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Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptional response of Schizosaccharomyces pombe to 5-Fluorouracil (5FU)

ABSTRACT: We use high-density tiling DNA microarray technology to obtain the specific transcriptome-wide response induced by 5-Fluorouracil (5FU) in the eukaryotic model Schizosaccharomyces pombe. Schizosaccharomyces pombe cultures with 5FU added to a final concentration of 500 M-NM-

ORGANISM(S): Schizosaccharomyces pombe

SUBMITTER: Luis Quintales

PROVIDER: E-GEOD-46919 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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New insights into the RNA-based mechanism of action of the anticancer drug 5'-fluorouracil in eukaryotic cells.

Mojardín Laura L Botet Javier J Quintales Luis L Moreno Sergio S Salas Margarita M

PloS one 20131101 11

5-Fluorouracil (5FU) is a chemotherapeutic drug widely used in treating a range of advanced, solid tumours and, in particular, colorectal cancer. Here, we used high-density tiling DNA microarray technology to obtain the specific transcriptome-wide response induced by 5FU in the eukaryotic model Schizosaccharomyces pombe. This approach combined with real-time quantitative PCR analysis allowed us to detect splicing defects of a significant number of intron-containing mRNA, in addition to identify ...[more]

PMID: 24223771

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Transcriptional response of Schizosaccharomyces pombe to 5-Fluorouracil (5FU)

Project description:We use high-density tiling DNA microarray technology to obtain the specific transcriptome-wide response induced by 5-Fluorouracil (5FU) in the eukaryotic model Schizosaccharomyces pombe.

2013-11-14 | GSE46919 | GEO

Clustered regulatory signals at nucleosome-depleted regions punctuate a constant nucleosomal landscape in Schizosaccharomyces pombe

Project description:Mononucleosomal DNA analysis of atf1D and pcr1D mutants of Schizosaccharomyces pombe and transcription analysis of exponential wild type 972 h-, atf1D, pcr1D and mitotic diploid pat1.114, and synchronous diploid pat1.114 at 0h, 3h and 5h into meiosis Mononucleosomal DNA vs. genomic input DNA in wildtype 972 h-, atf1D and pcr1D mutants of S. pombe was hybridized to Affymetrix GeneChip 1.0FR tiling microarrays (GPL7715). Total RNA for genome-wide transcription analysis from exponential wild type 972 h-, atf1D, pcr1D and mitotic diploid pat1.114 cells, and from synchronous diploid pat1.114 at 0h, 3h and 5h into meiosis was hybridized to the same microarrays.

2013-11-25 | E-GEOD-41770 | biostudies-arrayexpress

Schizosaccharomyces pombe

Project description:Transcriptional response of Schizosaccharomyces pombe to 5-Fluorouracil (5FU)

| PRJNA203034 | ENA

Analysis of DNA strand-specific differential expression with high density tiling microarrays

Project description:DNA microarray technology allows the analysis of genome structure and dynamics at genome-wide scale. Expression microarrays (EMA) contain probes for annotated open reading frames (ORF) and are widely used for the analysis of differential gene expression. By contrast, tiling microarrays (TMA) have a much higher probe density and provide unbiased genome-wide coverage. The purpose of this study was to develop a protocol that would take advantage of the high resolution of TMAs for quantitative measurement of DNA strand-specific differential expression of annotated and non-annotated transcripts. We extensively filtered probes present in Affymetrix Genechip Yeast Genome 2.0 expression and GeneChip S. pombe 1.0FR tiling microarrays to generate custom Chip Description Files (CDF) in order to compare the efficiency of both platforms. We experimentally tested the potential of our approach by measuring the differential expression of 4904 genes in the yeast Schizosaccharomyces pombe growing under conditions of oxidative stress. The results afforded a Pearson correlation coefficient of 0.943, indicating that TMAs are as reliable as EMAs for quantitative expression analysis. A significant advantage of TMAs over EMAs is the possibility of detecting non-annotated transcripts generated only under specific physiological conditions. We combined this property with a target-labelling protocol that preserves the original polarity of the transcripts with a view to determining the differential expression of non-annotated transcriptionally active regions. We have generated custom Chip Description Files (CDF) from Affymetrix Genechip Yeast Genome 2.0 expression and GeneChip S. pombe 1.0FR tiling microarrays to compare the efficiency of both platforms. We have experimentally tested the potential of our approach by measuring differential expression of the yeast Schizosaccharomyces pombe growing under conditions of oxidative stress.

2010-05-14 | E-GEOD-19020 | biostudies-arrayexpress

Genome-Wide Characterization of the Phosphate Starvation Response in Schizosaccharomyces pombe [ChIP-Seq data]

Project description:Inorganic phosphate is an essential nutrient required by organisms for growth. During phosphate starvation, Saccharomyces cerevisiae activates the phosphate signal transduction (PHO) pathway leading to the expression of the secreted acid phosphatase, PHO5. The fission yeast, Schizosaccharomyces pombe, regulates expression of the ScPHO5 homolog (pho1+) via a non-orthologous PHO pathway. The genes induced by phosphate limitation and the molecular mechanism by which the genetically identified positive (pho7+) and negative (csk1+) regulators function are not known. Here we use a combination of molecular biology, expression microarrays, and chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) to characterize the role of pho7+ and csk1+ in the PHO response. We define the set of genes that comprise the initial response to phosphate starvation in S. pombe. We identify a conserved PHO response for the ScPHO5 (pho1+), ScPHO84 (spbc8e4.01c+), and ScGIT1 (spbc1271.09+) orthologs. We use ChIP-Seq to identify members of the Pho7 regulon and characterize Pho7 binding in response to phosphate-limitation and Csk1 activity. We demonstrate that activation of pho1+ requires Pho7 binding to a UAS in the pho1+ promoter and that Csk1 repression does not regulate Pho7 enrichment. Further, we find that Pho7-dependent activation is not limited to phosphate-starvation, as additional environmental stress response pathways require pho7+ for maximal induction. We provide a global analysis of the PHO pathway in S. pombe. Our results elucidate the conserved core regulon required for responding to phosphate starvation between distantly related ascomycetes and a better understanding of flexibility in environmental stress response networks. ChIP Sequencing of the Schizosaccharomyces pombe 972h- transcription factor Pho7-TAP in high-Pi, no-Pi, and csk1M-NM-^T conditions

2013-01-02 | E-GEOD-39498 | biostudies-arrayexpress

Genomewide analysis of the human p53 transcriptional network unveils a lncRNA tumor suppressor signature (expression)

Project description:We report the application of high-throughput sequencing to performed the p53 regulated trancriptome in HCT116 colon cancer cells treated with the DNA damage 5FU. To study the direct targets of p53 we performed ChIP-seq to deterrmined the p53 biding sites and associated with the expression levels. With this study we identified the new genomic regions regulated by p53 and with special attention in those regions that are significally expressed by DNA damage and and are non- coding. HCT116 p53 wt cell transfected with the ASO-SC, ASO lncRNA-1 and ASO unassigned-1 for depletion of this new lncRNAs and treated with the DNA damage drug 5FU for 12h were analyzed in the affimetrix platform HTA2.

2014-12-22 | E-GEOD-58409 | biostudies-arrayexpress

Schizosaccharomyces pombe

Project description:Schizosaccharomyces pombe

| PRJNA601919 | ENA

Schizosaccharomyces pombe

Project description:Schizosaccharomyces pombe

| PRJNA239187 | ENA

Schizosaccharomyces pombe strain:ED668

Project description:Schizosaccharomyces pombe

| PRJNA295384 | ENA

CHD1 remodelers space nucleosomes in vitro and link regular arrays to 5M-bM-^@M-^Y ends of genes in S. Pombe

Project description:Nucleosome positioning governs access to eukaryotic genomes. Many genes show a stereotypic organisation at their 5M-bM-^@M-^Y end: a nucleosome free region just upstream of the transcription start site (TSS) followed by a regular nucleosomal array over the coding region. The determinants for this pervasive pattern are unclear, but nucleosome remodeling ATPases likely are critical. Now we employ deletion mutants to study the role of nucleosome remodeling ATPases in global nucleosome positioning in S. pombe and the corresponding changes in expression patterns. We find a striking evolutionary shift in remodeling enzyme usage between budding and fission yeast. The S. pombe RSC remodeling complex seems not involved in nucleosome positioning, despite its prominent role in S. cerevisiae. While lacking ISWI-type remodelers, S. pombe has two CHD1-type ATPases, Hrp1 and Hrp3. We demonstrate nucleosome spacing activity for both in vitro, and together they are essential for linking regular genic arrays to most TSSs in vivo. Impaired chromatin may but need not lead to changes in transcription. The absence of both causes changed expression for about 20% and increased antisense transcription for 15% of all annotated elements. For RNA expression: total RNA from hrp1D, hrp3D, hrp1Dhrp3D and wt (with actinomycin D) and total RNA from snf21ts at 25C and 34C, snf21ts swr1D at 25C and 34C, pht1D swr1D (without actinomycin D). For nucleosome mapping: Nucleosomal DNA in pht1M-NM-^T swr1M-NM-^T mutant, snf21- ts mutant, snf21- ts swr1M-NM-^T mutant, mit1M-NM-^T mutant, hrp1M-NM-^T mutant, hrp3M-NM-^T mutant and hrp1M-NM-^T hrp3M-NM-^T mutant S.pombe vs. Genomic Input DNA in wildtype and mit1M-NM-^T mutant S.pombe.

2012-10-11 | E-GEOD-41024 | biostudies-arrayexpress

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