Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1106184 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Heat shock response (HSR) is crucial for life’s adaptation to heat. Here, we discovered a novel mechanism of HSR controlled at the translational level, which depends on the multi-subunit translation initiation factor, eIF3. The cis-element for this regulation is called GUCG box and occurs degenerately within protein-coding regions of regulated mRNAs. Being positioned at ribosome leading-edge through -propeller subunit eIF3i, the RNA-binding subunit eIF3g binds the motif and stabilizes mRNA anchoring during translation under mild heat. The eIF3g/i-regulated HSR consists of 64 genes including heat shock protein genes, engaging a quarter of the cellular ribosomes. The 5’-terminal coding regions of the HSR mRNAs are enriched with more GUCG boxes, some of which are masked by weak secondary structures. This arrangement enables eIF3g/i-dependent enhancement in part through melting inhibitory secondary structures. GUCG boxes spread evenly across the entire protein-coding regions of strongly translated mRNAs ~20 nt. apart, as if to prevent ribosome collision. Thus, eIF3 not only stabilizes initiating ribosomes at its leading-edge but may contribute to anchoring elongating ribosomes throughout coding regions under heat insult.
2026-01-28 | GSE299621 | GEO
Project description:Steady state levels of SUMO post-translational modifications depend on the competing activities of the sumoylation and desumoylation machineries. Eukaryotic cells can modulate cellular levels of SUMO conjugation by regulating enzymes involved in these processes. For example, budding yeast exhibit an overall elevation of SUMO conjugation in response to heat shock, at least partly by triggering the degradation of the major SUMO protease, Ulp1. The effects of elevated sumoylation during heat shock, and whether they play a protective or adaptive role to the stress, remain unclear. Since a large number of transcription-related proteins are targets of sumoylation, one possibility is that increased sumoylation during heat shock facilitates the expression of heat shock genes by altering the properties of key transcription factors. To explore this, we analyzed the transcriptome of a yeast strain, ulp1-mt (ulp1-I615N), which expresses a mutant form of Ulp1 with reduced SUMO protease activity. The strain displays constitutively elevated levels of SUMO conjugation, mimicking the transient sumoylation surge observed during heat shock. Intriguingly, the ulp1-mt transcriptome largely resembles the transcriptome of heat-shocked yeast, suggesting that elevated sumoylation alone can drive much of the stress-induced gene expression program.
2026-04-30 | GSE290842 | GEO
Project description:FBXW7 modulates stress response by post-translational modification of HSF1 HSF1 orchestrates the heat-shock response upon exposure to heat stress and activates a transcriptional program vital for cancer cells. Genes positively regulated by HSF1 show increeased expression during heat shock while their expression is reduced during recovery. Genes negatively regulated by HSF1 show the opposite pattern. In this study we utilized the HCT116 FBXW7 KO colon cell line and its wild type counterpart to monitor gene expression changes during heat shock (42oC, 1 hour) and recovery (37oC for 2 hours post heat shock) using RNA sequencing. These results revealed that the heat-shock response pathway is prolonged in cells deficient for FBXW7.
2015-02-20 | GSE57397 | GEO
Project description:Disomic yeast response to heat shock
| PRJNA172729 | ENA
Project description:Voit2003 - Trehalose Cycle
This model is described in the article:
Biochemical and genomic
regulation of the trehalose cycle in yeast: review of
observations and canonical model analysis.
Voit EO.
J. Theor. Biol. 2003 Jul; 223(1):
55-78
Abstract:
The physiological hallmark of heat-shock response in yeast
is a rapid, enormous increase in the concentration of
trehalose. Normally found in growing yeast cells and other
organisms only as traces, trehalose becomes a crucial protector
of proteins and membranes against a variety of stresses,
including heat, cold, starvation, desiccation, osmotic or
oxidative stress, and exposure to toxicants. Trehalose is
produced from glucose 6-phosphate and uridine diphosphate
glucose in a two-step process, and recycled to glucose by
trehalases. Even though the trehalose cycle consists of only a
few metabolites and enzymatic steps, its regulatory structure
and operation are surprisingly complex. The article begins with
a review of experimental observations on the regulation of the
trehalose cycle in yeast and proposes a canonical model for its
analysis. The first part of this analysis demonstrates the
benefits of the various regulatory features by means of
controlled comparisons with models of otherwise equivalent
pathways lacking these features. The second part elucidates the
significance of the expression pattern of the trehalose cycle
genes in response to heat shock. Interestingly, the genes
contributing to trehalose formation are up-regulated to very
different degrees, and even the trehalose degrading trehalases
show drastically increased activity during heat-shock response.
Again using the method of controlled comparisons, the model
provides rationale for the observed pattern of gene expression
and reveals benefits of the counterintuitive trehalase
up-regulation.
To
induce a heat shock, set the parameter heat_shock from 0 to 1. This
changes the parameter values of X8 to X19 from 1 to the values
given in table 3 of the original publication.
As
this is an S-systems model, it does not contain any reactions
encoded in SBML.
This model is hosted on
BioModels Database
and identified by:
BIOMD0000000266.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2024-09-02 | BIOMD0000000266 | BioModels
Project description:The cells with the impaired Hsp40/Hsp70 chaperone complex Mas5/Ssa2 exhibit a transriptional response that is simillar to that of cells with the elevated levels of the heat-shock factor 1 (Hsf1) or heat-stressed wild type fission yeast cells
2013-09-20 | GSE50156 | GEO
Project description:Regulation of protein synthesis is fundamental for all aspects of eukaryotic biology by controlling development, homeostasis, and stress responses. The 13-subunit, 800-kDa eukaryotic initiation factor 3 (eIF3) organizes initiation factor and ribosome interactions required for productive translation. However, current understanding of eIF3 function does not explain genetic evidence correlating eIF3 deregulation with tissue-specific cancers and developmental defects. Here we report the genome-wide discovery of human transcripts that interact with eIF3 using photo-activatable crosslinking and immunoprecipitation (PAR-CLIP). eIF3 binds to a highly specific programme of messenger RNAs (mRNAs) involved in cell growth control processes, including cell cycling, differentiation, and apoptosis, via the mRNA 5' untranslated region (5' UTR). Surprisingly, functional analysis of the interaction between eIF3 and two mRNAs encoding cell proliferation regulators, c-Jun and BTG1, reveals that eIF3 employs different modes of RNA stem loop binding to exert either translational activation or repression. Our findings illuminate a new role for eIF3 in governing a specialized repertoire of gene expression and suggest that binding of eIF3 to specific mRNAs could be targeted to control carcinogenesis. 293T cells were treated with 4-thiouridine and protein-RNA complexes were crosslinked, and eIF3-RNA complexes were immunoprecipitated.
2015-04-06 | E-GEOD-65004 | biostudies-arrayexpress
Project description:FBXW7 modulates stress response by post-translational modification of HSF1 HSF1 orchestrates the heat-shock response upon exposure to heat stress and activates a transcriptional program vital for cancer cells. Genes positively regulated by HSF1 show increeased expression during heat shock while their expression is reduced during recovery. Genes negatively regulated by HSF1 show the opposite pattern. In this study we utilized the HCT116 FBXW7 KO colon cell line and its wild type counterpart to monitor gene expression changes during heat shock (42oC, 1 hour) and recovery (37oC for 2 hours post heat shock) using RNA sequencing. These results revealed that the heat-shock response pathway is prolonged in cells deficient for FBXW7. Whole RNA was extracted from 1 million HCT116 WT or FBXW7KO cells using the RNAeasy kit (Qiagen) according to the manufacturer’s protocol. Poly-A+ (magnetic oligodT-containing beads (Invitrogen)) or Ribominus RNA was used for library preparation. cDNA preparation and strand-specific library construction was performed using the dUTP method. Libraries were sequenced on the Illumina HiSeq 2000 using 50bp single-read method. Differential gene expression analysis was performed for each matched recovery versus heat-shock pairs, separately in each biological replicate and cell line (WT or KO). Two types of comparisons were tested: (a) WT recovery vs WT heat shock, (b) FBXW7 KO recovery vs heat shock.
2015-02-20 | E-GEOD-57397 | biostudies-arrayexpress
Project description:To determine the transcriptional responses to heat shock of inner ear sensory hair cells and supporting cells, we performed cell-type-specific transcriptional profiling using the RiboTag method, which allows for immunoprecipitation of actively translating mRNAs from specific cell types. RNA-Seq differential gene expression analyses demonstrated that RiboTag identified known cell type-specific markers as well as new markers for hair cells and supporting cells. Gene expression differences suggest that both hair cells and supporting cells exhibit a transcriptional heat shock response. However, hair cells and supporting cells expressed different members of the heat shock protein family in response to heat stress, and supporting cells expressed a larger number of HSPs. Only one HSP, Chaperonin Containing T-Complex Polypeptide 1 Subunit 8, (CCT8) was uniquely induced in hair cells. Together our data indicate that hair cells exhibit a limited but unique heat shock response, and supporting cells exhibit a broader and more robust transcriptional response to protective heat stress.
2020-05-05 | GSE139593 | GEO
Project description:Translational and transcriptional responses of fission yeast to heat shock
| PRJEB36274 | ENA