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Genetic and Epigenetic Determinants Establish a Continuum of Hsf1 Occupancy and Activity Across the Yeast Genome

ABSTRACT: Genetic and Epigenetic Determinants Establish a Continuum of Hsf1 Occupancy and Activity Across the Yeast Genome

PROVIDER: PRJNA482832 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7591552_1.fastq.gz	Fastqsanger.gz
	SRR7591552_2.fastq.gz	Fastqsanger.gz
	SRR7591553_1.fastq.gz	Fastqsanger.gz
	SRR7591553_2.fastq.gz	Fastqsanger.gz
	SRR7591554_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Genetic and Epigenetic Determinants Establish a Continuum of Hsf1 Occupancy and Activity Across the Yeast Genome

Project description:We performed ChIP-seq of Hsf1 under non heat shock, 5-minute heat shock and 120 minute heat shock conditions. We used the conditional chemical genetics approach known as “anchor away” (AA) to rapidly inactivate Hsf1. We coupled Hsf1-AA to and nascent RNA seq (NAC)-seq to define the genes whose expression depends on Hsf1 during heat shock.

2018-07-26 | GSE117653 | GEO

Genetic and epigenetic determinants establish a continuum of Hsf1 occupancy and activity across the yeast genome.

Project description:Heat shock factor 1 is the master transcriptional regulator of molecular chaperones and binds to the same cis-acting heat shock element (HSE) across the eukaryotic lineage. In budding yeast, Hsf1 drives the transcription of ∼20 genes essential to maintain proteostasis under basal conditions, yet its specific targets and extent of inducible binding during heat shock remain unclear. Here we combine Hsf1 chromatin immunoprecipitation sequencing (seq), nascent RNA-seq, and Hsf1 nuclear depletion to quantify Hsf1 binding and transcription across the yeast genome. We find that Hsf1 binds 74 loci during acute heat shock, and these are linked to 46 genes with strong Hsf1-dependent expression. Notably, Hsf1's induced DNA binding leads to a disproportionate (∼7.5-fold) increase in nascent transcription. Promoters with high basal Hsf1 occupancy have nucleosome-depleted regions due to the presence of "pioneer factors." These accessible sites are likely critical for Hsf1 occupancy as the activator is incapable of binding HSEs within a stably positioned, reconstituted nucleosome. In response to heat shock, however, Hsf1 accesses nucleosomal sites and promotes chromatin disassembly in concert with the Remodels Structure of Chromatin (RSC) complex. Our data suggest that the interplay between nucleosome positioning, HSE strength, and active Hsf1 levels allows cells to precisely tune expression of the proteostasis network.

| S-EPMC6340206 | biostudies-literature

HSF2 cooperates with HSF1 to drive a transcriptional program critical for the malignant state

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

HSF1 Activation Can Restrict HIV Replication

Project description:Host protein folding stress responses can play important roles in RNA virus replication and evolution. Intriguingly, prior work revealed a complicated interplay between the cytosolic proteostasis stress response, controlled by its master regulator heat shock factor 1 (HSF1) and human immunodeficiency virus-1 (HIV-1). We sought to isolate HSF1 transcription factor activity from proteostasis stress and elucidate the function of HSF1 in HIV-1 lifecycle in absence of cellular stress. We used chemical genetic, stress-independent control of HSF1 activity to establish whether and how HSF1 influences HIV-1 replication. Stress-independent HSF1 induction decreased both the total quantity and infectivity of HIV-1 virions. Moreover, HIV-1 was unable to escape HSF1-mediated restriction over the course of several serial passages. These results promote continued consideration of the heat shock response as a potential target for antiviral drugs.

2022-01-30 | GSE137591 | GEO

Yeast HSF1 vs hsf1-ba1

Project description:Upon heat shock, Hsf1 protein is extensively phosphorylated, however, this modification is inhibited by an hsf1-bal mutation. To get genome-wide effect of the hyperphosphorylation on Hsf1-regulated transcription, the heat-induced gene expression profiles in HSF1 and hsf1-bal cells were compared. Keywords: stress response

2005-09-27 | GSE3361 | GEO

Excess protein synthesis, denatured proteins or molecular crowding spontaneously induce HSF1 trimerisation and activation

Project description:Stress responses are a key feature of normal physiology and are usurped by cancer cells to ensure enhanced protein synthesis for growth, to compensate for genomic instability, and to protect cancer cells from therapy induced stress. Heat shock factor-1 (HSF1) is a major stress-response transcription factor, and its activity is markedly enhanced in cancer. Stress induces HSF1 conformational changes and post-translational modifications, leading to assembly of active HSF1 trimers that bind DNA to control target gene expression. Although the function of HSF1 in transcription is relatively well-known, the mechanisms leading to HSF1 activation and enhanced stress response in tumours are unclear. To investigate whether HSF1 is a primary sensor of proteotoxic stress in vivo, we studied the range of conditions that can cause HSF1 activation in vitro and in cells, and conditions that prevent its activation. We show that purified recombinant HSF1 adopts a stable monomeric conformation in vitro. Heat stress caused a conformational change and the assembly of HSF1 trimers. Conditions leading to protein denaturation, including heat stress, crowding, Hsp90 inhibition, or proteasome inhibition, all directly lead to HSF1 activation. In contrast, HSF1 activation in vivo is prevented by proteosynthesis inhibition, which reduces the amount of denatured proteins in the cell. These results establish that HSF1 is a direct sensor of proteotoxic stress, independent of post-translational modification, where abrupt environmental changes that cause protein denaturation simultaneously induce a conformational change in monomeric HSF1 leading to its activation. This mechanism explains the universal ability of cells to respond to proteotoxic stress and trigger a protective response when increased chaperone activities are required to restore homeostasis.

2024-08-14 | PXD037662 | Pride

Genome-wide Analysis of Sp2 Occupancy and Expression Profiling Establish Sp2 as a Sequence-specific Transcription Factor Regulating Fundamental Cellular Processes - ChIPseq

Project description:Genome-wide Analysis of Sp2 Occupancy and Expression Profiling Establish Sp2 as a Sequence-specific Transcription Factor Regulating Fundamental Cellular Processes - ChIPseq

2012-05-24 | E-MTAB-994 | biostudies-arrayexpress

Transcription profiling of mouse HSF1+/+ and HSF1-/- fibroblasts heat shock time series

Project description:Mouse HSF1+/+ and HSF1-/- Fibroblasts Heat Shock Time Courses Scanned on Scanner 7 (Axon 4000B)

2005-07-21 | E-SMDB-1853 | biostudies-arrayexpress

Identification of genes regulated by human HSF1, chicken HSF1 and chicken HSF3

Project description:To examine whether human HSF1, chicken HSF1 and chicken HSF3 regulates the expression of different genes, we performed DNA microarray analysis.

2024-09-18 | GSE262549 | GEO

yeast hsf1-R206S/F256S mutant

Project description:Effect of hsf1-R206S/F256S mutation on heat-induced transcription of genes is analyzed. Total RNA was isolated from HSF1 wild type and hsf1-R206S/F256S cells grown at 39oC for 15 min. Probe cDNA was primed by oligo(dT) and was synthesized in the presence of 33P-dCTP. Hybridization was carried out using the same GF100 GeneFilter. Value higher than 30 in HSF1 wild type cells is confident. Values from duplicate experiments were averaged, and the average fold changes were calculated. Keywords = yeast Keywords = HSF1 Keywords: other

2004-12-24 | GSE2103 | GEO

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