Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression analysis using RNA Sequencing of the Saccharomyces cerevisiae HTA1-S121A strain upon thermo and osmotic stress.

ABSTRACT: To study the relevance of the post-translational modification in the H2A histone residue S121, we assessed the genome-wide transcriptional response of the non-phosphorylatable histone mutant HTA1-S121A (H2AS121A) upon two different stress conditions; osmostress and heat shock. Results point out that the unphosphorylatable H2AS121A protein showed an impaired stress responsive gene expression indicating that this specific histone residue plays a relevant role in stress responsive transcriptional regulation.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE80512 | GEO | 2016/11/04

SECONDARY ACCESSION(S): PRJNA319164

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Gene expression analysis using RNA Sequencing of the Saccharomyces cerevisiae BY4741 Spt4-T42A/S43A mutant strain upon osmotic stress.

Project description:To study the relevance of the phosphorylation of Spt4 in residues T42 and S43, we assessed the genome-wide transcriptional response of the non-phosphorylatable Spt4-T42A/S43A mutant (Spt4-AA) upon osmotic stress. Results point out that the unphosphorylatable Spt4-T42A/S43A protein showed an impaired stress responsive gene expression indicating that these specific residues play a relevant role in osmotic stress responsive transcriptional regulation.

2017-11-20 | GSE98352 | GEO

Data-driven identification of inherent features of eukaryotic stress-responsive genes

Project description:Virtually all living organisms are challenged by changes in their environment, such as sudden increases in osmolarity. To survive, cells have developed stress-responsive mechanisms that tune functions such as metabolism and gene expression. The response of Saccharomyces cerevisiae to osmostress includes a massive reprogramming of gene expression. Identifying the inherent features of stress-responsive genes is of significant interest for understanding the basic principles underlying the rewiring of gene expression upon stress. Here we generated a comprehensive catalog of osmotress-responsive genes from 5 independent RNA-seq experiments. We explored 30 features of yeast genes and found that 25 (83.34%) were distinct in osmostress-responsive genes. We then identified a subset of 13 non-redundant minimal osmostress gene traits and used statistical modeling to generate a ranking of the most stress-predictive features. Our findings reveal that the most relevant features of osmostress-responsive genes are the number of transcription factors targeting a gene and gene conservation. The same features that define yeast osmostress-responsive genes can also be used to predict osmostress-responsive genes in humans, although the most predictive features in humans are GC content and mRNA half-life. Our study provides a holistic understanding of the basic principles of the regulation of stress-responsive gene expression across eukaryotes.

2022-02-14 | GSE171427 | GEO

Study of ribosome dynamics after osmotic stress in Lsm1 and Pat1 deletions

Project description:In this study, we aim to understand how the fates of stress-activated mRNAs are determined under stress conditions by isolating individual osmostress-activated mRNA species, quantitating the proteins associated in vivo with each of them, and analyzing how deletion of these proteins impact on the expression of stress-activated genes. By comparison with the proteome associated with individual not stress-related mRNA species, we show specific proteins to be preferentially binding to osmostress-activated mRNAs, notably members of the cytoplasmic Pat1 / Lsm1 – 7 complex. We evaluated the impact of this complex on the stress response by analyzing expression of osmostress-activated genes, production of osmo-protein and, mapping ribosome transit at single nucleotide resolution using 5’-phosphate sequencing of mRNAs in lsm1 and pat1 mutants. We conclude that our biochemical co-purification approach has successfully identified RNA-binding proteins with a particular role in regulating post-transcriptional expression of stress-activated mRNAs.

2018-07-18 | GSE107250 | GEO

Gene expression analysis using RNA Sequencing of the Saccharomyces cerevisiae BY4741 H4-T30 and S47 mutant strains upon heat and osmotic stress

Project description:To study the relevance of the phosphorylation of H4 in residues T30 and S47, we assessed the genome-wide transcriptional response of the non-phosphorylatable H4-T30A and the phospho-mimetic H4-T30D mutants upon heat stress and the phospho-mimetic H4-S47D mutant upon osmotic stress . Results point out that H4-T30(A/D) and H4-S47D mutants showed an impaired stress responsive gene expression indicating that these specific residues play a relevant role in, respectively, heat and osmotic stress responsive transcriptional regulation.

2020-01-30 | GSE130549 | GEO

Hog1 bypasses stress-mediated down-regulation of transcription by PolII redistribution and chromatin remodeling

Project description:Cells are subjected to dramatic changes on gene expression upon environmental changes. Stress causes a general down-regulation of gene expression together with the induction of a set of stress-responsive genes. Genome wide localisation studies showed major changes on Pol II localisation towards stress-responsive genes in contrast to housekeeping genes. Pol II relocalisation requires of the Hog1 SAPK, which also associates at stress-responsive loci. Chromatin structure was not significantly altered upon stress except for those genes that displayed Hog1 association. Together, Hog1 serves to bypass the general down-regulation of gene expression by targeting RNA Pol II machinery and inducing chromatin remodeling at stress-responsive loci. Hog1 and Pol II ChIP-Seq and Mnase-Seq experiments in both strains WT and Hog1 mutant, for 2 conditions: Exposed and not exposed to osmostress

2012-10-30 | E-GEOD-41494 | biostudies-arrayexpress

Glutamine methylation on Histone H2A is an RNA Polymerase I dedicated modification

Project description:Nucleosomes are decorated with numerous post-translational modifications capable of influencing many DNA processes. Here, we describe a new class of modification, methylation of glutamine, occurring on yeast histone H2A at position 105 (Q105) and human H2A at Q104. We identify Nop1 as the methyltransferase in yeast and we demonstrate that Fibrillarin is the equivalent enzyme in human cells. Glutamine methylation of H2A is restricted to the nucleolus. Global analysis in yeast, using a H2AQ105me specific antibody, show that this modification is exclusively enriched over the 35S rDNA transcriptional unit. We show that the Q105 residue is part of the binding site for the histone chaperone FACT (Facilitator of Transcription) complex. Methylation of Q105 or its substitution to alanine disrupts binding to FACT in vitro. A yeast strain mutated at Q105 exhibits a defect in histone incorporation and shows increased transcription at rDNA genes. This defect is phenocopied by mutations in FACT that decrease its activity. Together these data identify glutamine methylation of H2A as the first histone epigenetic mark dedicated to a specific RNA polymerase and define its function as a regulator of FACT interaction with nucleosomes.

2014-01-21 | E-MTAB-1447 | biostudies-arrayexpress

smRNA under high osmotic stress

Project description:To identifiy osmotic stress responsive smRNAs, we used a deep-sequencing technique to profile small RNA populations in leaf and root tissues of plants under high osmotic stress and control conditions. We treated 30day-old plants with high osmotic stress and sampled leaves and roots from the same plant with 3 biologial replicates. Then, 3 replicates were pooled and total RNA was extracted and prepared for smRNA deep sequencing. After normalization and annotation, we selected potential osmotic stress responsive smRNAs.

2012-09-19 | E-GEOD-36560 | biostudies-arrayexpress

smRNA under high osmotic stress

2012-09-19 | GSE36560 | GEO

Genome-wide distribution maps of histone variants H2A.Lap1 and H2A.Z in 30do mouse spermatids [ChIP_seq]

Project description:Chromatin performs numerous functions during cellular differentiation, and therefore it must be capable of adopting a multitude of different structures. How these various structures are established is poorly understood, but we propose that specific histone H2A variants will have a key role in remodelling chromatin during differentiation. Structurally, we show here that the gain of just a single acidic amino acid residue has generated a new mouse H2A.Bbd-like histone variant, H2A.Lap1, and that when incorporated into nucleosomal arrays imparts on them unique biophysical properties that are distinct from arrays containing either H2A or human H2A.Bbd. Functionally, we identify H2A.Lap1 as a novel chromatin component of active genes that are expressed during spermatogenesis, and in combination with H2A.Z create a unique chromatin landscape at the start site of transcription. During round spermatid differentiation, H2A.Lap1 dramatically loads onto the inactive X chromosome enabling a subset of its genes to be transcriptionally activated Examination of 2 different histone variants in mouse spermatids.

2012-01-20 | E-GEOD-29913 | biostudies-arrayexpress

Saccharomyces cerevisiae

Project description:Histone H2A K4,7G

| PRJNA98029 | ENA