Cyclin-dependent kinases are regulators and effectors of oscillations driven by a transcription factor network
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ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae Schizosaccharomyces pombe
PROVIDER: GSE32974 | GEO | 2012/02/03
SECONDARY ACCESSION(S): PRJNA146419
REPOSITORIES: GEO
Similar Datasets
Project description:Yeast cell cycle transcription dynamics in two S. cerevisae strains grown at 37°C: BF264-15DU (MATa ade1 his2 leu2-3, 112 trp1-1 ura3Dns, bar1) (wild type) and a mutant of the wild type strain lacking all Cdk1 activity, cdc28-4. We compared transcript levels of genes previously shown to be periodically expressed in wild-type cells (Orlando et al, 2008, Nature) to transcript levels in the absence of Cdk1 activity. Two replicate time courses from cells lacking all Cdk1 activity and one control time course from cells with wild-type Cdk1 activity are included.
2012-02-03 | E-GEOD-32974 | biostudies-arrayexpress
Project description:Yeast cell cycle transcription dynamics in two S. cerevisae strains: BF264-15DU (MATa ade1 his2 leu2-3, 112 trp1-1 ura3Dns, bar1) [referred to as wild type] and a mutant of the wild type strain, clb1,2,3,4,5,6 GAL1-CLB1, [referred to as cyclin mutant] that does not express S-phase and mitotic cyclins. Both strains were synchronized by elutriation and released into YEP 2% dextrose/1M sorbitol at 30c. 15 samples were taken at 16 min intervals covering ~2 cycles in wild-type and ~1.5 cycles for the mutants. A significant fraction of the Saccharomyces cerevisiae genome is transcribed periodically during the cell division cycle, suggesting that properly timed gene expression is important for regulating cell cycle events. Genomic analyses of transcription factor localization and expression dynamics suggest that a network of sequentially expressed transcription factors could control the temporal program of transcription during the cell cycle. However, directed studies interrogating small numbers of genes indicate that their periodic transcription is governed by the activity of cyclin-dependent kinases (CDKs). To determine the extent to which the global cell cycle transcription program is controlled by cyclin/CDK complexes, we compared genome-wide transcription dynamics in wild type budding yeast to mutants that do not express S-phase and mitotic cyclins. Keywords: cell cycle, strain comparison
2008-05-07 | GSE8799 | GEO
Project description:Yeast cell cycle transcription dynamics in two S. cerevisae strains: BF264-15DU (MATa ade1 his2 leu2-3, 112 trp1-1 ura3Dns, bar1) [referred to as wild type] and a mutant of the wild type strain, clb1,2,3,4,5,6 GAL1-CLB1, [referred to as cyclin mutant] that does not express S-phase and mitotic cyclins. Both strains were synchronized by elutriation and released into YEP 2% dextrose/1M sorbitol at 30c. 15 samples were taken at 16 min intervals covering ~2 cycles in wild-type and ~1.5 cycles for the mutants. A significant fraction of the Saccharomyces cerevisiae genome is transcribed periodically during the cell division cycle, suggesting that properly timed gene expression is important for regulating cell cycle events. Genomic analyses of transcription factor localization and expression dynamics suggest that a network of sequentially expressed transcription factors could control the temporal program of transcription during the cell cycle. However, directed studies interrogating small numbers of genes indicate that their periodic transcription is governed by the activity of cyclin-dependent kinases (CDKs). To determine the extent to which the global cell cycle transcription program is controlled by cyclin/CDK complexes, we compared genome-wide transcription dynamics in wild type budding yeast to mutants that do not express S-phase and mitotic cyclins. Experiment Overall Design: Cell cycle synchrony/time series experiments. G1 cells collected by elutriation was examined over time for 2 cell cycles. Strains compared: wild type vs cyclin mutants. 15 samples per time course at 16 min resolution. 2 biological replicates per strain.
2008-06-20 | E-GEOD-8799 | biostudies-arrayexpress
Project description:All yeast strains were in the genetic background W303-1A (MATa leu2-3,112 trp1-1 ura3-1 can1-100 ade2-1 his3-11,15). Gene expression profiles of the following mutant strains were compared with WT: YIA29 (mdl1::HIS3); YIA30 (yme1::KAN); YIA31 (mdl1::HIS3 yme1::KAN); 2 independent RNA preparations per strain were used (A and B); 2 independent array hybridisations per RNA preparation were performed (color switch experiments).
2005-12-31 | E-EMBL-5 | biostudies-arrayexpress
Project description:Experiment Design: •Type of experiment: time course after GAL (galactose) induction •Experimental factor: time, genotype •Number of hybridizations performed in the experiment: 24 (eight conditions with three biological replicates each) Samples used, extract preparation and labeling: •The origin of the biological sample: Species: S. cerevisiae Cell type: wild-type (YSS37, IFH1-13myc-TRP1, MATa) UASIFH1::HIS3-UASGAL1 (YSS89, UASGAL1-IFH1-13myc-TRP1, MATa) •Growth conditions: log phase (2x107/mL) at 30°C in YPLG medium, then addition of Galactose to 2% •Treatments: all cells were harvested by rapid centrifugation at 4°C then flash frozen in liquid nitrogen. Keywords = IFH1 Keywords = Transcriptional control of RP genes Keywords: time-course
2004-11-06 | GSE1934 | GEO
Project description:Experiment Design: Type of experiment: time course after GAL (galactose) induction. Experimental factor: time, genotype, Number of hybridizations performed in the experiment: 24 (eight conditions with three biological replicates each),Samples used, extract preparation and labeling: The origin of the biological sample: Species: S. cerevisiae,Cell type: wild-type (YSS37, IFH1-13myc-TRP1, MATa),UASIFH1::HIS3-UASGAL1 (YSS89, UASGAL1-IFH1-13myc-TRP1, MATa), Growth conditions: log phase (2x107/mL) at 30°C in YPLG medium, then addition of Galactose to 2%, Treatments: all cells were harvested by rapid centrifugation at 4°C then flash frozen in liquid nitrogen.
2007-07-09 | E-GEOD-1934 | biostudies-arrayexpress
Project description:Saccharomyces cerevisiae strain BY4741 (MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0) was grown in YPD medium. For control conditions, cells were grown in mid-log phase at 30°C for 20 min or 2 hours. Stress conditions were heat shock (37°C for 20 min), diauxic shift (harvested at 2 hours after glucose depletion), DNA damage (harvested after 2 hours of treatment with 5 µg/ml 4-nitroquinoline 1-oxide (Sigma)). Moreover, four conditions of the yeast metabolic cycle were analyzed. S. cerevisiae strain CEN.PK (MATa URA3 TRP1 LEU2 HIS3 MAL2-8C SUC2) was used and cultivated as described elsewhere (Nocetti and Whitehouse, Genes Dev, 2016). The period of metabolic oscillation was approximately 3.2 h. Cells were harvested at 16, 32, 48, and 60 min from the start of each cycle for one oxidative, two reductive/building, and one reductive/charging phase points. Total RNA from each sample was extracted by the hot phenol method and used for library preparation. 3′-seq libraries were prepared as described previously (Lianoglou et al., Genes Dev, 2013). Each condition was sequenced in three biological replicates. The 27 individual libraries were pooled and subjected to sequencing with HiSeq with SR50 at the Integrated Genomics Operation (MSKCC).
2023-09-30 | GSE213720 | GEO
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.
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Project description:Effect of HgCl2-treatment (dose-response:15min, 30min, 2h, and 24h) on cellular metabolism, resp on transcription. Differences between BY-4741 (MATa leu2 ura3 his3 met15 can1) + BYstb5 (MATa stb5::canMX4) to gain new insights into Hg-toxicity itself and adaptation to Hg-stress in yeast Saccharomyces cerevisiae.
2011-05-01 | E-MEXP-2991 | biostudies-arrayexpress
Project description:It is unclear how the amount of active nuclear MAPK over time quantitatively affects transcription. Here, we seek to address this issue by studying signal transduction and transcriptional response in a system that separates signalling from adaptation and hence signal strength from signal duration. The system is based on Saccharomyces cerevisiae osmoadaptation and allows modulation of the period of HOG-dependent responses without changing the initial stress intensity. The conditional osmotic stress system includes (i) a yeast mutant (gpd1 gpd2) unable to produce its main osmolyte glycerol, subsequently stressed with (ii) a stress inductor (polyols of different sizes) and allowed to adapt by (iii) expression of polyol flux-mediating aquaglyceroporin (rat AQP9). As there is no endogenous glycerol production, the osmoadaptation rate depends only on the size dependent equilibration rate over the plasma membrane of the polyol used as both stress inductor and compatible solute. Hence, we apply initially identical stresses but with differential durations, and determine the global transcriptional response. Saccharomyces cerevisiae W303-1A (MATa leu2-3/112 ura3-1 trp1-1 his3-11/15 gpd1::TRP1 gpd2::URA3) osmotically stressed with 1M of glycerol, erythritol, xylitol or sorbitol. Samples are taken in triplicates (except for sorbitol 20 an 90 min and 20 min xylitol were duplicates were taken) in time course series after stress application. Total of 45 samples. RNA from from cultures of gpd1 gpd2 cells expressing rAQP9 prior to polyol exposure was used as reference RNA for all microarrays.
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