GEO DataSets

(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; Expression profiling by high throughput sequencing; Other

Platforms:

GPL17342 GPL19756

52 Samples

Download data

(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) Using ribosome profiling, we find globally reduced translation efficiency during mitotic / replicative aging in budding yeast. Two mechanisms contribute to this: Firstly, the mRNA binding protein Ssd1 is induced during aging, sequestering mRNAs to P-bodies and stress granules that are abundant in old cells. Indeed, overexpression of Ssd1 reduced protein synthesis in young cells and extended lifespan, while loss of Ssd1 reduced the translational deficit of old cells and shortened lifespan. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL13821

18 Samples

Download data: WIG, XLS

(Submitter supplied) We have shown that multiple tRNA synthetase inhibitors can increase lifespan in both the nematode C. elegans and the budding yeast S. cerevisiae by acting through the conserved transcription factor Gcn4 (yeast) / ATF-4 (worms). To further understand the biology downstream of this conserved transcription factor in the yeast model system, we looked at two different yeast models known to have both upregulated Gcn4, and GCN4-dependent increased replicative lifespan. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19756

96 Samples

Download data: TSV

(Submitter supplied) Gcn4 is a yeast transcriptional activator induced by amino acid starvation. ChIP-seq analysis revealed 546 genomic sites occupied by Gcn4 in starved cells, representing ~30% of all Gcn4 binding-motifs. Deviation from the consensus motif and nucleosome occupancy are key negative determinants of Gcn4 binding. Surprisingly, only ~40% of the bound sites are in promoter regions, and only ~50-67% of these activate transcription, indicating extensive negative control over Gcn4 function. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19756

12 Samples

Download data: TDF

(Submitter supplied) Gcn4 is a yeast transcriptional activator induced by amino acid starvation. ChIP-seq analysis revealed 546 genomic sites occupied by Gcn4 in starved cells, representing ~30% of all Gcn4 binding-motifs. Deviation from the consensus motif and nucleosome occupancy are key negative determinants of Gcn4 binding. Surprisingly, only ~40% of the bound sites are in promoter regions, and only ~50-67% of these activate transcription, indicating extensive negative control over Gcn4 function. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23014

42 Samples

Download data: BW

(Submitter supplied) The Snf1 kinase plays a critical role in recalibrating cellular metabolism in response to glucose depletion. Hundreds of genes show changes in expression levels when the SNF1 gene is deleted. However, cells can adapt to the absence of a specific gene when grown in long term culture. Here we apply a chemical genetic method to rapidly and selectively inactivate a modified Snf1 kinase using a pyrazolopyrimidine inhibitor. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL90

4 Samples

Download data: CEL, CHP

(Submitter supplied) Caloric restriction (CR) is the only non-genetic intervention to retard aging and increase longevity in a variety of species. It is important to understand the fundamental mechanism by which CR extends lifespan that remains elusive. Owing to well-established genomic tools and convenience of culture system, we used a single cell organism, Saccharomyces cerevisiae, to clarify the mechanisms of CR. In order to identify genes responsible for CR-mediated longevity, we performed microarray experiments across the longevity assurance time-points.

Organism:

Schizosaccharomyces pombe; Saccharomyces cerevisiae BY4741; Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL2529

24 Samples

Download data: CEL, CHP

(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

Download data

(Submitter supplied) Paired-end sequencing study of nucleosomal DNA prepared from budding yeast by micrococcal nuclease digestion.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9377

4 Samples

Download data: TXT

(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) Transcriptional regulation plays an important role in the control of gene expression during aging. However, translation efficiency likely plays an equally important role in determining protein abundance, but has been relatively under studied in this context. Here we used RNA-seq and ribosome profiling to investigate the role of translational regulation in lifespan extension by CAN1 gene deletion in yeast. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

16 Samples

Download data: TXT

(Submitter supplied) Sequence-specific DNA-binding transcription factors are central to gene regulation. They are often associated with consensus binding sites that predict far more genomic sites than are bound in vivo. One explanation is that most sites are blocked by nucleosomes, such that only sites in nucleosome-depleted regulatory regions are bound. Alternatively, the consensus site may be poorly defined. We compared the binding of the yeast transcription factor Gcn4 in vivo using published ChIP-seq data (546 sites) and in vitro, using a modified SELEX method ("G-SELEX"), which utilizes short genomic DNA fragments to quantify binding at all sites. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19756

5 Samples

Download data: BW

(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) Complex biological processes are often regulated, at least in part, by the binding of transcription factors to their targets. Recently, considerable effort has been made to analyze the binding of relevant factors to the suite of targets they regulate, thereby generating a regulatory circuit map. However, for most studies the dynamics of binding have not been analyzed and thus the temporal order of events and mechanisms by which this occur are poorly understood. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL3541

60 Samples

Download data: PAIR

(Submitter supplied) Iron dyshomeostasis contributes to aging, but little information is available about the molecular mechanisms. Here, we provide evidence that, in Saccharomyces cerevisiae, aging is associated with altered expression of genes involved in iron homeostasis. We further demonstrate that defects in the conserved mRNA-binding protein Cth2, which controls stability and translation of mRNAs encoding iron-containing proteins, increase lifespan by alleviating its repressive effects on mitochondrial function. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

15 Samples

Download data: TXT

(Submitter supplied) Studies using yeast have advanced our understanding of both replicative and chronological aging, leading to the discovery of longevity genes that have homologues in higher eukaryotes. Chronological lifespan in yeast is conventionally defined as the lifespan of a non-dividing cell. To date, this parameter has only been estimated under calorically restricted (CR) conditions, mimicked by starvation. Since post-mitotic cells in higher eukaryotes are rarely calorically-restricted, we sought to develop an alternative experimental system where non-dividing yeast would age chronologically, in the presence of excess nutrients. more...

Organism:

Saccharomyces cerevisiae; Schizosaccharomyces pombe

Type:

Expression profiling by array

Platform:

GPL2529

26 Samples

Download data: CEL, CHP

(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) Application of microfluidic platforms facilitated high-precision measurements of yeast replicative lifespan (RLS); however, comparative quantification of lifespan across strain libraries has been missing. Here we microfluidically measured RLS of 307 yeast strains, each deleted for a single gene. Despite previous reports of extended lifespan in these strains, we found that 56% of them did not actually live longer than the wild-type; while the remaining 44% showed extended lifespans, the degree of extension was often different from what was previously reported. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27812

4 Samples

Download data: TXT