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 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 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.

scholarly journals Mammalian Heat Shock Response and Mechanisms Underlying Its Genome-wide Transcriptional Regulation

2016 ◽  
Vol 62 (1) ◽  
pp. 63-78 ◽  
Author(s):  
Dig B. Mahat ◽  
H. Hans Salamanca ◽  
Fabiana M. Duarte ◽  
Charles G. Danko ◽  
John T. Lis
Keyword(s):  
Transcriptional Regulation ◽  
Heat Shock ◽  
Heat Shock Response ◽  
Genome Wide ◽  
Shock Response

Distinctive heat-shock response of bioleaching microorganismAcidithiobacillus ferrooxidansobserved using genome-wide microarray

2012 ◽  
Vol 58 (5) ◽  
pp. 628-636 ◽  
Author(s):  
Huaqun Yin ◽  
Min Tang ◽  
Zhijun Zhou ◽  
Xian Fu ◽  
Li Shen ◽  
...  
Keyword(s):  
Heat Shock ◽  
Heat Shock Response ◽  
Heterotrophic Bacteria ◽  
Expression Profiles ◽  
Central Carbon Metabolism ◽  
Autotrophic Bacteria ◽  
Genome Wide ◽  
Shock Response ◽  
Shock Proteins ◽  
Genome Wide Expression

Temperature plays an important role in the heap bioleaching. The maldistribution of ventilation in the heap leads to local hyperthermia, which does exert a tremendous stress on bioleaching microbes. In this study, the genome-wide expression profiles of Acidithiobacillus ferrooxidans at 40 °C were detected using the microarray. The results showed that some classic proteases like Lon and small heat-shock proteins were not induced, and heat-inducible membrane proteins were suggested to be under the control of σE. Moreover, expression changes of energy metabolism are noteworthy, which is different from that in heterotrophic bacteria upon heat stress. The induced enzymes catalyzed the central carbon metabolism pathway that might mainly provide precursors of amino acids for protein synthesis. These results will deepen the understanding of the mechanisms of heat-shock response on autotrophic bacteria.

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