Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of heat stress response in Arabidopsis wild type and hsf1x3 double knockout mutant lines

ABSTRACT: The aim of the expression profiling was to define and to apply criteria that allow discrimination between the effects of heat stress (HS) and HSF-dependent gene expression in Arabidopsis. Therefore we determined and analyzed the expression profiles of wild type (WT) and homozygous hsf1--/hsf3-- double knock out mutant plants (abbreviated hsf1/3). Hsf1/3 plants are deficient in HSF1 and HSF3 activity and unable to induce the fast transient expression of mRNAs of a number of HS genes tested (Lohmann et al., 2004).
The effects of HS on gene expression were analyzed after one hour heat treatment (37C) of leaf tissue.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Wolfgang Busch

PROVIDER: E-MEXP-98 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Identification of novel heat shock factor-dependent genes and biochemical pathways in Arabidopsis thaliana.

Busch Wolfgang W Wunderlich Markus M Schöffl Fritz F

The Plant journal : for cell and molecular biology 20050101 1

In order to assess specific functional roles of plant heat shock transcription factors (HSF) we conducted a transcriptome analysis of Arabidopsis thaliana hsfA1a/hsfA1b double knock out mutants and wild-type plants. We used Affymetrix ATH1 microarrays (representing more than 24 000 genes) and conducted hybridizations for heat-treated or non-heat-treated leaf material of the respective lines. Heat stress had a severe impact on the transcriptome of mutant and wild-type plants. Approximately 11% of ...[more]

PMID: 15610345

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Project description:HSF1 binds DNA via the DBD domain, causing gene upregulation during HS. We assessed the effect of RD-mediated phase separation on chromatin targeting of HSF1 using Cut&Tag followed by high-throughput sequencing to map genome-wide binding of LLPS-competent versus LLPS-incompetent HSF1 mutants under both HS and NHS conditions. Comparing with WT HSF1 under NHS, both WT under HS and M1 under NHS showed increased and broad binding to enhancers and distal intergenic region, with binding most enriched in expected motifs of HSF-related transcription factors. To further assess the role for IDR-induced LLPS in chromatin targeting of HSF1, we used several additional strategies. First, the treatment of 1,6-hexanediol markedly decreased chromatin occupancy both of WT under HS and M1 under NHS conditions. Second, we interrogate chromatin binding of LLPS-deficient mutant M3. Cut&Tag analysis revealed that M3 showed decreased chromatin binding compared to WT under HS and M1 under NHS. The decreased chromatin binding of M3 to chromatin was not due to the loss of its DNA binding ability, as the EMSA assay revealed that M3 was still capable of binding HSE. Instead, the decreased chromatin binding reflects the loss of inter-molecular interaction between HSF1 that holds LLPS. Furthermore, M3 in heat shocked cells shows similar reduced genomic targeting and shallow binding pattern as NHS cells . Third, the enrichment of transcriptional apparatus RNA Pol II, CYCT1, BRD4 to HSF1 target genes also depend on whether HSF1 can phase separate at these sites. Lastly, we conducted live cell single molecule imaging to evaluate chromatin binding kinetics of LLPS-deficient mutant M3 relative to WT HSF1. Measurements of single molecule displacement and diffusion coefficient showed M3 to be significantly more mobile than WT under HS, which suggests M3 was less confined within phase-separated puncta compared with LLPS-competent HSF1. Consistent with this result, super resolution imaging of M3 also showed decreased cluster formation at HSP gene foci but maintained nSBs formation. Altogether, LLPS-forming capability of HSF1 is essential for the efficient recruitment of HSF1 and transcriptional apparatus to HSP gene loci.

Dataset Information

Transcription profiling of heat stress response in Arabidopsis wild type and hsf1x3 double knockout mutant lines

Publications

Identification of novel heat shock factor-dependent genes and biochemical pathways in Arabidopsis thaliana.

Similar Datasets

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