Heat Shock Factor 1 drives intergenic association of its target gene loci during heat shock
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA505985 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8206073.fastq.gz | Fastqsanger.gz | |||
| SRR8206074.fastq.gz | Fastqsanger.gz | |||
| SRR8206075.fastq.gz | Fastqsanger.gz | |||
| SRR8206076.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 4 of 4 |
Similar Datasets
Project description:Transcriptional induction of Heat Shock Protein (HSP) genes in yeast is accompanied by dynamic changes in their 3D structure and spatial organization, yet the molecular basis for these phenomena remains unknown. Using chromosome conformation capture and single cell imaging, we show that genes transcriptionally activated by Heat Shock Factor 1 (Hsf1) specifically interact across chromosomes and coalesce into diffraction-limited intranuclear foci. Genes activated by the alternative stress regulators Msn2 and Msn4, in contrast, do not interact among themselves nor with Hsf1 targets. Likewise, constitutively expressed genes, even those interposed between HSP genes, show no detectable interaction. Hsf1 forms discrete subnuclear puncta when stressactivated, and these puncta dissolve in concert with transcriptional attenuation, paralleling the kinetics of HSP gene coalescence and dissolution. Nuclear Hsf1 and RNA Pol II are both necessary for intergenic HSP gene interactions, while DNA-bound Hsf1 is necessary and sufficient to drive coalescence of a heterologous gene. Our findings demonstrate that Hsf1 can dynamically restructure the yeast genome.
2018-11-20 | GSE122666 | GEO
Project description:Cells adapt to environmental stressors such as heat shock and extracellular acidosis through formation of nuclear membrane-less compartments called Amyloid bodies (A-bodies). Stressors activate formation of Amyloid bodies (A-bodies) via induction of ribosomal intergenic spacer RNA (rIGSRNA). RNA-seq on non-ribosome depleted RNA from human MCF7 cells exposed to heat shock (43C, 30 minutes) revealed the heat shock-specific expression profile of rIGSRNA.
2018-08-02 | GSE115731 | GEO
Project description:Heat shock-induced ribosomal intergenic spacer RNA
| PRJNA475962 | ENA
Project description:Transcriptional induction of heat shock protein (HSP) genes is accompanied by dynamic changes in their 3D structure and spatial organization, yet the molecular basis for these phenomena remains unknown. Using chromosome conformation capture and single-cell imaging, we show that genes transcriptionally activated by Hsf1 specifically interact across chromosomes and coalesce into diffraction-limited intranuclear foci. Genes activated by the alternative stress regulators Msn2/Msn4, in contrast, do not interact among themselves nor with Hsf1 targets. Likewise, constitutively expressed genes, even those interposed between HSP genes, show no detectable interaction. Hsf1 forms discrete subnuclear puncta when stress activated, and these puncta dissolve in concert with transcriptional attenuation, paralleling the kinetics of HSP gene coalescence and dissolution. Nuclear Hsf1 and RNA Pol II are both necessary for intergenic HSP gene interactions, while DNA-bound Hsf1 is necessary and sufficient to drive heterologous gene coalescence. Our findings demonstrate that Hsf1 can dynamically restructure the yeast genome.
| S-EPMC6435272 | biostudies-literature
Project description:Whole-genome analysis of heat shock factor binding sites in Drosophila melanogaster. Heat shock factor IP DNA or Mock IP DNA from heat shocked Kc 167 cells compared to whole cell extract on Agilent 2x244k tiling arrays.
2011-01-05 | GSE19744 | GEO
Project description:mRNAs associate with single or multiple ribosomes; these ribosomal assemblies —monosomes and polysomes — translate the mRNAs before degradation. The impact of heat stress on this mRNA turnover remains unclear. In heat-shocked yeast cells, the proportion of monosomes within the ribosomal assemblies rises without a corresponding increase in the number of mRNAs associated with them. As a result, most monosomes are devoid of mRNAs and silent, lacking translational initiation factors and proteins facilitating posttranslational folding. The accumulation of silent ribosomes generally reduces the rate of association of transcripts with the ribosomes. However, elevated temperatures enhance the ribosomal association of specific mRNAs, primarily those encoding heat-shock proteins, allowing them to balance their increased degradation rates. Additionally, reduced binding of the Xrn1 exonuclease to mRNAs diminishes the influence of codon optimality on mRNA stability. These mechanisms reconfigure the translation machinery to prioritize heat-shock protein synthesis over ribosome biogenesis.
2025-09-10 | GSE289484 | 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).
2011-11-09 | GSE24197 | GEO
Project description:mRNAs associate with single or multiple ribosomes these ribosomal assemblies monosomes and polysomes translate the mRNAs before degradation. The impact of heat stress on this mRNA turnover remains unclear. We show that in heat-shocked yeast cells, the proportion of monosomes increases without a corresponding rise in the number of associated mRNAs. Consequently, most monosomes are devoid of mRNAs and silent, lacking translational initiation factors and proteins facilitating posttranslational folding. Such silent monosomes also appear under other stress conditions, with proportions varying according to stress type, suggesting they represent a general feature of cellular adaptation. In parallel with the induction of silent ribosomes, elevated temperatures reduce the overall rate of mRNA ribosome association with few exceptions. Notably, heat-shock promotes the ribosomal association of transcripts encoding heatshock proteins, without extension of the halflives of these mRNAs. These mechanisms dynamically reorganize mRNA turnover to prioritize translation of heat-shock proteins over other proteins.
| MSV000099165 | MassIVE
Project description:Recombinant Escherichia coli cultures are used to manufacture numerous therapeutic proteins and industrial enzymes, where many of these processes use elevated temperatures to induce recombinant protein production. The heat-shock response in wild-type E. coli has been well studied. In this study, the transcriptome profiles of recombinant E. coli subjected to a heat-shock and to a dual heat-shock recombinant protein induction were examined. Most classical heat-shock protein genes were identified as regulated in both conditions. The major transcriptome differences between the recombinant and reported wild-type cultures were heavily populated by hypothetical and putative genes, which indicates recombinant cultures utilize many unique genes to respond to a heat-shock. Comparison of the dual stressed culture data with literature recombinant protein induced culture data revealed numerous differences. The dual stressed response encompassed three major response patterns: induced-like, in-between, and greater than either individual stress response. Also, there were no genes that only responded to the dual stress. The most interesting difference between the dual stressed and induced cultures was the amino acid-tRNA gene levels. The amino acid-tRNA genes were elevated for the dual cultures compared to the induced cultures. Since tRNAs facilitate protein synthesis via translation, this observed increase in amino acid-tRNA transcriptome levels, in concert with elevated heat-shock chaperones, might account for improved productivities often observed for thermo-inducible systems. Most importantly, the response of the recombinant cultures to a heat-shock was more profound than wild-type cultures, and further, the response to recombinant protein induction was not a simple additive response of the individual stresses. The objective of the present work is to gain a better understanding of the heat-shock response in recombinant cultures and how this response might impact recombinant protein production. To accomplish this objective, the transcriptome response of recombinant cultures subjected to a heat-shock and a dual heat-shock recombinant protein induction were analyzed. The transcriptome levels were determined using Affymetrix E. coli Antisense DNA microarrays, such that the entire genome was evaluated. These two transcriptome responses were also compared to recombinant cultures at normal growth temperature that were not over-expressing the recombinant protein and a set of literature recombinant culture data that were chemically induced to over-express the recombinant protein. Additionally, the heat-shock response of the recombinant cultures was compared to the literature report of the heat-shock response in wild-type cultures. The results of the global transcriptome analysis demonstrated that recombinant cultures respond differently to a heat-shock stress than wild-type cultures, where the transcriptome response of the recombinant cultures is further modified by production of a recombinant protein.
2009-08-07 | GSE17507 | GEO
Project description:This study aimed to establish a genome-wide association for heat tolerance using the newly developed 66K SNP array for Mercenaria mercenaria. Northern quahogs from three local farms were combined for a heat challenge by increasing temperature at 1°C per day from 24°C to 35°C (Phase I), maintaining at 35°C for two days before decreasing to 27°C within the next 24 hr, then to 24°C within 24 hr. Survival-time analysis showed different survivals among quahogs from these three farms during the heat challenge. Mortality during the temperature increase period (Phase I) was 38, 46, and 55%, and after the temperature decrease was 36, 30, and 29%. For the survivors, no changes were found in body weight before and after the heat shock challenges (p < 0.265). The PCA analyses of SNP frequencies indicated significant genetic differences associated with clam survival under heat stress across the different farms. The fastStructure analysis also revealed the proportions of different ancestral components within the clams, highlighting the genetic factors that may contribute to their varying survival rates under heat stress. The heritability of the heat tolerance traits was 0.680 ± 0.063. GWAS analysis indicated that one SNP exhibited a significant association with the time-to-death trait of northern quahogs and was in chromosome 7. More significant SNPs (p < 10-3.5) were inside genes that have been reported to function in heat tolerance such as serine/threonine-protein kinase 31 and carbohydrate sulfotransferase 11, and some genes found within 50K bp far from SNP sites have a relationship with heat tolerance such as toll-like receptors 4 and 6 (TLRs 4 and TLRs 6), uracil-DNA glycosylase, and a disintegrin and metalloproteinase with thrombospondin motifs gon-1 (ADAMTs). Overall, these findings highlight the power of high-throughput approaches for the identification of superior clam genotypes for further breeding.
2025-02-26 | GSE290453 | GEO