Saccharomyces cerevisiae strain:sigma 1278b
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ABSTRACT:
PROVIDER: PRJDB10543 | ENA |
REPOSITORIES: ENA
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Project description:Short-read RNA-seq was performed on rRNA-depleted RNA isolated from spores of the budding yeast Saccharomyces cerevisiae that were sorted by mating type.
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Project description:To characterize cellular response to the anti-cancer ruthinium complex KP1019, budding yeast Saccharomyces cerevisiae transcripitonal response to KP1019 was measured using microarray analysis. Although KP1019 molecular mechanism of action remains a matter of debate, the drug has been shown to bind DNA in biophysical assays and to damage DNA of colorectal and ovarian cancer cells in vitro. KP1019 has also been shown to induce mutations and induce cell cycle arrest in Saccharomyces cerevisiae, suggesting that budding yeast can serve as an appropriate model for characterizing the cellular response to the drug. Here we use a transcriptomic approach to characterize KP1019 induced transcriptional changes.
2015-10-26 | GSE71805 | GEO
Project description:To characterize cellular response to the anti-cancer ruthinium complex KP1019, budding yeast Saccharomyces cerevisiae transcripitonal response to KP1019 was measured using microarray analysis. Although KP1019 molecular mechanism of action remains a matter of debate, the drug has been shown to bind DNA in biophysical assays and to damage DNA of colorectal and ovarian cancer cells in vitro. KP1019 has also been shown to induce mutations and induce cell cycle arrest in Saccharomyces cerevisiae, suggesting that budding yeast can serve as an appropriate model for characterizing the cellular response to the drug. Here we use a transcriptomic approach to characterize KP1019 induced transcriptional changes. Two concentrations of KP1019 (40 micrograms/mL and 80 micrograms/ml were assayed by microarray analysis to obtain comparative expression data for treated and untreated cells of the budding yeast Saccharomyces cerevisiae (strain BY4741). Two biological replicates of each concentration were done. Each biological replicate was done in duplicate to allow for dye reversal controls.
2015-10-26 | E-GEOD-71805 | biostudies-arrayexpress
Project description:Transcriptome-wide Analysis of Exosome Targets in the Budding Yeast Saccharomyces cerevisiae
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Project description:Post-translational modification of proteins by lysine acetylation plays important regulatory roles in living cells. The budding yeast Saccharomyces cerevisiae is a widely used unicellular eukaryotic model organism in biomedical research. S. cerevisiae contains several evolutionary conserved lysine acetyltransferases and deacetylases. However, only a few dozen acetylation sites in S. cerevisiae are known, presenting a major obstacle for further understanding the regulatory roles of acetylation in this organism. Here we use high resolution mass spectrometry to identify about 4000 lysine acetylation sites in S. cerevisiae. Acetylated proteins are implicated in the regulation of diverse cytoplasmic and nuclear processes including chromatin organization, mitochondrial metabolism, and protein synthesis. Bioinformatic analysis of yeast acetylation sites shows that acetylated lysines are significantly more conserved compared with nonacetylated lysines. A large fraction of the conserved acetylation sites are present on proteins involved in cellular metabolism, protein synthesis, and protein folding. Furthermore, quantification of the Rpd3-regulated acetylation sites identified several previously known, as well as new putative substrates of this deacetylase. Rpd3 deficiency increased acetylation of the SAGA (Spt-Ada-Gcn5-Acetyltransferase) complex subunit Sgf73 on K33. This acetylation site is located within a critical regulatory domain in Sgf73 that interacts with Ubp8 and is involved in the activation of the Ubp8-containing histone H2B deubiquitylase complex. Our data provides the first global survey of acetylation in budding yeast, and suggests a wide-ranging regulatory scope of this modification. The provided dataset may serve as an important resource for the functional analysis of lysine acetylation in eukaryotes
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Project description:Oxidative stress is a harmful condition in a cell, tissue, or organ, caused by an imbalnace between reactive oxygen species and other oxidants and the capacity of antioxidant defense systems to remove them. The budding yeast S. cerevisiae has been the major eukaryotic model for studies of response to oxidative stress. We used microarrays to study the genome-wide temporal response of the yeast S. cerevisiae to oxidative stress induced by cumene hydroperoxide. Keywords: time course
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Project description:We investigated the genome-wide distribution of Okazaki fragments in the commonly used laboratory Saccharomyces cerevisiae strain S288C to study the DNA replication model adopted by the budding yeast. The method based upon lambda exonuclease digestion for purification of RNA-primed replication intermediates was first improved to be suitable for the purification of Okazaki fragments. Then, we used this improved method to purify Okazaki fragments from S288C yeast cells, followed by Illumina sequencing. We found that the expected asymmetric distribution of Okazaki fragments around confirmed replication origins, which was derived from the semi-discontinuous DNA replication model, was not observed on S. cerevisiae chromosomes. Even around two highly efficient replication origins, ARS522 and ARS416, the ratios of Okazaki fragments on both strands were inconsistent with the semi-discontinuous DNA replication model. Our study supported the discontinuous DNA replication model. Besides, we also observed that Okazaki fragments were overpresented in the transcribed regions in S. cerevisiae mitochondrial genome, which indicated the interplay between transcription and DNA replication. Examination of the distribution of Okazaki fragments in Saccharomyces cerevisiae strain S288C.
2013-06-18 | E-GEOD-42929 | biostudies-arrayexpress
Project description:We investigated the genome-wide distribution of Okazaki fragments in the commonly used laboratory Saccharomyces cerevisiae strain S288C to study the DNA replication model adopted by the budding yeast. The method based upon lambda exonuclease digestion for purification of RNA-primed replication intermediates was first improved to be suitable for the purification of Okazaki fragments. Then, we used this improved method to purify Okazaki fragments from S288C yeast cells, followed by Illumina sequencing. We found that the expected asymmetric distribution of Okazaki fragments around confirmed replication origins, which was derived from the semi-discontinuous DNA replication model, was not observed on S. cerevisiae chromosomes. Even around two highly efficient replication origins, ARS522 and ARS416, the ratios of Okazaki fragments on both strands were inconsistent with the semi-discontinuous DNA replication model. Our study supported the discontinuous DNA replication model. Besides, we also observed that Okazaki fragments were overpresented in the transcribed regions in S. cerevisiae mitochondrial genome, which indicated the interplay between transcription and DNA replication.
2013-06-18 | GSE42929 | GEO