Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

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

ABSTRACT: 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

ORGANISM(S): Schizosaccharomyces pombe 972h-

SUBMITTER: Ian Carter-O'Connell

PROVIDER: E-GEOD-39498 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Genome-wide characterization of the phosphate starvation response in Schizosaccharomyces pombe.

Carter-O'Connell Ian I Peel Michael T MT Wykoff Dennis D DD O'Shea Erin K EK

BMC genomics 20121212

<h4>Background</h4>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 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 involving genetically identified positive (pho7+) and negative (csk1+) regulators. The genes ind ...[more]

PMID: 23231582

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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. Schizosaccharomyces pombe 972 h- cells were starved for inorganic phosphate for 0, 30, 60, 120, or 240 minutes pior to microarray preparation to determine the extent and temporal resolution of the phosphate starvation response. At 120 minutes post-starvation we define a set of genes that are directly and specifically induced by phosphate starvation, providing a time-point at which all other experiments were performed. We characterize the pho7+- and csk1+- dependency of this PHO response at 120 minutes post-starvation in pho7+csk1+, pho7M-NM-^T, csk1M-NM-^T, and pho7M-NM-^Tcsk1M-NM-^T cells. In a seperate set of experiments we characterized the S. pombe stress response to copper limitation, iron limitation, and carbon switching at 120 minutes post-stress and osmotic shift at 20 minutes post-stress in both pho7+ and pho7M-NM-^T cells.

Project description:Binding of transcription factors to DNA is a key regulatory step in the control of gene expression. DNA sequences with high affinity for transcription factors occur more frequently in the genome than instances of genes bound or regulated by these factors. How specific gene regulation is achieved by transcription factors remains unclear. We used genome-wide approaches to study how trans factors shape the binding and regulatory landscape of Pho4, a budding yeast transcription factor that activates gene expression in response to phosphate limitation. In no phosphate (0mM phosphate) medium, Pho4 is transported into the nucleus and activates transcription of a set of genes (PHO) that are necessary for cell survival in phosphate limited environment. In high phosphate (10mM phosphate) medium, Pho4 is transported outside of the nucleus and the transcription program of PHO genes are turned off. Here we examined the transcription profiling of S. cerevisiae (W303) in various strains treated in media with 10mM or 0mM inorganic phosphate, to study the the transcription activation by Pho4 its cooperative binding factor Pho2, and its competitive binding factor Cbf1. (I) To infer how much Pho4 itself, Pho2 itself, and the interaction between Pho2 and Pho4 contribute to transcriptional activation in response to Pi starvation, we applied mutant cycle analysis to compare wild type, pho2Δ, pho4Δ and pho2Δ pho4Δ strains in both 10 mM and 0 mM Pi conditions. Mutant cycle analysis is a cyclic comparison among all various mutants. For example, by comparing pho2Δ and pho2Δ pho4Δ, we can directly infer the contribution from Pho4 alone to gene activation. And by comparing wild type and pho2Δ, we can infer the contribution from Pho2 alone together with that from the interaction between Pho2 and Pho4. (II) Compare two strains or one strain in two treatments in multiple replicates with dye-swap method. wt no vs high Pi, to identify genes that are induced in response to Pi starvation. cbf1Δ vs wt in high Pi, to identify the influence of Cbf1 on gene expression in high Pi condition. cbf1Δpho4Δ vs wt in high Pi, to identify the influence of Cbf1 on gene expression that is mediated through Pho4, in high Pi condition. rtg3Δtye7Δ vs wt in high Pi, to identify the influence of Rtg3 and Tye7 on gene expression in high Pi condition. pho80Δ vs pho80Δpho4Δ, to identify the genes that are activated Pho4 when Pho4 is fully nuclear localized. pho80Δcbf1Δ vs pho80Δcbf1Δpho4Δ, to identify the influence of Cbf1 on gene expression that is mediated through Pho4, when Pho4 is fully nuclear localized.

Dataset Information

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

Publications

Genome-wide characterization of the phosphate starvation response in Schizosaccharomyces pombe.

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