24857: Expression analysis of Candida albicans WO-1 grown in glucose or xylose Refer to individual Series

2011-10-19 | E-GEOD-24858 | biostudies-arrayexpress

Rpd3 and histone H3 and H4 deletions/mutations

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2004-09-04 | GSE1639 | GEO

S. paradoxus wt strains: glucose vs. xylulose growth

Project description:Transcription profile of 12 wt S.paradoxus strains originating from diverse geographical origins and natural habitats. Transcription profiles in two conditioins were compared: growth on glucose and growth on the naturally rare pentose sugar xylulose. Two condition experiment, growth on glucose and on xylulose, 12 wt S.paradoxus strains

2013-08-23 | E-GEOD-50125 | biostudies-arrayexpress

S. cerevisiae wt strains: glucose vs. xylulose growth

Project description:Transcription profile of 12 wt S.cerevisiae strains originating from diverse geographical origins and natural habitats. Transcription profiles in two conditioins were compared: growth on glucose and growth on the naturally rare pentose sugar xylulose. Two condition experiment, growth on glucose and on xylulose, 12 wt S. cerevisiae strains, two biological replicates

2013-08-23 | E-GEOD-50124 | biostudies-arrayexpress

The Rpd3 Core Complex is a Chromatin Stabilization Module

2012-01-01 | GSE33829 | GEO

Different nucleosomal landscapes at early and late replicating origins in Saccharomyces cerevisiae

Project description:Sequencing of mononucleosomal DNA during G1 and S phases in Saccharomyces cerevisiae Samples from mononucleosomal DNA from WT and rpd3 mutant strains (W303-1a background) in G1 or in S phase in the presence of 0.2 M HU were sequenced (Illumina Genome Analyzer IIx) using the single-end read protocol

2014-09-09 | E-GEOD-54377 | biostudies-arrayexpress

An integrated SAGA and TFIID PIC assembly pathway selective for poised and induced promoters [RNA-Seq]

Project description:Genome-wide, little is understood about how proteins organize at inducible promoters before and after in-duction, and to what extent inducible and constitutive architectures depend on cofactors. We report that se-quence-specific transcription factors and their tethered cofactors (e.g., SAGA, Mediator, TUP, NuA4, SWI/SNF, RPD3-L) are already bound to promoters prior to induction (“poised”), rather than recruited upon induction, whereas induction recruits the pre-initiation complex (PIC). Through depletion and/or deletion ex-periments we show that SAGA does not function at constitutive promoters, although a SAGA-independent Gcn5 does acetylate +1 nucleosomes there. At poised promoters, SAGA catalyzes +1 nucleosome acetylation but not PIC assembly. At induced promoters, SAGA catalyzes acetylation, deubiquitylation, and PIC assembly. Surprisingly, SAGA mediates induction by creating a PIC that allows TFIID to stably associate, rather than creating a TFIID-independent PIC, as is generally thought. These findings suggest that inducible systems, where present, evolved on top of constitutive systems.

2022-10-27 | GSE212653 | GEO

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