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Ribonucleoprotein immunoprecipitation of Schizosaccharomyces pombe cells using the RNA-binding protein Meu5

ABSTRACT: Ribonucleoprotein immunoprecipitation microarray (RIp-chip) study using the RNA-binding protein Meu5 from the fission Schizosaccaromyces pombe

ORGANISM(S): Schizosaccharomyces pombe

SUBMITTER: Juan Mata

PROVIDER: E-TABM-932 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcription profiling of fission yeast with deletion or overexpression of ste11 and changes in gene expression after nitrogen starvation of h plus, h minus, h90fus1 and h90ste11 cells to investigate control of gene expression during early sexual differentiation

Project description:Fission yeast cells belong to one of two specialized cell types, M or P. Specific environmental conditions trigger sexual differentiation, which leads to an internal program starting with pheromone signalling between M and P cells, followed by mating, meiosis and sporulation. The initial steps of this process are controlled by Ste11p, a master transcriptional regulator that activates the expression of cell type-specific genes (only expressed in either M or P cells) as well as genes expressed in both M and P cells. <br><br> Pheromone signalling is activated by Ste11p-dependent transcription, and in turn enhances some of this transcription in a positive feedback. To obtain a genome-wide view of Ste11p target genes, their cell-type specificity, and their dependence on pheromone, we used DNA microarrays along with different genetic and environmental manipulations of fission yeast cells.We directly compared the transcriptome of homothallic wild-type cells (h90 fus1) with that of ste11 delta mutants under conditions that induce sexual differentiation. To allow for indirect effects of the ste11 delta mutation, we took advantage of the fact that ectopic expression of ste11 can drive cells into sexual differentiation and therefore is expected to cause the expression of Ste11p targets. We thus defined Ste11p targets as those genes whose expression was significantly reduced in a ste11 delta mutant and significantly increased when ste11 is overexpressed in vegetative cells.<br> <br> This study looked at the effect of deletion or overexpression of ste11, and changes in gene expression after nitrogen starvation of h plus, h minus, h90fus1 and h90ste11 cells.

2006-09-22 | E-TABM-139 | biostudies-arrayexpress

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Project description:Ribonucleoprotein immunoprecipitation microarray (RIp-chip) study using various myosin proteins and other cytoskeletal components from the fission Schizosaccaromyces pombe

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Ribonucleoprotein immunoprecipitation of fission yeast to study myosin proteins and myosin-specific chaperones

Project description:Ribonucleoprotein immunoprecipitation microarray (RIp-chip) study using various myosin proteins and myosin-specific chaperones from the fission Schizosaccaromyces pombe. Two strains were used. In rng3TAP the rng3 protein has been tagged with TAP to allow its detection and immunoprecipitation. The TAP strain expresses the TAP sequence alone (without being attached to an other protein)

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Ribonucleoprotein immunoprecipitation of S. pombe cells during meiosis using TAP-tagged RNA-binding protein Meu5

Project description:Ribonucleoprotein immunoprecipitation microarray (RIp-chip) study using the RNA-binding protein Meu5 from the fission Schizosaccaromyces pombe

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RNP immunoprecipitation of fission yeast using Rng3p myosin-specific chaperones to investigate if the association of Rng3p with RNAs occurs on ribosomes

Project description:Ribonucleoprotein immunoprecipitation microarray (RIp-chip) study using the Rng3p myosin-specific chaperones from the fission Schizosaccaromyces pombe. Rng3p associates with RNAs encoding myosins. To investigate if the association of Rng3p with these RNAs occurs on ribosomes, Rng3-purified fractions were immunoprecipitated with antibodies against a ribosomal RNA or an unrelated antibody. The RNAs present in the second immunoprecipitate were analysed using DNA microarrays

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Ribonucleoprotein immunoprecipitation of myosin proteins and myosin-specific chaperones in fission yeast

Project description:Ribonucleoprotein immunoprecipitation microarray (RIp-chip) study using various myosin proteins and myosin-specific chaperones from the fission Schizosaccaromyces pombe

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A coordintate global control over cellular transcription

Project description:Although much is known about the regulation of eukaryotic transcription, the global controls which determine rates of total transcription within a cell are not well understood. We have investigated the effects that the DNA to protein ratio has on both total cellular transcription and the transcription of individual mRNA genes in the unicellular eukaryote fission yeast. Mutants altered in cell size and those blocked in cell cycle progression were used to vary the DNA to protein ratio over a fivefold range around the wild type value. We find that cells of sizes within twofold of wild type value regulate global transcription to maintain similar transcription rates per protein regardless of the cellular DNA content. These changes in total transcription were correlated with coordinated changes in gene occupancy by RNA polymerase II. In large cell cycle arrested mutants, when the DNA to protein ratio falls to a low level, total transcription rates plateau as DNA becomes limiting for transcription1. Unexpectedly, expression levels of individual genes remained tightly coordinated with each other over the entire range of cell sizes. We propose that there is a coordinated, global cellular control which determines the rate of transcription of most genes in the genome and that this control plays a role in regulating the overall growth rate of the cell. Normalized data generated using protocol P-TABM-1335 is available in file ZHURINSKY_NORMALISED_DATA.txt in the additional data archive.

2011-09-23 | E-TABM-1075 | biostudies-arrayexpress

Transcription profiling of fission yeast SAGA mutants shows that the SAGA complex controls the switch from proliferation to sexual differentiation through the opposing roles of its subunits Gcn5 and Spt8

Project description:The SAGA complex is a conserved multifunctional coactivator known to play broad roles in eukaryotic transcription. To gain new insights into its functions, we have performed biochemical and genetic analyses of SAGA in the fission yeast, Schizosaccharomyces pombe. Purification of the S. pombe SAGA complex showed that its subunit composition is identical to that of Saccharomyces cerevisiae. Analysis of S. pombe SAGA mutants revealed that SAGA has two opposing roles regulating sexual differentiation. First, in nutrient rich conditions, the SAGA histone acetyltransferase, Gcn5, represses ste11+, which encodes the master regulator of the mating pathway. In contrast, the SAGA subunit Spt8 is required for the induction of ste11+ upon nutrient starvation. Chromatin immunoprecipitation experiments suggest that these regulatory effects are direct, as SAGA is physically associated with the ste11+ promoter independent of nutrient levels. Genetic tests suggest that nutrient levels do cause a switch in SAGA function, as spt8? suppresses gcn5? with respect to ste11+ derepression in rich medium, whereas the opposite relationship, gcn5? suppression of spt8?, occurs during starvation. Thus, SAGA plays distinct roles in the control of the switch from proliferation to differentiation in S. pombe through the dynamic and opposing activities of Gcn5 and Spt8.

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Transcription profiling of Salmonella enterica serovar Typhimurium definitive phage type 104 (DT104) isolates

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2008-09-05 | E-MTAB-20 | biostudies-arrayexpress

RIp-chip experiments with proteins that do not contain RNA-binding domains

Project description:In order to assess the prevalence of cotranslational assembly of protein complexes we performed RIp-chip experiments with many proteins that do not conatin RNA-binding motifs

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