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E2F coregulates an essential HSF developmental program that is distinct from the heat-shock response

ABSTRACT: E2F coregulates an essential HSF developmental program that is distinct from the heat-shock response

PROVIDER: PRJNA321849 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3535760.fastq.gz	Fastqsanger.gz
	SRR3535770.fastq.gz	Fastqsanger.gz
	SRR3535780.fastq.gz	Fastqsanger.gz
	SRR3535790.fastq.gz	Fastqsanger.gz
	SRR3535761.fastq.gz	Fastqsanger.gz

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Genome-wide binding profile for Heat Shock Factor (HSF).

Project description:Sequence-specific transcription factors (TFs) are critical for specifying patterns and levels of gene expression, but the DNA elements to which they can bind are not always sufficient to specify their binding in vivo. In eukaryotes, the binding of a TF is in competition with a constellation of other proteins, including histones which package DNA into nucleosomes. Here, we examine using the ChIP-seq assay, the genome-wide distribution of Drosophila Heat Shock Factor (HSF), a TF whose binding activity is mediated by heat shock-induced trimerization. We detect HSF binding to 464 sites, the vast majority of which contain HSF Sequence-binding Elements (HSEs) in Drosophila S2 cells, but these HSF-bound sites represent only a small fraction of HSEs present in the genome. We find a strong correlation of bound HSEs to active chromatin marks present prior to HSF binding, indicating an HSE’s residence in open chromatin is a primary determinant of whether HSF can bind following heat shock.

2010-09-02 | GSE19025 | GEO

Genome-wide binding profile for Heat Shock Factor (HSF).

Project description:Sequence-specific transcription factors (TFs) are critical for specifying patterns and levels of gene expression, but the DNA elements to which they can bind are not always sufficient to specify their binding in vivo. In eukaryotes, the binding of a TF is in competition with a constellation of other proteins, including histones which package DNA into nucleosomes. Here, we examine using the ChIP-seq assay, the genome-wide distribution of Drosophila Heat Shock Factor (HSF), a TF whose binding activity is mediated by heat shock-induced trimerization. We detect HSF binding to 464 sites, the vast majority of which contain HSF Sequence-binding Elements (HSEs) in Drosophila S2 cells, but these HSF-bound sites represent only a small fraction of HSEs present in the genome. We find a strong correlation of bound HSEs to active chromatin marks present prior to HSF binding, indicating an HSEM-bM-^@M-^Ys residence in open chromatin is a primary determinant of whether HSF can bind following heat shock. A single mock immunoprecipitation (IP) using the pre-innoculated animal serum was used as a background dataset for this study. For each condition (NHS and 20minute HS), we performed two independent HSF-ChIP-seq experiments. In addition, we performed two independent HSF-ChIP-seq experiments for each condition (NHS and 20minute HS) in cells that were highly depleted of HSF by RNAi.

2010-09-02 | E-GEOD-19025 | biostudies-arrayexpress

E2F coregulates an essential HSF developmental program that is distinct from the heat-shock response.

Project description:Heat-shock factor (HSF) is the master transcriptional regulator of the heat-shock response (HSR) and is essential for stress resilience. HSF is also required for metazoan development; however, its function and regulation in this process are poorly understood. Here, we characterize the genomic distribution and transcriptional activity of Caenorhabditis elegans HSF-1 during larval development and show that the developmental HSF-1 transcriptional program is distinct from the HSR. HSF-1 developmental activation requires binding of E2F/DP to a GC-rich motif that facilitates HSF-1 binding to a heat-shock element (HSE) that is degenerate from the consensus HSE sequence and adjacent to the E2F-binding site at promoters. In contrast, induction of the HSR is independent of these promoter elements or E2F/DP and instead requires a distinct set of tandem canonical HSEs. Together, E2F and HSF-1 directly regulate a gene network, including a specific subset of chaperones, to promote protein biogenesis and anabolic metabolism, which are essential in development.

| S-EPMC5066613 | biostudies-literature

ChIP-seq of HSF-1 and Pol II in C. elegans larval development and heat shock

Project description:To understand the function and regulation of the C. elegans heat shock factor (HSF-1) in larval development, we have used ChIP-seq to analyze the occupancy of HSF1 and RNA Pol II in L2 larvae and young adult (YA) animals grown at 20°C or upon heat shock at 34°C for 30 min. In addition, we have used RNA-seq to analyze the transcriptomes of wild type (N2), hsf-1(ok600) mutants and hsf-1(ok600); rmSi1[hsf-1::gfp] L2 larvae grown at 20°C and characterized the gene expression change by heat shock in wild type (N2) animals at L2 stage.

2016-10-12 | GSE81521 | GEO

Age-dependent heat shock hormesis to HSF-1 deficiency suggests a compensatory mechanism mediated by the unfolded protein response and innate immunity in young Caenorhabditis elegans

Project description:The goal of this RNA-Seq analysis was to identify genes differentially expressed in wild type (N2) and a hypomorphic mutant of the gene encoding heat shock factor 1 {hsf-1(sy441)} at normal conditions and upon heat shock. This study aimed to identify genes that are up- or downregulated when HSF-1 activity is impaired at 20 ºC. We also aimed to identify gene that are regulated by HSF-1 upon heat stress by comparing differentially expressed genes upon heat shock in wild type and in hsf-1(sy441) mutant background.

2024-06-29 | GSE241011 | GEO

E2F coregulates an essential HSF developmental program that is distinct from the heat-shock response

Project description:This SuperSeries is composed of the SubSeries listed below.

2016-10-12 | GSE81523 | GEO

Using Auxin-inducible-degradation System to Interrogate Tissue-specific Transcriptional Programs of HSF-1 in Reproduction and Heat Shock Response. [Germline - Timecourse]

Project description:To understand the roles of HSF-1 and its regulation in reproduction and heat shock response in a tissue-specific manner, we coupled tissue-specific HSF-1 depletion in C. elegans by auxin-inducible degron (AID) with genome-wide transcriptional analyses in whole animals. We used ChIP-seq to analyze the occupancy of HSF-1 (tagged with AID::GFP) and RNA Pol II in young adult (YA) animals grown at 20°C or upon heat shock (HS) at 34°C for 30 min following an acute depletion of HSF-1 by AID for 2 hours either in the somatic or in the germline cells. Depletion by AID was performed by transferring worms expressing the E3 ligase TIR1 and carrying AID insertion to endogenous HSF-1 (JTL611 or JTL621) to NGM plates containing 1mM auxin (indole- 3-acetic acid, Sigma). The mock treatment was done by transferring worms to plates only containing the vehicle ethanol (EtOH). In parallel, we used RNA-seq to analyze the heat shock respnse upon depletion of HSF-1 in the soma or the germline for 2 hours. In addition, we also analyzed the transcriptomic changes by RNA-seq upon tissue-specific depletion of HSF-1 initiated at young adult stage for different length of time. In all RNA-seq analyses, we included the strains that only express TIR1 but do not have degron insertion at HSF-1 (CA1200 and CA1199) to control for the effects of auxin treatment and AID insertion into HSF-1.

2021-07-01 | GSE162066 | GEO

Using Auxin-inducible-degradation System to Interrogate Tissue-specific Transcriptional Programs of HSF-1 in Reproduction and Heat Shock Response. [HS response]

2021-07-01 | GSE162064 | GEO

Using Auxin-inducible-degradation System to Interrogate Tissue-specific Transcriptional Programs of HSF-1 in Reproduction and Heat Shock Response. [ChIP-Seq]

2021-07-01 | GSE162063 | GEO

RNA-seq analysis in C. elegans larval development and heat shock

2016-10-12 | GSE81520 | GEO