GEO DataSets

(Submitter supplied) We found ribosomal transcription factor Ifh1p is dynamically acetylated and phosphorylated in response to nutrient cues. ChIP-seq data revealed dynamic binding to ribosomal genes (RP) during the OX growth phase of the yeast metabolic cycle (YMC) when RP genes are highly induced, and weaker binding in the RC quiescent-like phase. Besides RP genes, our ChIP-seq data also reveals binding of Ifh1p to non-RP genes such as translation factors and metabolic genes.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13272

4 Samples

Download data: WIG

(Submitter supplied) Affymetrix experiment performed on RNA isolated from Wild type, FHL1 deleted and FHL1,IFH1 double deleted strains. Data aquired in duplicate. In S. cerevisiae the mRNAs from the 138 ribosomal protein (RP) genes are amongst the most abundant in the cell, and their transcription is regulated tightly so that they are the most prominent cluster in most transcriptome experiments. It has recently been observed that the proteins Fhl1p and Ifh1p are found almost exclusively at RP genes (Lee et al., Science, 298, 799-804, 2002;Jorgensen et al., Genes Dev, 18, 2491-2505 2004; Schawalder et al Nature in press; Rudra et al , EMBO J. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Dataset:

GDS1033

Platform:

GPL90

6 Samples

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Expression profiling of fhl1 single deletion mutant and ifh1 fhl1 double deletion mutant. Mutants generated from W303 strain. Results indicate that Ifh1p and Fhl1p function together to regulate the transcription of ribosomal protein genes.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, transformed count, 3 genotype/variation sets

Platform:

GPL90

Series:

GSE2096

6 Samples

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(Submitter supplied) Array design -Platform: amino-silane coated glass slides (GAPS II, Corning) -S. cerevisiae intergenic regions amplified from S288C genomic DNA (ResGen) using the intergenic region primer oligonucleotides (ResGen) (Harismendy et al. EMBO J. 22(18): 4738-4747, 2003). The primers allow the amplification of the sequence located on either side of elements such as open reading frames, tRNAs, small nuclear RNAs, Ty elements, solo δ, etc. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL1695

15 Samples

Download data: TIFF

(Submitter supplied) Sgf73, a core component of the SAGA (Spt-Ada-Gcn5 Acetyltransferase) co-activator complex, is the yeast orthologue of ataxin-7, which in humans undergoes CAG ? polyglutamine repeat expansion to produce the neurodegenerative disease spinocerebellar ataxia type 7 (SCA7). We recently documented that deletion of SGF73 dramatically extends replicative lifespan (RLS) in yeast. To define the basis for Sgf73-mediated RLS extension, and to further explore the molecular function of Sgf73/ataxin-7 we performed ChIP-Seq for Sgf73 in yeast to identify its regions of DNA binding. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13821

5 Samples

Download data: BED, TXT

(Submitter supplied) Fhl1-9myc ChIP-chip, YPD, OD600=0.8, 2 arrays with duplicate spotting of yeast intergenic regions. AND Ifh1-9myc ChIP-chip, cells grown in YPD, OD600=0.8, 2 arrays with duplicate spotting of yeast intergenic regions. Keywords = Fhl1 Keywords: other

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by array

Platform:

GPL1689

8 Samples

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(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19756 GPL27812

46 Samples

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(Submitter supplied) Acetyl-CoA is a key intermediate in metabolism situated at the intersection of many metabolic pathways. The reliance of histone acetylation on acetyl-CoA enables gene expression to be coordinated with metabolic state. Previous studies have linked abundant histone acetylation to activation of genes involved in cell growth or tumorigenesis. However, under glucose starvation, the extent to which histone acetylation is important for gene expression remains poorly understood. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19756 GPL27812

16 Samples

Download data: TXT

(Submitter supplied) Acetyl-CoA is a key intermediate in metabolism situated at the intersection of many metabolic pathways. The reliance of histone acetylation on acetyl-CoA enables gene expression to be coordinated with metabolic state. Previous studies have linked abundant histone acetylation to activation of genes involved in cell growth or tumorigenesis. However, under glucose starvation, the extent to which histone acetylation is important for gene expression remains poorly understood. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19756

30 Samples

Download data: BW

(Submitter supplied) Ribosome biogenesis is a complex and energy-demanding process requiring tight coordination of ribosomal RNA (rRNA) and ribosomal protein (RP) production. Alteration of any step in this process may impact growth by leading to proteotoxic stress. Although the transcription factor Hsf1 has emerged as a central regulator of proteostasis, how its activity is coordinated with ribosome biogenesis is unknown. more...

Organism:

Saccharomyces cerevisiae W303

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25517

63 Samples

Download data: BW

(Submitter supplied) To study the TORC1-mediated transcriptional regulation of the genes involved in ribosome biosynthesis in fission yeast

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16192

4 Samples

Download data: XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13272

25 Samples

Download data: BAM, BIGWIG

(Submitter supplied) TORC1 is a structurally and functionally conserved multiprotein complex that regulates many aspects of eukaryote growth including the synthesis and assembly of ribosomes. The protein kinase activity of this complex is responsive to environmental cues and is potently inhibited by the natural product macrolide rapamycin. Insights into how TORC1 regulates growth have been provided with the recent identification of the rapamycin-sensitive phosphoproteome in yeast. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13272

9 Samples

Download data: BAM, BIGWIG

(Submitter supplied) TORC1 is a structurally and functionally conserved multiprotein complex that regulates many aspects of eukaryote growth including the synthesis and assembly of ribosomes. The protein kinase activity of this complex is responsive to environmental cues and is potently inhibited by the natural product macrolide rapamycin. Insights into how TORC1 regulates growth have been provided with the recent identification of the rapamycin-sensitive phosphoproteome in yeast. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13272

16 Samples

Download data: BAM

(Submitter supplied) In this study, we elucidate the common logic of the RPGs regulatory network by evaluating both the architecture and activity of promoters under conditions of stress or modulation of TF levels, and we identified the proteins regulating the activity of promoters lacking Rap1 binding, thus demonstrating that RPG co-regulation requires the complementary action of two different mechanisms involving both Ifh1 and Sfp1.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL17342

22 Samples

Download data: BIGWIG, BW

(Submitter supplied) 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.

Organism:

Saccharomyces cerevisiae; Schizosaccharomyces pombe

Type:

Expression profiling by array

Platform:

GPL2529

12 Samples

Download data: CEL

(Submitter supplied) In Saccharomyces cerevisiae, deletion of genes encoding proteins of the large ribosomal subunit (RPLs) increases the replicative lifespan in a Gcn4-dependent manner. However, how Gcn4, a key transcriptional activator of amino acid biosynthesis genes, increases lifespan, is unknown. Here we show that Gcn4 acts as a repressor of protein synthesis. By analyzing the mRNA and protein abundance, the ribosome occupancy and protein synthesis rate in various yeast strains, we demonstrate that Gcn4 is sufficient to reduce protein synthesis and to increase yeast lifespan. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other

Platforms:

GPL17342 GPL19756

52 Samples

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(Submitter supplied) In Saccharomyces cerevisiae, deletion of genes encoding proteins of the large ribosomal subunit (RPLs) increases the replicative lifespan in a Gcn4-dependent manner. However, how Gcn4, a key transcriptional activator of amino acid biosynthesis genes, increases lifespan, is unknown. Here we show that Gcn4 acts as a repressor of protein synthesis. By analyzing the mRNA and protein abundance, the ribosome occupancy and protein synthesis rate in various yeast strains, we demonstrate that Gcn4 is sufficient to reduce protein synthesis and to increase yeast lifespan. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL17342 GPL19756

50 Samples

Download data: CSV, TXT

(Submitter supplied) In Saccharomyces cerevisiae, deletion of genes encoding proteins of the large ribosomal subunit (RPLs) increases the replicative lifespan in a Gcn4-dependent manner. However, how Gcn4, a key transcriptional activator of amino acid biosynthesis genes, increases lifespan, is unknown. Here we show that Gcn4 acts as a repressor of protein synthesis. By analyzing the mRNA and protein abundance, the ribosome occupancy and protein synthesis rate in various yeast strains, we demonstrate that Gcn4 is sufficient to reduce protein synthesis and to increase yeast lifespan. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

2 Samples

Download data: CSV

(Submitter supplied) Coordinated regulation of ribosomal RNA (rRNA) and ribosomal protein gene (RPG) transcription by eukaryotic RNA polymerases (RNAP) is a key requirement for growth control. Although evidence for balance between RNPI-mediated 35S rRNA production and RNAPII-mediated RPG transcription have been described, the molecular basis is obscure. Here, we found that Rph1 modulates the transcription status of both rRNA and RPG in yeast. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27812

24 Samples

Download data: TXT, XLSX