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

ABSTRACT: 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.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE130549 | GEO | 2020/01/30

REPOSITORIES: GEO

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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

A genetic analysis reveals novel histone residues required for transcriptional reprogramming upon stress

Project description:Cells have the ability to sense, respond and adapt to environmental fluctuations. Stress causes a massive reorganization of the transcriptional program. Many examples of histone post-translational modifications (PTMs) have been associated with transcriptional activation or repression under steady-state growth conditions. Comparatively less is known about the role of histone PTMs in the cellular adaptive response to stress. Here, we performed high-throughput genetic screenings that provide a novel global map of the histone residues required for transcriptional reprogramming in response to heat and osmotic stress. Of note, we observed that the histone residues needed depend on the type of gene and/or stress, thereby suggesting a “personalized”, rather than general, subset of histone requirements for each chromatin context. In addition, we identified a number of new residues that unexpectedly serve to regulate transcription. As a proof of concept, we characterized the function of the histone residues H4-S47 and H4-T30 in response to osmotic and heat stress, respectively. Our results uncover novel roles for the kinases Cla4 and Ste20, yeast homologs of the mammalian PAK2 family, which phosphorylate H4-S47 and for the kinase Ste11 that targets H4-T30. This study provides new insights into the role of histone residues in transcriptional regulation under stress conditions.

2020-05-27 | PXD017134 | Pride

Transcriptome profiling of the effects of Aurora B mediated phosphoregulation of CNOT3 in differentiating mesendodermal cells

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Gene expression responses to ABA and to osmotic stress in the bon123 triple mutant

Project description:Hyperosmotic stress caused by drought and salinity is a significant environmental threat that limits plant growth and agricultural productivity. Osmotic stress induces diverse responses in plants including Ca2+ signaling, accumulation of the stress hormone abscisic acid (ABA), reprogramming of gene expression, and altering growth. Despite intensive investigation, no global regulators of all of these responses have been identified. Here, we show that the Ca2+-responsive phospholipid binding BONZAI (BON) proteins are critical for all of these osmotic stress responses. A Ca2+-imaging-based forward genetic screen identified a loss-of-function bon1 mutant with a reduced cytosolic Ca2+ signal in response to hyperosmotic stress. The loss-of-function mutants of the BON1 gene family, bon1bon2bon3, are impaired in the induction of gene expression and ABA accumulation in response to osmotic stress. In addition, the bon mutants are hypersensitive to osmotic stress in growth inhibition. BON genes have been shown to negatively regulate plant immune responses mediated by intracellular immune receptor NLR genes including SNC1. We found that the defects of the bon mutants in osmotic stress responses were suppressed by mutations in the NLR gene SNC1 or the immunity regulator PAD4. Our findings indicate that NLR signaling represses osmotic stress responses and that BON proteins suppress NLR signaling to enable global osmotic stress responses in plants.

2020-09-04 | GSE157435 | GEO

Label-free proteome analysis of small extracellular vesicles (sEV) expressing different HRS mutants.

Project description:Label-free proteome analysis of small extracellular vesicles (sEV) derived from WM9 cells expressing different HRS mutants: wild type (HRSWT), phospho-deficient (HRSS345A), and phospho-mimetic mutant HRS (HRSS345D).

2022-02-16 | MSV000088846 | MassIVE

Stress-dependent dynamics of chromatin remodeling in yeast: Dual roles for SWI/SNF in heat shock stress response

Project description:Total H4 and acetyl H4 IP, time course Total H4 and acetyl H4 occupancy, Snf2 occupancy, gene expression analysis Keywords: stress response, time course S cerevisiae were subjected to heat shock and stationary phase stress. The histone occupancy and H4 acetylation levels were monitored in parallel with gene expression studies, and Snf2 occupancy before and after stress.

2010-05-26 | E-GEOD-7665 | biostudies-arrayexpress

Analysis of Rice microRNAs Expression under Drought Stress

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2007-02-14 | GSE5986 | GEO

Contribution of time of day and the circadian clock to the heat stress responsive transcriptome in Arabidopsis

Project description:In Arabidopsis, a large subset of heat responsive genes exhibits diurnal or circadian oscillations. However, to what extent the dimension of time and/or the circadian clock contribute to heat stress responses remains largely unknown. To determine the direct contribution of time of day and/or the clock to differential heat stress responses, we probed wild-type and mutants of the circadian clock genes CCA1, LHY, PRR7, and PRR9 following exposure to heat (37°C) and moderate cold (10°C) in the early morning (ZT1) and afternoon (ZT6). Thousands of genes were differentially expressed in response to temperature, time of day, and/or the clock mutation. Approximately 30% more genes were differentially expressed in the afternoon compared to the morning, and heat stress significantly perturbed the transcriptome. Of the DEGs (~3000) specifically responsive to heat stress, ~70% showed time of day (ZT1 or ZT6) occurrence of the transcriptional response. For the DEGs (~1400) that are shared between ZT1 and ZT6, we observed changes to the magnitude of the transcriptional response. In addition, ~2% of all DEGs showed differential responses to temperature stress in the clock mutants. The findings in this study highlight a significant role for time of day in the heat stress responsive transcriptome, and the clock through CCA1 and LHY, appears to have a more profound role than PRR7 and PRR9 in modulating heat stress responses during the day. Our results emphasize the importance of considering the dimension of time in studies on abiotic stress responses in Arabidopsis.

2019-03-18 | GSE116004 | GEO

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

Espression data of control and heat-stressed Arabidopsis WT, hd2c-3, brm-1 and brm-1 hd2c-3 plants

Project description:Studies in yeast and animals have revealed that histone deacetylases (HDACs) often act as components of multiprotein complexes, including chromatin remodeling complexes (CRCs). In our group, we found evidence for the interaction between Arabidopsis HD2C deacetylase and a BRM-containing SWI/SNF chromatin remodeling complex. Moreover, we revealed a novel function of HD2C as a regulator of the heat stress response. HD2C transcript levels were strongly induced in plants subjected to heat treatment and the expression of selected heat-responsive genes was up-regulated in heat-stressed hd2c mutant, suggesting that HD2C acts to down-regulate heat-activated genes. Microarray transcriptome analysis of brm and hd2c mutants identified a subset of commonly regulated heat-responsive genes, and the effect of the double brm hd2c mutation on the expression of these genes was non-additive. Moreover, heat treated hd2c, brm and brm hd2c mutants displayed similar rates of growth retardation. Taken together, our findings suggest that HD2C and BRM act in a common genetic pathway to regulate the Arabidopsis heat stress response.

2015-12-04 | GSE75646 | GEO

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