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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of S. cerevisiae RPD3 deletion mutants and histone H3 and H4 amino-terminus mutants

ABSTRACT: Signal intensity data for rpd3 delete, H3delta(1-28), H3(K4,9,14,18,23,27Q), H4delta(2-26), H4(K5,8,12,16Q), rpd3 delete H3delta(1-28), and rpd3 delete H4(K5,8,12,16Q) yeast grown in rich (YPD) media

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Randall Heywood Morse

PROVIDER: E-GEOD-1639 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-wide analysis of the relationship between transcriptional regulation by Rpd3p and the histone H3 and H4 amino termini in budding yeast.

Sabet Nevin N Volo Sam S Yu Cailin C Madigan James P JP Morse Randall H RH

Molecular and cellular biology 20041001 20

The histone amino termini have emerged as key targets for a variety of modifying enzymes that function as transcriptional coactivators and corepressors. However, an important question that has remained largely unexplored is the extent to which specific histone amino termini are required for the activating and repressive functions of these enzymes, Here we address this issue by focusing on the prototypical histone deacetylase, Rpd3p, in the budding yeast Saccharomyces cerevisiae. We show that tar ...[more]

PMID: 15456858

Similar Datasets

Rpd3 and histone H3 and H4 deletions/mutations

Project description:Signal intensity data for rpd3 delete, H3delta(1-28), H3(K4,9,14,18,23,27Q), H4delta(2-26), H4(K5,8,12,16Q), rpd3 delete H3delta(1-28), and rpd3 delete H4(K5,8,12,16Q) yeast grown in rich (YPD) media Keywords = histones Keywords = chromatin Keywords = rpd3 Keywords = HDAC Keywords = histone deacetylase Keywords = yeast Keywords: other

2004-09-04 | GSE1639 | GEO

Transcription profiling of S. cerevisiae wild type and amino-terminal mutant histone H3 and H4 strains

Project description:Yeast lacking the H3 or H4 amino termini, and corresponding wild type strains, were grown in synthetic media. These conditions induce Gcn4-activated transcription. Experiment Overall Design: Three replicates of the H4del(2-26) and corresponding wild type strains, and four replicates of the H3del(1-28) and corresponding wild type strains, were performed. Note the strains are congenic, but differ in whether the histones were present on TRP1 marked (H4) or LEU2 marked (H3) plasmids. Samples were analysed using Affymetrix S98 microarrays.

2007-09-21 | E-GEOD-4135 | biostudies-arrayexpress

Characterization of H3 density, H3 or H4 acetylation, Rpd3 binding, TFIIB binding, and Rpb3 (pol II) binding in wild type and rpd3 cells as they transition from logarithmic growth to diauxic shift to quiescence [ChIP-Seq]

Project description:Binding profiles for H3 and H4ac were determined as cells transition from log growth to quiescence. We found that massive chromatin changes that reflect global transcriptional repression occur after the diauxic shift in an Rpd3-dependent manner. Binding of Rpd3 is dramatically expanded to reflect binding at thousands of genes after quiescence entry, demonstrating an Rpd3-driven mechanism to change chromatin and repress transcription after entry into quiescence.

2015-08-20 | GSE67150 | GEO

Quantitative analysis of acetylome reveals the roles of Rpd3 and Sir2 in asexual development, virulence and multiple stress responses in Beauveria bassiana.

Project description:Lysine acetylation is one of the most prevalent post-translational modifications and has since been found to regulate histone functions and affect chromatin structure and gene expression. Here, we charactered Rpd3, a histone deacetylase of Beauveria bassiana, played important roles in the deacetylation of histone H3 and H4. We unveil the role of Rpd3 in asexual development and show that a ΔRpd3 mutant strain has severe growth defects and is defective in conidiophores and blastospores development. Acetylomic analyses indicated that Rpd3 functions in asexual development and virulence and multiple stress responses via broad genetic pathways in B. bassiana. Therefore, we conclude that BbRpd3 is vital for asexual development, virulence and multiple stress responses in Beauveria bassiana.

2021-08-12 | PXD006714 | Pride

Quantitative analysis of proteome reveals the roles of Rpd3 and Sir2 in asexual development, virulence and multiple stress responses in Beauveria bassiana.

Project description:Lysine acetylation is one of the most prevalent post-translational modifications and has since been found to regulate histone functions and affect chromatin structure and gene expression. Here, we charactered Rpd3, a histone deacetylase of Beauveria bassiana, played important roles in the deacetylation of histone H3 and H4. We unveil the role of Rpd3 in asexual development and show that a ΔRpd3 mutant strain has severe growth defects and is defective in conidiophores and blastospores development. Proteomic analyses indicated that Rpd3 functions in asexual development and virulence and multiple stress responses via broad genetic pathways in B. bassiana. Therefore, we conclude that BbRpd3 is vital for asexual development, virulence and multiple stress responses in Beauveria bassiana.

2021-08-12 | PXD006713 | Pride

Histone H4 N-terminal tail mutants

Project description:A series of yeast carrying K->R mutations in the histone H4 N-terminal tail were profiled by gene expression array in mid-log phase. Keywords: repeat sample

2005-03-05 | GSE2324 | GEO

Rpd3 drives transcriptional quiescence

Project description:Rpd3 drives transcriptional quiescence

| PRJNA279126 | ENA

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.

2012-01-01 | GSE33829 | GEO

Histone H4 N-terminal tail mutants

Project description:A series of yeast carrying K->R mutations in the histone H4 N-terminal tail were profiled by gene expression array in mid-log phase.

2010-06-10 | E-GEOD-2324 | biostudies-arrayexpress

The Rpd3 Core Complex is a Chromatin Stabilization Module

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

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