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Transcriptome analysis of wild type, sbp1 and scd6 deletion Saccharomyces cerevisiae strains upon RNA granule inducing sodium azide stress

ABSTRACT: Transcriptome analysis of wild type, sbp1 and scd6 deletion Saccharomyces cerevisiae strains upon RNA granule inducing sodium azide stress

PROVIDER: PRJNA606249 | ENA |

REPOSITORIES: ENA

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Transcriptome analysis of wild type, sbp1 and scd6 deletion Saccharomyces cerevisiae strains upon RNA granule inducing sodium azide stress

Project description:We report here transcriptome wide changes in S. cerevisiae in response to sodium azide treatment. The observed changes are consistent with those observed in response to oxidative stress such as H2O2. We also identify transcripts that are specifically affected by Scd6 and/or Sbp1. Some of these mRNAs could be direct targets of Scd6/Sbp1.

2020-05-23 | GSE145162 | GEO

Quantitative global proteomics of yeast PBP1 deletion mutants and their stress responses reveals glucose metabolism, translation and stress granule changes

Project description:The yeast protein PBP1 has been implicated in diverse pathways such as polyadenylation, translation, RNA-DNA hybrid formation, stress granule homeostasis, mitochondrial dysfunction, and TORC1 sequestration. Intriguingly, its deletion mitigates the toxicity of human neurodegeneration factors, but the molecular mechanisms of these effects are poorly understood. Here we performed label-free quantitative global proteomics to identify crucial downstream factors, comparing two PBP1 deletion strains (DB and SM) and two cell stress conditions (heat and NaN3). In all four analyses, downregulations of key bioenergetics enzymes (CIT1, SDH1, MLS1), cell wall mannoproteins (HSP150, PST1) and the prion protein RNQ1 as well as upregulations of the leucine biosynthesis enzyme LEU1 and the transcription factor TAF6 were documented. Consistently for both unstressed PBP1-deleted strains, over 2-fold dysregulations were documented for potential PBP1 interactors such as MKT1 or RPL39 and the stress granule component NRP1. Upregulation of the ribosomal biogenesis factor NOP10 was observed as in the mouse mutant. Consistently for both PBP1 deletion strains, heat stress triggered changes of the stress granule component GIS2 and several of its interactors.

2016-12-23 | PXD003868 | Pride

The Transcriptional Response to Oxidative Stress is Independent of Stress-Granule Formation

Project description:We characterized oxidative-stress-induced transcriptional changes in Drosophila S2 cells and assessed how these were altered under conditions that disrupted stress granule (SG) assembly. Sodium-arsenite stress for 3 hours resulted predominantly in the induction or upregulation of stress-responsive mRNAs whose levels peaked during cell recovery after stress cessation. RNAi-mediated knock down of the conserved G3BP1/ Rasputin protein inhibited stress-granule assembly. However, this disruption had no significant effect on the stress-induced transcriptional response.

2022-01-24 | GSE178464 | GEO

Identification of Stress Granule interactor proteins in yeast S. cerevisiae

Project description:We investigated the sub-cellular architecture of Stress Granules in the context of glucose starvation. In order to uncover transient and peripheral Stress Granule interactors, we optimized the proximity-dependent biotinylation (BioID) approach for use in yeast. This approach allowed us to visualize Stress Granule formation while simultaneously inducing the biotinylation of SG components and nearby proteins in live cells. We used two independent Stress Granule components Pub1 and Pab1.

2020-03-23 | PXD016988 | Pride

Fusarium verticillioides wild type versus LAE1 deletion mutant at 6 days on fumonisin inducing medium

Project description:Investigation of whole genome gene expression level changes after 6 days growth of Fusarium verticillioides wild-type and LAE1 deletion mutant in liquid fumonisin inducing media (GYAM) Fusarium verticillioides produces a polyketide derived mycotoxin, fumonsin, over time in liquid media, Proctor et al, Co-expression of 15 contiguous genes delineates a fumonisin biosynthetic gene cluster in Gibberella moniliformis, Fungal Genetics and Biology, 38:237-249. 6 arrays: Two samples (wild type, LAE1 deletion mutant), one time point (6 days), three biological replicates.

2012-12-01 | E-GEOD-32608 | biostudies-arrayexpress

Elucidation of the RNA-granule inducing sodium azide stress response through transcriptome analysis.

Project description: Not available

| S-EPMC7116212 | biostudies-literature

Gene expression of cerebellar granule cell layer

Project description:We performed gene-expression analysis of mouse cerebellar granule cell layer as compared to that of Purkinje cells. DNA microarray analysis detected genes in cerebellar granule cell layer, most of which are classified into functional molecule categories. Our comparative analysis between Purkinje cells and the granule cell layer showed that the characteristic expression pattern in Purkinje cells was particularly represented by M-bM-^@M-^\the neural communication systemM-bM-^@M-^] components. Pukinje cells and granule cell layer of the mouse cerebellum were collected by laser microdissection for RNA extraction and hybridization on Affymetrix microarrays.

2013-01-17 | E-GEOD-26750 | biostudies-arrayexpress

Fusarium verticillioides wild type versus LAE1 deletion mutant at 6 days on fumonisin inducing medium

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mRNA Expression data from sodium butyrate or sodium phenylbutyrate treated A549 cells

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2017-06-10 | GSE86928 | GEO

Gene expression of cerebellar granule cell layer

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