Chaperone condensates buffer the heat shock response against pleiotropic inputs [RNA-seq]
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ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE339192 | GEO | 2026/08/26
REPOSITORIES: GEO
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Project description:Heat shock response (HSR) is a cellular defense mechanism against various stresses. Both heat shock and proteasome inhibitor MG132 cause the induction of heat shock proteins, a distinct feature of HSR. To better understand the molecular basis of HSR, we subjected the mouse fibrosarcoma cell line, RIF-1, and its thermotolerant variant, TR-RIF-1 cells, to heat shock and MG132. We compared mRNA expressions using microarray analysis during recovery after heat shock and MG132 treatment. This study led us to group the 3,245 up-regulated genes by heat shock and MG132 into three families: genes regulated 1) by both heat shock and MG132 (e.g. chaperones); 2) by heat shock (e.g. DNA-binding proteins including histones); and 3) by MG132 (e.g. innate immunity and defense-related molecules).
2011-11-09 | GSE24197 | GEO
Project description:Heat shock response (HSR) is a cellular defense mechanism against various stresses. Both heat shock and proteasome inhibitor MG132 cause the induction of heat shock proteins, a distinct feature of HSR. To better understand the molecular basis of HSR, we subjected the mouse fibrosarcoma cell line, RIF-1, and its thermotolerant variant, TR-RIF-1 cells, to heat shock and MG132. We compared mRNA expressions using microarray analysis during recovery after heat shock and MG132 treatment. This study led us to group the 3,245 up-regulated genes by heat shock and MG132 into three families: genes regulated 1) by both heat shock and MG132 (e.g. chaperones); 2) by heat shock (e.g. DNA-binding proteins including histones); and 3) by MG132 (e.g. innate immunity and defense-related molecules). RIF-1 and TR cells were heat shock treated or MG132 treated and harvested after various times of recovery. mRNA expressions were compared to untreated samples. Biological replication was done.
2011-11-09 | E-GEOD-24197 | biostudies-arrayexpress
Project description:Cells respond to many different types of stresses by overhauling gene expression patterns, both at the transcriptional and translational level. Under heat stress, global transcription and translation are inhibited, while the expression of chaperone proteins are preferentially favored. As the direct link between mRNA transcription and protein translation, tRNA expression is intricately regulated during the stress response. Despite extensive research into the heat shock response (HSR), the regulation of tRNA expression by RNA Polymerase III (Pol III) transcription has yet to be fully elucidated in mammalian cells. Here, we examine the regulation of Pol III transcription during different stages of heat shock stress in mouse embryonic stem cells (mESCs). We observe that global transcription of tRNAs is downregulated after 30 minutes of heat shock, followed by an overall increase in tRNA transcription after 60 minutes of heat shock. This effect is more evident in tRNAs, though other RNA Pol III gene targets are also similarly affected. Notably, we show that the down-regulation at 30 minutes of heat shock is independent of HSF1, the master transcription factor of the HSR, but that the subsequent increase in expression at 60 minutes requires HSF1. Taken together, these results demonstrate an adaptive RNA Pol III response to heat stress, and an intricate relationship between the canonical HSR and tRNA expression.
2025-03-04 | GSE282678 | GEO
Project description:Environmental stress, such as oxidative or heat stress, induces the activation of the heat shock response
(HSR) and leads to an increase in the heat shock proteins (HSPs) level. These HSPs act as molecular
chaperones to maintain cellular proteostasis. Controlled by highly intricate regulatory mechanisms,
having stress-induced activation and feedback regulations with multiple partners, the HSR is still
incompletely understood. In this context, we propose a minimal molecular model for the gene
regulatory network of the HSR that reproduces quantitatively different heat shock experiments both
on heat shock factor 1 (HSF1) and HSPs activities. This model, which is based on chemical kinetics
laws, is kept with a low dimensionality without altering the biological interpretation of the model
dynamics. This simplistic model highlights the titration of HSF1 by chaperones as the guiding line of
the network. Moreover, by a steady states analysis of the network, three different temperature stress
regimes appear: normal, acute, and chronic, where normal stress corresponds to pseudo thermal
adaption. The protein triage that governs the fate of damaged proteins or the different stress regimes
are consequences of the titration mechanism. The simplicity of the present model is of interest in
order to study detailed modelling of cross regulation between the HSR and other major genetic
networks like the cell cycle or the circadian clock.
Sivéry, A., Courtade, E., Thommen, Q. (2016). A minimal titration model of the mammalian dynamical heat shock response. Physical biology, 13(6), 066008.
2022-01-25 | MODEL2201210001 | BioModels
Project description:The heat shock response (HSR) is a mechanism to cope with proteotoxic stress by inducing the expression of molecular chaperones and other heat shock response genes. The HSR is evolutionarily well conserved and has been widely studied in bacteria, cell lines and lower eukaryotic model organisms. However, mechanistic insights into the HSR in higher eukaryotes, in particular in mammals, are limited. We have developed an in vivo heat shock protocol to analyze the HSR in mice and dissected heat shock factor 1 (HSF1)-dependent and -independent pathways. Whilst the induction of proteostasis-related genes was dependent on HSF1, the regulation of circadian function related genes, indicating that the circadian clock oscillators have been reset, was independent of its presence. Furthermore, we demonstrate that the in vivo HSR is impaired in mouse models of Huntington’s disease but we were unable to corroborate the general repression of transcription after a heat shock found in lower eukaryotes.
2017-03-03 | GSE95602 | GEO
Project description:Background. The Heat Shock Response (HSR) is an evolutionarily conserved mechanism that helps cells adapt to environmental stresses. Heat Shock Factor 1 (HSF1) is a master HSR transcription factor that is long known to bind at promoters of its target HSP genes to rapidly activate their transcription. However, recent genome-wide studies revealed HSF1 binding at thousands of sites outside of heat-shock responsive gene promoters, implying a broader role of HSF1 in HSR. Results. We asked how the widespread HSF1 binding is established and to what extent it may be related to transcription activation. To answer these questions, we examined responses of two different human cancer cell lines to two stimuli that induce HSR, exposure to 42C and inorganic arsenic at the ambient temperature, by manually integrating ChIP-sequencing against HSF1, RNA Pol II, H3K4Me3 with nascent RNA- and ATAC-sequencing datasets in cells before and during HSR induced by these two stimuli. We show that widespread HSF1 binding is a temperature-agnostic hallmark of HSR whose genome-wide patterns combine cell type specificity with robustness to the nature of a stimulus and magnitude of activation. Mechanistically, HSR involves amplification of pre-existing low level HSF1 binding with few changes in accessible chromatin. HSF1 binding patterns show more stability than transcriptionally activated genes both between conditions and between cell lines. Conclusions. Comparing responses of distant cell lines to two HSR-inducing stimuli allowed us to define several features of HSR. Genome-wide HSF1 binding is a sensitive readout of HSR whose genome-wide patterns retain cell type identity across a broad dynamic range. The pre-existing genomic architecture is retained during HSR down to individual loci. Context-specific transcription involving common HSF1 binding favors a model of regulation by combinatory interplay of rigid transcription factor patterns.
2023-10-30 | GSE209675 | GEO
Project description:Background. The Heat Shock Response (HSR) is an evolutionarily conserved mechanism that helps cells adapt to environmental stresses. Heat Shock Factor 1 (HSF1) is a master HSR transcription factor that is long known to bind at promoters of its target HSP genes to rapidly activate their transcription. However, recent genome-wide studies revealed HSF1 binding at thousands of sites outside of heat-shock responsive gene promoters, implying a broader role of HSF1 in HSR. Results. We asked how the widespread HSF1 binding is established and to what extent it may be related to transcription activation. To answer these questions, we examined responses of two different human cancer cell lines to two stimuli that induce HSR, exposure to 42C and inorganic arsenic at the ambient temperature, by manually integrating ChIP-sequencing against HSF1, RNA Pol II, H3K4Me3 with nascent RNA- and ATAC-sequencing datasets in cells before and during HSR induced by these two stimuli. We show that widespread HSF1 binding is a temperature-agnostic hallmark of HSR whose genome-wide patterns combine cell type specificity with robustness to the nature of a stimulus and magnitude of activation. Mechanistically, HSR involves amplification of pre-existing low level HSF1 binding with few changes in accessible chromatin. HSF1 binding patterns show more stability than transcriptionally activated genes both between conditions and between cell lines. Conclusions. Comparing responses of distant cell lines to two HSR-inducing stimuli allowed us to define several features of HSR. Genome-wide HSF1 binding is a sensitive readout of HSR whose genome-wide patterns retain cell type identity across a broad dynamic range. The pre-existing genomic architecture is retained during HSR down to individual loci. Context-specific transcription involving common HSF1 binding favors a model of regulation by combinatory interplay of rigid transcription factor patterns.
2023-10-30 | GSE209685 | GEO
Project description:Background. The Heat Shock Response (HSR) is an evolutionarily conserved mechanism that helps cells adapt to environmental stresses. Heat Shock Factor 1 (HSF1) is a master HSR transcription factor that is long known to bind at promoters of its target HSP genes to rapidly activate their transcription. However, recent genome-wide studies revealed HSF1 binding at thousands of sites outside of heat-shock responsive gene promoters, implying a broader role of HSF1 in HSR. Results. We asked how the widespread HSF1 binding is established and to what extent it may be related to transcription activation. To answer these questions, we examined responses of two different human cancer cell lines to two stimuli that induce HSR, exposure to 42C and inorganic arsenic at the ambient temperature, by manually integrating ChIP-sequencing against HSF1, RNA Pol II, H3K4Me3 with nascent RNA- and ATAC-sequencing datasets in cells before and during HSR induced by these two stimuli. We show that widespread HSF1 binding is a temperature-agnostic hallmark of HSR whose genome-wide patterns combine cell type specificity with robustness to the nature of a stimulus and magnitude of activation. Mechanistically, HSR involves amplification of pre-existing low level HSF1 binding with few changes in accessible chromatin. HSF1 binding patterns show more stability than transcriptionally activated genes both between conditions and between cell lines. Conclusions. Comparing responses of distant cell lines to two HSR-inducing stimuli allowed us to define several features of HSR. Genome-wide HSF1 binding is a sensitive readout of HSR whose genome-wide patterns retain cell type identity across a broad dynamic range. The pre-existing genomic architecture is retained during HSR down to individual loci. Context-specific transcription involving common HSF1 binding favors a model of regulation by combinatory interplay of rigid transcription factor patterns.
2023-10-30 | GSE209667 | GEO
Project description:Heat shock factor 1 (HSF1) is well known for its role in the heat shock response (HSR), where it drives a transcriptional program comprising heat shock protein (HSP) genes, and in tumorigenesis, where it drives a program comprising HSPs and many non-canonical target genes that support malignancy. Here, we find that HSF2, an HSF1 paralog with no significant role in the HSR, physically and functionally interacts with HSF1 across diverse types of cancer. HSF1 and HSF2 have strikingly similar chromatin occupancy and regulate a common set of genes which include both HSPs and non-canonical transcriptional targets with roles critical in supporting malignancy. Loss of either HSF1 or HSF2 results in a dysregulated response to nutrient stresses in vitro and reduced tumor progression in cancer cell line xenografts. Taken together, these findings establish HSF2 as a critical cofactor of HSF1 in driving a cancer cell transcriptional program to support the anabolic malignant state.
2022-03-15 | GSE194098 | GEO
Project description:How heat shock induces the heat shock response (HSR) - a gene expression program encoding chaperones and other protein homeostasis (proteostasis) factors - remains an unresolved question in eukaryotic cell biology. Here we show that subcellular localization of the conserved J-protein Sis1 is a key regulator of the HSR in yeast. Under nonstress conditions, nucleoplasmic Sis1 promotes interaction between the chaperone Hsp70 and the transcription factor Hsf1 to repress the HSR. Heat shock triggers Sis1 to localize to the periphery of the nucleolus and to condense on the ER surface. Sis1 recruits the proteasome to this spatial network along with disaggregases and the ribosome quality control complex. Through localization dynamics, Sis1 relays the condition of the proteome to Hsf1. We conclude that the activation state of the HSR is determined by the spatial organization of the proteostasis network.
2020-02-26 | GSE145936 | GEO