Transcription profile of fission yeast
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae Schizosaccharomyces pombe
PROVIDER: GSE15108 | GEO | 2010/11/04
SECONDARY ACCESSION(S): PRJNA114859
REPOSITORIES: GEO
Similar Datasets
Project description:Wild-type cells were cultured at 30 deg and cells were harvested. Total RNAs were purified from 3 populations. Microarray data of 3 samples were background-corrected with Mas5.0.
2010-11-04 | E-GEOD-15108 | biostudies-arrayexpress
Project description:Wild-type and the acs2Ts1 mutant yeasts were shifted from 25deg to 37deg. After 60 minutes, Yeasts were harvested and divided into 2 x 2 cell samples. Total RNAs were purified from 4 populations. Keywords: WT vs mutant
2006-10-01 | GSE2806 | GEO
Project description:Large-scale interactome screen for 89 transcription factors (TFs) in fission yeast. TFs are tagged at the endogenous locus with a 3xFLAG affinity epitope. Cells cultured under optimal conditions (30°C, rich medium) were subjected to IP-MS at 150 mM an 500 mM NaCl.
2024-08-30 | PXD054070 | Pride
Project description:An branched-chain amino acids auxotroph eca39∆ mutant fission yeast exhibits an unusual adaptive growth phenotype on solid minimal media containing Ile, Leu and Val when other strains are growing nearby. The transcriptional profiles of an eca39∆ mutant before and after the adaptation were determined using Affymetrix DNA microarrays. Wild-type, the eca39∆ mutant, and the adapted eca39∆ mutant fission yeasts were inoculated in YE+2mM Ile, Leu and Val, and harvested at OD ~ 1. Total RNAs were purified from the 3 samples.
2012-09-21 | E-GEOD-29355 | biostudies-arrayexpress
Project description:We systematically examined transcription and RNA-processing in mitochondria of the petite-negative fission yeast Schizosaccharomyces pombe. Two presumptive transcription initiation sites at opposite positions on the circular-mapping mtDNA were confirmed by in vitro capping of primary transcripts with guanylyl-transferase. The major promoter (Pma) is located adjacent to the 5'-end of the rnl gene, and a second, minor promoter (Pmi) upstream from cox3. The primary 5'-termini of the mature rnl and cox3 transcripts remain unmodified. A third predicted accessory transcription initiation site is within the group IIA1 intron of the cob gene (cobI1). The consensus promoter motif of S. pombe closely resembles the nonanucleotide promoter motifs of various yeast mtDNAs. We further characterized all mRNAs and the two ribosomal RNAs by Northern hybridization, and precisely mapped their 5'- and 3'-ends. The mRNAs have leader sequences with a length of 38 up to 220 nt and, in most instances, are created by removal of tRNAs from large precursor RNAs. Like cox2 and rnl, cox1 and cox3 are not separated by tRNA genes; instead, transcription initiation from the promoters upstream from rnl and cox3 compensates for the lack of tRNA-mediated 5'-processing. The 3'-termini of mRNAs and of SSU rRNA are processed at distinct, C-rich motifs that are located at a variable distance (1-15 nt) downstream from mRNA and SSU-rRNA coding regions. The accuracy of RNA-processing at these sites is sequence-dependent. Similar 3'-RNA-processing motifs are present in species of the genus Schizosaccharomyces, but not in budding yeasts that have functionally analogous A+T-rich dodecamer processing signals.
| S-EPMC1370763 | biostudies-literature
Project description:BackgroundFission yeast cells undergo sexual differentiation in response to nitrogen starvation. In this process haploid M and P cells first mate to form diploid zygotes, which then enter meiosis and sporulate. Prior to mating, M and P cells communicate with diffusible mating pheromones that activate a signal transduction pathway in the opposite cell type. The pheromone signalling orchestrates mating and is also required for entry into meiosis.ResultsHere we use DNA microarrays to identify genes that are induced by M-factor in P cells and by P-factor in M-cells. The use of a cyr1 genetic background allowed us to study pheromone signalling independently of nitrogen starvation. We identified a total of 163 genes that were consistently induced more than two-fold by pheromone stimulation. Gene disruption experiments demonstrated the involvement of newly discovered pheromone-induced genes in the differentiation process. We have mapped Gene Ontology (GO) categories specifically associated with pheromone induction. A direct comparison of the M- and P-factor induced expression pattern allowed us to identify cell-type specific transcripts, including three new M-specific genes and one new P-specific gene.ConclusionWe found that the pheromone response was very similar in M and P cells. Surprisingly, pheromone control extended to genes fulfilling their function well beyond the point of entry into meiosis, including numerous genes required for meiotic recombination. Our results suggest that the Ste11 transcription factor is responsible for the majority of pheromone-induced transcription. Finally, most cell-type specific genes now appear to be identified in fission yeast.
| S-EPMC1693924 | biostudies-literature
Project description:We report gene expression profiling in the fission yeast Schizosaccharomyces pombe. We performed high-throughput sequencing of RNA isolated from wild-type, clr6-1, ago1∆, red1∆, rrp6∆, clr4∆, ccr4∆, ccr4∆fep1, wild-type cells treated with an iron chelator (2,2′-bipyridyl; DIP) grown at 30°C or 18°C and ccr4∆fep1 cells treated with DIP at 18C. We find that many stress response genes, transmembrane transporters, and non-coding RNAs are up-regulated in cells cultured at 18°C. Our analyses concluded that Clr4 and Ccr4 are important for controlling transcript levels at 18°C and uncovered a role for iron homeostasis in adaptive genome control.
2018-05-08 | GSE104546 | GEO
Project description:To discover the fission yeast prolyl hydroyxlome. Five biological replicates of WT and Ofd1D cells were cultured. The whole cell lysates were analysed by TMT mass spectrometry for prolyl hydroxylation
2022-03-03 | PXD009371 | Pride
Project description:In Schizosaccharomyces pombe, over 90% of transcription factor genes are nonessential. Moreover, the majority do not exhibit significant growth defects under optimal conditions when deleted, complicating their functional characterization and target gene identification. Here, we systematically overexpressed 99 transcription factor genes with the nmt1 promoter and found that 64 transcription factor genes exhibited reduced fitness when ectopically expressed. Cell cycle defects were also often observed. We further investigated three uncharacterized transcription factor genes (toe1(+)-toe3(+)) that displayed cell elongation when overexpressed. Ectopic expression of toe1(+) resulted in a G1 delay while toe2(+) and toe3(+) overexpression produced an accumulation of septated cells with abnormalities in septum formation and nuclear segregation, respectively. Transcriptome profiling and ChIP-chip analysis of the transcription factor overexpression strains indicated that Toe1 activates target genes of the pyrimidine-salvage pathway, while Toe3 regulates target genes involved in polyamine synthesis. We also found that ectopic expression of the putative target genes SPBC3H7.05c, and dad5(+) and SPAC11D3.06 could recapitulate the cell cycle phenotypes of toe2(+) and toe3(+) overexpression, respectively. Furthermore, single deletions of the putative target genes urg2(+) and SPAC1399.04c, and SPBC3H7.05c, SPACUNK4.15, and rds1(+), could suppress the phenotypes of toe1(+) and toe2(+) overexpression, respectively. This study implicates new transcription factors and metabolism genes in cell cycle regulation and demonstrates the potential of systematic overexpression analysis to elucidate the function and target genes of transcription factors in S. pombe.
| S-EPMC3730917 | biostudies-literature
Project description:In ribosome biogenesis, a large fraction of ribosomes is used for producing ribosomal proteins. Here, we deal with the question what fraction of ribosomes should be allocated for synthesis of ribosomal proteins to optimize the cellular economy for growth. We define the "r-fraction" as the fraction of mRNA of the ribosomal protein genes out of the total mRNA and simulated how the amount of the total protein is affected by the r-fraction. Then, we empirically measured the amount of protein and RNA in fission yeast cells cultured at a high or low nitrogen source. In the cells cultured at a low nitrogen source, the r-fraction decreased from 0.46 to 0.42 with a 40% reduction of rRNA, but the reduction of the total protein was smaller at 30%. These results indicate that the r-fraction is internally controlled to optimize the efficiency of protein synthesis at a limited cellular cost.
2015-10-22 | GSE68173 | GEO