Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Communication between mitochondria and nucleus: defining a retrograde response in fission yeast

ABSTRACT: Retrograde response was widely studied in budding yeast but the main transcription factors that transmit it (RTG1,2 and 3) are not conserved in other organisms, thus it is interesting to study how communication between mitochondria and nucleus evolved in distantly related fission yeast, and which are the common aspects of this conserved pathway between yeast and higher organisms.To analyse any retrograde response in fission yeast, we inhibited the electron transport chain activity by antimycin A and studied cellular gene expression changes by microarrays. Cells treated with antimycin A in fermentative medium (YE with 3% glucose), showed the same growth rate as untreated cells, but they reached a lower biomass in stationary phase. Antimycin A treated cells consumed glucose at a faster rate and produced more ethanol, indicating that the energy metabolism was shifted even more towards fermentation. We analyzed the transcriptomes of antimycin A-treated cells to untreated control cells during early exponential growth phase (OD 0.5).

INSTRUMENT(S): Axon GenePix 4000B scanning hardware

ORGANISM(S): Schizosaccharomyces pombe

SUBMITTER: Mimoza Hoti

PROVIDER: E-MTAB-4520 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

A histone H3K36 chromatin switch coordinates DNA double-strand break repair pathway choice.

Project description:Wildtype and set2delta strains, with samples taken at t=0 and following 30 minutes treatment with 5 µg/ml bleomycin.

2014-06-09 | E-MTAB-2549 | biostudies-arrayexpress

Meta-stable structural variants alter gene expression and quantitative traits in the fission yeast

Project description:To examine whether naturally occurring duplications are altering gene expression we chose eight pairs of closely related strains (less than 150 SNPS between each pair) that contained at least one unshared duplication and performed pair-wise two-colour microarray analysis.

2017-05-30 | E-MTAB-4019 | biostudies-arrayexpress

Functional and Regulatory Profiling of Energy Metabolism in Fission Yeast: dynamic gene regulation during adaptation to respiratory medium.

Project description:Fission yeast in high glucose media preferentially uses fermentation for energy production, even under aerobic conditions, an analogous metabolic programme, aerobic glycolysis, is a hallmark of cancer and enables the proliferation of tumor cells. Fission yeast, unlike budding yeast, requires mitochondrial genomes and oxidative phosphorylation for survival, mitochondrial inheritance, genome organisation and RNA processing are strikingly different between the two yeasts, and S. pombe mitochondria resemble more the human mitochondria. However, mitochondrial biology and respiratory control is poorly understood in fission yeast. In this study, we used microarrays to profile gene expression before and at six time points after the shift from fermentative to respiratory medium. Cells were grown in yeast extract based media with 3% glucose to early exponential phase (time point 0), then the carbon source was changed to 3% glycerol, 0.1% glucose. Transcript levels were monitored by microarrays at several time points after the switch (0.2, 0.5, 1, 2; 04 and 24 hours). Sample from each time point is hybrydized with sample of all pooled time points. Experiment was repeated twice with the dye swap.

2016-11-01 | E-MTAB-4518 | biostudies-arrayexpress

wild-type and gaf1 mutant cells treated with Torin1 or with a combination of caffeine/rapamycin

Project description:Target of Rapamycin Complex 1 (TORC1) signaling promotes growth and ageing. Inhibition of TORC1 leads to a down-regulation of factors that stimulate protein translation, which in turn contributes to longevity. TORC1-dependent post-transcriptional regulation of protein translation has been well studied, while analogous transcriptional regulation is less understood. Here we screened fission yeast deletion mutants for resistance to Torin1, which inhibits TORC1 and cell growth. Cells lacking the GATA transcription factor Gaf1 (gaf1Δ) grew normally even in high doses of Torin1. The gaf1Δ mutation shortened the chronological lifespan of non-dividing cells and diminished the longevity triggered by Torin1 treatment. Expression profiling and genome-wide binding experiments showed that, upon TORC1 inhibition, Gaf1 directly up-regulated genes for small-molecule metabolic pathways and indirectly repressed genes for protein translation. Surprisingly, Gaf1 bound to, and down-regulated the tRNA genes, so also functions as a transcription factor for genes transcribed by RNA polymerase III. Thus, Gaf1 controls the transcription of both coding and tRNA genes to inhibit translation and growth downstream of TORC1.

2020-03-02 | E-MTAB-8569 | biostudies-arrayexpress

Abo1, a conserved bromodomain AAA-ATPase, interacts with FACT and maintains global nucleosome occupancy and organization

Project description:Determination the global transcriptional contributions of Abo1 and Abo2 using microarray analyses.

2016-03-07 | E-MTAB-3455 | biostudies-arrayexpress

An essential role for dNTP homeostasis following CDK-induced replication stress

Project description:dNTP supply and demand model in which maintaining dNTP homeostasis is essential in preventing replication catastrophe in response to CDK-induced replication stress

2018-10-31 | E-MTAB-6795 | biostudies-arrayexpress

Fission yeast Cactin restricts telomere transcription and elongation by promoting Rap1 pre-mRNA splicing and protein stabilization

Project description:RNA transcriptome analysis of S.pombe fission yeast cells deleted for cay1+/SPBC2F12.12c (cay1D) and wildtype The transcriptome of cay1+ deleted fission yeast cells was characterized and compared to wildtype yeasts to identify differentially expressed genes controlled by Cay1 on a transcriptional or post-transcriptional level. 3 biological replicates of wildtype and cay1D fission yeast cells were prepared in parallel. Based on poor quality array hybridization one cay1D replicate was excluded from further analysis

2014-09-27 | E-GEOD-61792 | biostudies-arrayexpress

Proteome of fission yeast RNA degradation mutants

Project description:We measured total proteomes of 15 different fission yeast strains : wild type, Δcid1, Δdis32, Δcid1Δdis32, Δlsm1, Δski2, Δcid1Δlsm1, Δdis32Δski2, Δcid1Δski2, Δcid1Δdis32Δski2, Δcid1Δdis32Δlsm1, Δdis32Δlsm1, Δlsm1Δski2, Δlsm1Δski2Δdis32, Δlsm1Δski2Δcid1. All mutantions affected cytoplasmic mRNA decay. At least 5 repeats were measured for each mutant.

2024-06-21 | PXD051392 | Pride

Transcriptome regulation in response to respiratory inhibition with antimycin A in: (a) wild type fission yeast grown in minimal media (EMM) (b) minimal media supplemented with arginine or in (c) strain with deletion of ssp1 gene.

Project description:We observed that in fission yeast respiration inhibition with drug antimycin A results in arginine auxotrophy. To get insights into transcriptional response for respiratory inhibition and attenuating role of arginine supplementation we performed microarray experiment. Yeast were growing exponentially (OD600 around 0.5) in minimal media (EMM), transcript abundance was monitored immediately prior (Time 0), and 30 and 120 minutes after addition to the media antimycin A (to the concentration 0.15 µg/ml). We performed such experiment for wild type yeast (strain 972 h-), wild type yeast grown in minimal media supplemented with arginine (to the concentration 0.2g/L), and for ssp1 deletion strain grown in minimal media. Ssp1 regulates AMPK kinase and our microarray data show that is can modulate response for respiration block. Two biological samples for each condition (EMM, EMM with arginine and ssp1 deletion) was collected. Part of all the samples were pooled and used as reference in dye swap design.

2020-03-30 | E-MTAB-8805 | biostudies-arrayexpress

Distinctive responses to nitrogen starvation in the dominant active mutants of the fission yeast Rheb GTPase.

Project description:Rheb, a ras-like small GTPase conserved from human to yeast, controls Tor kinase and plays a central role in regulation of cell growth depending on extracellular conditions. Fission yeast Rheb regulates amino acid uptake as well as response to nitrogen starvation. In this study we generated two mutants of Rheb, rhb1-DA4 and rhb1-DA8, and characterized them genetically. V17A mutation within the G1 box defined for the ras-like GTPases was responsible for rhb1-DA4, and Q52R I76F within the switch II domain for rhb1-DA8. In fission yeast, two events, induction of a meiosis initiating gene mei2+ and cell division without cell growth, are a typical response to nitrogen starvation. Under nitrogen-rich conditions, Rheb stimulates Tor kinase, which, in turn, suppresses the response to nitrogen starvation. While amino acid uptake was prevented by both rhb1-DA4 and rhb1-DA8 in a dominant fashion, the response to nitrogen starvation was prevented only by rhb1-DA4. rhb1-DA8 thereby allowed genetic dissection of the Rheb-dependent signaling cascade. We postulate that Rheb in fission may have two downstream elements, Tor kinase for regulation of the response to nitrogen starvation and the other element for regulation of amino acid uptake. Gene expression profile under nitrogen starvation in fission yeast. Type of experiment: Comparing between vegetatively-growing control cells and cells 3 hrs after nitrogen starvation. Experimental factor: Gene expression profile after nitrogen starvation in the rhb1-D4 or rhb1-D8 cells. Quality control steps taken: All experiments were repeated more than twice except for the tsc2D which was previously reported. Keywards: Nitrogen starvation, rhb1-D4, rhb1-D8

2009-09-28 | E-GEOD-14626 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data