scholarly journals ReporterSeq reveals genome-wide dynamic modulators of the heat shock response across diverse stressors

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Brian D Alford ◽  
Eduardo Tassoni-Tsuchida ◽  
Danish Khan ◽  
Jeremy J Work ◽  
Gregory Valiant ◽  
...  
Keyword(s):  
Heat Shock ◽  
Heat Shock Response ◽  
Cellular Stress Response ◽  
Response Dynamics ◽  
Time Resolved ◽  
Genetic Method ◽  
Genome Wide ◽  
Activity Measurements ◽  
Shock Response ◽  
Time Specific

Understanding cellular stress response pathways is challenging because of the complexity of regulatory mechanisms and response dynamics, which can vary with both time and the type of stress. We developed a reverse genetic method called ReporterSeq to comprehensively identify genes regulating a stress-induced transcription factor under multiple conditions in a time-resolved manner. ReporterSeq links RNA-encoded barcode levels to pathway-specific output under genetic perturbations, allowing pooled pathway activity measurements via DNA sequencing alone and without cell enrichment or single-cell isolation. We used ReporterSeq to identify regulators of the heat shock response (HSR), a conserved, poorly understood transcriptional program that protects cells from proteotoxicity and is misregulated in disease. Genome-wide HSR regulation in budding yeast was assessed across 15 stress conditions, uncovering novel stress-specific, time-specific, and constitutive regulators. ReporterSeq can assess the genetic regulators of any transcriptional pathway with the scale of pooled genetic screens and the precision of pathway-specific readouts.

scholarly journals Genome-wide, time-sensitive interrogation of the heat shock response under diverse stressors via ReporterSeq

2020 ◽  
Author(s):  
Brian D. Alford ◽  
Gregory Valiant ◽  
Onn Brandman
Keyword(s):  
Heat Shock ◽  
Heat Shock Response ◽  
Cellular Stress Response ◽  
Response Dynamics ◽  
Time Resolved ◽  
Genetic Method ◽  
Genome Wide ◽  
Activity Measurements ◽  
Shock Response ◽  
Time Specific

AbstractInterrogating cellular stress response pathways is challenging because of the complexity of regulatory mechanisms and response dynamics, which can vary with both time and the type of stress. We developed a reverse genetic method called ReporterSeq to comprehensively identify genes regulating a stress-induced transcription factor under multiple conditions in a time-resolved manner. ReporterSeq links RNA-encoded barcode levels to pathway-specific output under genetic perturbations, allowing pooled pathway activity measurements via DNA sequencing alone and without cell enrichment or single cell isolation. Here, we used ReporterSeq to identify regulators of the heat shock response (HSR), a conserved, poorly understood transcriptional program that protects cells from proteotoxicity and is misregulated in disease. We measured genome-wide HSR regulation in budding yeast across thirteen stress conditions, uncovering novel stress-specific, time-specific, and constitutive regulators. ReporterSeq can assess the genetic regulators of any transcriptional pathway with the scale of pooled genetic screens and the precision of pathway-specific readouts.

Genome-wide chromatin remodeling modulates the Alu heat shock response

Gene ◽  
2001 ◽  
Vol 276 (1-2) ◽  
pp. 127-133 ◽  
Author(s):  
Cheonkoog Kim ◽  
Carol M. Rubin ◽  
Carl W. Schmid
Keyword(s):  
Heat Shock ◽  
Chromatin Remodeling ◽  
Heat Shock Response ◽  
Genome Wide ◽  
Shock Response

scholarly journals Stochastic and Age‐Dependent Proteostasis Decline Underlies Heterogeneity in Heat‐Shock Response Dynamics

Small ◽  
2021 ◽  
pp. 2102145
Author(s):  
Nadia Vertti‐Quintero ◽  
Simon Berger ◽  
Xavier Casadevall i Solvas ◽  
Cyril Statzer ◽  
Jillian Annis ◽  
...  
Keyword(s):  
Heat Shock ◽  
Heat Shock Response ◽  
Response Dynamics ◽  
Shock Response ◽  
Age Dependent

scholarly journals Microfluidics: Stochastic and Age‐Dependent Proteostasis Decline Underlies Heterogeneity in Heat‐Shock Response Dynamics (Small 30/2021)

Small ◽  
2021 ◽  
Vol 17 (30) ◽  
pp. 2170157
Author(s):  
Nadia Vertti‐Quintero ◽  
Simon Berger ◽  
Xavier Casadevall i Solvas ◽  
Cyril Statzer ◽  
Jillian Annis ◽  
...  
Keyword(s):  
Heat Shock ◽  
Heat Shock Response ◽  
Response Dynamics ◽  
Shock Response ◽  
Age Dependent

scholarly journals Heterogeneity in heat shock response dynamics caused by translation fidelity decline and proteostasis collapse

2019 ◽  
Author(s):  
Nadia Vertti-Quintero ◽  
Simon Berger ◽  
Xavier Casadevall i Solvas ◽  
Cyril Statzer ◽  
Jillian Annis ◽  
...  
Keyword(s):  
Heat Shock ◽  
Heat Shock Response ◽  
Early Adulthood ◽  
Surrogate Marker ◽  
Protein Translation ◽  
Single Individual ◽  
Response Dynamics ◽  
C Elegans ◽  
Translation Fidelity ◽  
Shock Response

AbstractGenetics, environment, and stochasticity influence the rate of ageing in living organisms. Individual Caenorhabditis elegans that are genetically identical and cultured in the same environment have different lifespans, suggesting a significant role of stochasticity in ageing. We have developed a novel microfluidic methodology to measure heat-shock response as a surrogate marker for heterogeneity associated with lifespan and have quantified the heat-shock response of C. elegans at the population, single individual, and tissue levels. We have further mathematically modelled our data to identify the major drivers determining such heterogeneity. This approach demonstrates that protein translation and degradation rate constants explain the individuality of the heat-shock time-course dynamic. We observed a decline of protein turnover capacity in early adulthood, co-incidentally occurring as the predicted proteostasis collapse. We identified a decline of intestinal response as the tissue that underlies the individual heterogeneity. Additionally, we verified that individuals with enhanced translation fidelity in early adulthood live longer. Altogether, our results reveal that the stochastic onset of proteostasis collapse of somatic tissues during early adulthood reflects individual protein translation capacity underlying heterogenic ageing of isogenic C. elegans.

scholarly journals The Role of Heat Shock Transcription Factor 1 in the Genome-wide Regulation of the Mammalian Heat Shock Response

2004 ◽  
Vol 15 (3) ◽  
pp. 1254-1261 ◽  
Author(s):  
Nathan D. Trinklein ◽  
John I. Murray ◽  
Sara J. Hartman ◽  
David Botstein ◽  
Richard M. Myers
Keyword(s):  
Transcription Factor ◽  
Heat Shock ◽  
Heat Shock Response ◽  
Mammalian Cells ◽  
Transcriptional Response ◽  
Heat Shock Transcription Factor ◽  
Genome Wide ◽  
Shock Response ◽  
Inducible Genes ◽  
Transcription Factor 1

Previous work has implicated heat shock transcription factor 1 (HSF1) as the primary transcription factor responsible for the transcriptional response to heat stress in mammalian cells. We characterized the heat shock response of mammalian cells by measuring changes in transcript levels and assaying binding of HSF1 to promoter regions for candidate heat shock genes chosen by a combination of genome-wide computational and experimental methods. We found that many heat-inducible genes have HSF1 binding sites (heat shock elements, HSEs) in their promoters that are bound by HSF1. Surprisingly, for 24 heat-inducible genes, we detected no HSEs and no HSF1 binding. Furthermore, of 182 promoters with likely HSE sequences, we detected HSF1 binding at only 94 of these promoters. Also unexpectedly, we found 48 genes with HSEs in their promoters that are bound by HSF1 but that nevertheless did not show induction after heat shock in the cell types we examined. We also studied the transcriptional response to heat shock in fibroblasts from mice lacking the HSF1 gene. We found 36 genes in these cells that are induced by heat as well as they are in wild-type cells. These results provide evidence that HSF1 does not regulate the induction of every transcript that accumulates after heat shock, and our results suggest that an independent posttranscriptional mechanism regulates the accumulation of a significant number of transcripts.

scholarly journals Urocortin 3 overexpression reduces ER stress and heat shock response in 3T3-L1 adipocytes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sina Kavalakatt ◽  
Abdelkrim Khadir ◽  
Dhanya Madhu ◽  
Heikki A. Koistinen ◽  
Fahd Al-Mulla ◽  
...  
Keyword(s):  
Stress Response ◽  
Heat Shock ◽  
Er Stress ◽  
Glucose Uptake ◽  
Heat Shock Response ◽  
Cellular Stress Response ◽  
Mrna Levels ◽  
Obesity And Diabetes ◽  
Shock Response ◽  
Urocortin 3

AbstractThe neuropeptide urocortin 3 (UCN3) has a beneficial effect on metabolic disorders, such as obesity, diabetes, and cardiovascular disease. It has been reported that UCN3 regulates insulin secretion and is dysregulated with increasing severity of obesity and diabetes. However, its function in the adipose tissue is unclear. We investigated the overexpression of UCN3 in 3T3-L1 preadipocytes and differentiated adipocytes and its effects on heat shock response, ER stress, inflammatory markers, and glucose uptake in the presence of stress-inducing concentrations of palmitic acid (PA). UCN3 overexpression significantly downregulated heat shock proteins (HSP60, HSP72 and HSP90) and ER stress response markers (GRP78, PERK, ATF6, and IRE1α) and attenuated inflammation (TNFα) and apoptosis (CHOP). Moreover, enhanced glucose uptake was observed in both preadipocytes and mature adipocytes, which is associated with upregulated phosphorylation of AKT and ERK but reduced p-JNK. Moderate effects of UCN3 overexpression were also observed in the presence of 400 μM of PA, and macrophage conditioned medium dramatically decreased the UCN3 mRNA levels in differentiated 3T3-L1 cells. In conclusion, the beneficial effects of UCN3 in adipocytes are reflected, at least partially, by the improvement in cellular stress response and glucose uptake and attenuation of inflammation and apoptosis.

scholarly journals Quantitative proteomics identifies the universally conserved ATPase Ola1p as a positive regulator of heat shock response in Saccharomyces cerevisiae

2021 ◽  
Author(s):  
Stefan Dannenmaier ◽  
Christine Desroches Altamirano ◽  
Lisa Schueler ◽  
Ying Zhang ◽  
Johannes Hummel ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Heat Stress ◽  
Heat Shock ◽  
Heat Shock Response ◽  
De Novo ◽  
Stress Granules ◽  
Cellular Stress Response ◽  
Protein Ubiquitination ◽  
Shock Response

The universally conserved P-loop ATPase Ola1 is implicated in various cellular stress response pathways, as well as in cancer and tumor progression. However, Ola1p functions are divergent between species and the involved mechanisms are only poorly understood. Here, we studied the role of Ola1p in the heat shock response of the yeast Saccharomyces cerevisiae using a combination of quantitative and pulse labeling-based proteomics approaches, in vitro studies and cell-based assays. Our data show that when heat stress is applied to cells lacking Ola1p, the expression of stress-protective proteins is enhanced. During heat stress Ola1p associates with detergent-resistant protein aggregates and rapidly forms assemblies that localize to stress granules. The assembly of Ola1p was also observed in vitro using purified protein and conditions, which resembled those in living cells. We show that loss of Ola1p results in increased protein ubiquitination of detergent-insoluble aggregates recovered from heat-shocked cells. When subsequently cells lacking Ola1p were relieved from heat stress, reinitiation of translation was delayed, whereas, at the same time, de novo synthesis of central factors required for protein refolding and the clearance of aggregates was enhanced when compared to wildtype cells. The combined data suggest that upon acute heat stress, Ola1p is involved in the stabilization of misfolded proteins, which become sequestered in cytoplasmic stress granules. This function of Ola1p enables cells to resume translation in a timely manner as soon as heat stress is relieved.

scholarly journals Mathematical Modeling of the Eukaryotic Heat-Shock Response: Dynamics of the hsp70 Promoter

2005 ◽  
Vol 88 (3) ◽  
pp. 1646-1658 ◽  
Author(s):  
Theodore R. Rieger ◽  
Richard I. Morimoto ◽  
Vassily Hatzimanikatis
Keyword(s):  
Mathematical Modeling ◽  
Heat Shock ◽  
Heat Shock Response ◽  
Response Dynamics ◽  
Hsp70 Promoter ◽  
Shock Response

scholarly journals Heat-responsive and time-resolved transcriptome and metabolome analyses of Escherichia coli uncover thermo-tolerant mechanisms

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Sinyeon Kim ◽  
Youngshin Kim ◽  
Dong Ho Suh ◽  
Choong Hwan Lee ◽  
Seung Min Yoo ◽  
...  
Keyword(s):  
Heat Stress ◽  
Heat Shock ◽  
Heat Shock Response ◽  
Late Stage ◽  
Full Range ◽  
Thermal Adaptation ◽  
Morphological Plasticity ◽  
Growth Stages ◽  
Time Resolved ◽  
Shock Response

Abstract Current understanding of heat shock response has been complicated by the fact that heat stress is inevitably accompanied by changes in specific growth rates and growth stages. In this study, a chemostat culture was successfully performed to avoid the physico-chemical and biological changes that accompany heatshock, which provided a unique opportunity to investigate the full range of cellular responses to thermal stress, ranging from temporary adjustment to phenotypic adaptation at multi-omics levels. Heat-responsive and time-resolved changes in the transcriptome and metabolome of a widely used E. coli strain BL21(DE3) were explored in which the temperature was upshifted from 37 to 42 °C. Omics profiles were categorized into early (2 and 10 min), middle (0.5, 1, and 2 h), and late (4, 8, and 40 h) stages of heat stress, each of which reflected the initiation, adaptation, and phenotypic plasticity steps of the stress response. The continued heat stress modulated global gene expression by controlling the expression levels of sigma factors in different time frames, including unexpected downregulation of the second heatshock sigma factor gene (rpoE) upon the heat stress. Trehalose, cadaverine, and enterobactin showed increased production to deal with the heat-induced oxidative stress. Genes highly expressed at the late stage were experimentally validated to provide thermotolerance. Intriguingly, a cryptic capsular gene cluster showed considerably high expression level only at the late stage, and its expression was essential for cell growth at high temperature. Granule-forming and elongated cells were observed at the late stage, which was morphological plasticity occurred as a result of acclimation to the continued heat stress. Whole process of thermal adaptation along with the genetic and metabolic changes at fine temporal resolution will contribute to far-reaching comprehension of the heat shock response. Further, the identified thermotolerant genes will be useful to rationally engineer thermotolerant microorganisms.

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