Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1314291 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Plants as sessile organisms can adapt to environmental stress to mitigate its adverse effects. As part of such adaptation they maintain an active memory of heat stress for several days that mediates a more efficient response to recurring stress. We identified a mutant that is specifically affected in this heat stress memory. The forgetter1 (frg1) mutant is defective in the Arabidopsis orthologue of Strawberry notch and displays reduced maintenance of heat-induced gene expression. FRG1 globally associates with the promoter region of actively expressed genes in a heat-dependent fashion. FRG1 interacts with chromatin remodelers of the SWI/SNF and ISWI families, which also display reduced heat stress memory. Accordingly, nucleosome dynamics at loci with altered maintenance of heat-induced expression are affected in frg1. Thus, FRG1 is required to sustain a transcription-competent chromatin environment by nucleosome positioning. Our findings suggest a mechanism for the highly conserved Strawberry notch proteins in development and pathologies.
2016-10-10 | GSE79453 | GEO
Project description:In HuntingtonM-bM-^@M-^Ys disease (HD), polyglutamine expansions in the huntingtin (Htt) protein cause subtle changes in cellular functions that, over-time, lead to neurodegeneration and death. Studies have indicated that activation of the heat shock response can reduce many of the effects of mutant Htt in disease models, suggesting that the heat shock response is impaired in the disease. To understand the basis for this impairment, we have used genome-wide chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq) to examine the effects of mutant Htt on the master regulator of the heat shock response, HSF1. We find that, under normal conditions, HSF1 function is highly similar in cells carrying either wild-type or mutant Htt. However, polyQ-expanded Htt severely blunts the HSF1-mediated stress response. Surprisingly, we find that the HSF1 targets most affected upon stress are not directly associated with proteostasis, but with cytoskeletal binding, focal adhesion and GTPase activity. Our data raise the intriguing hypothesis that the accumulated damage from life-long impairment in these stress responses may contribute significantly to the etiology of Huntington's disease. ChIP-Seq experiments for HSF-1 were performed in striatal cells that express either wild-type or mutant Htt using ChIP-Seq technology under normal (33M-BM-0C) and heat shock (42M-BM-0C for six hours) conditions. The cells were crosslinked with 1% formaldehyde and immunoprecipitated using antibody sc-9144 (Santa Cruz Biotech) for HSF-1. Sequencing was performed using the Illumina Genome Analyzer II.
2012-06-19 | E-GEOD-38000 | biostudies-arrayexpress
Project description:In Huntington’s disease (HD), polyglutamine expansions in the huntingtin (Htt) protein cause subtle changes in cellular functions that, over-time, lead to neurodegeneration and death. Studies have indicated that activation of the heat shock response can reduce many of the effects of mutant Htt in disease models, suggesting that the heat shock response is impaired in the disease. To understand the basis for this impairment, we have used genome-wide chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq) to examine the effects of mutant Htt on the master regulator of the heat shock response, HSF1. We find that, under normal conditions, HSF1 function is highly similar in cells carrying either wild-type or mutant Htt. However, polyQ-expanded Htt severely blunts the HSF1-mediated stress response. Surprisingly, we find that the HSF1 targets most affected upon stress are not directly associated with proteostasis, but with cytoskeletal binding, focal adhesion and GTPase activity. Our data raise the intriguing hypothesis that the accumulated damage from life-long impairment in these stress responses may contribute significantly to the etiology of Huntington's disease.
2012-06-19 | GSE38000 | GEO
Project description:This project was conducted in collaboration with the Stachowicz and Dorrestein labs exploring the effects of eelgrass genotypic diversity on rhizosphere exometabolome production under marine heat wave versus ambient conditions. This data was collected from cultures of eelgrass genotypes grown in various levels of poly or monoculture under marine heat wave or ambient conditions in mesocosm. After simulating a 15 week marine heat wave regime, we sampled for each culture type-treatment combination’s rhizosphere metabolome and used non-targeted LC-MS/MS to examine how root exudates at the culture-level interact with genotypic diversity and temperature stress in a marine habitat forming species. Untargeted LC-MS/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 150 x 2.1 mm (Phenomenex, Torrance, CA).
2024-11-19 | MSV000096471 | GNPS
Project description:This project was conducted in collaboration with the Stachowicz and Dorrestein labs exploring the effects of eelgrass genotypic diversity on rhizosphere exometabolome production under marine heat wave versus ambient conditions. This data was collected from cultures of eelgrass genotypes grown in various levels of poly or monoculture under marine heat wave or ambient conditions in mesocosm. After simulating a 15 week marine heat wave regime, we sampled for each culture type-treatment combination’s rhizosphere metabolome and used non-targeted LC-MS/MS to examine how root exudates at the culture-level interact with genotypic diversity and temperature stress in a marine habitat forming species. Untargeted LC-MS/MS acquisition was performed on a Vanquish Flex UHPLC system coupled to an Orbitrap Exploris 240 (Thermo Fisher Scientific, Bremen, Germany). Chromatographic separation was performed on a Kinetex 1.7 um 100 A pore size C18 reversed phase UHPLC column 150 x 2.1 mm (Phenomenex, Torrance, CA).
2024-11-19 | MSV000096470 | GNPS
Project description:To understand affected genes by overexpression of origouridylate binding protein 1b (UBP1b) under heat stress conditions, transcriptional profiling of UBP1box and control plants were analyzed under normal and heat stress (40°C) conditions using Arabidopsis custom microarrays.
2016-08-21 | GSE78713 | GEO
Project description:In Huntington's disease (HD), polyglutamine expansions in the huntingtin (Htt) protein cause subtle changes in cellular functions that, over-time, lead to neurodegeneration and death. Studies have indicated that activation of the heat shock response can reduce many of the effects of mutant Htt in disease models, suggesting that the heat shock response is impaired in the disease. To understand the basis for this impairment, we have used genome-wide chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq) to examine the effects of mutant Htt on the master regulator of the heat shock response, HSF1. We find that, under normal conditions, HSF1 function is highly similar in cells carrying either wild-type or mutant Htt. However, polyQ-expanded Htt severely blunts the HSF1-mediated stress response. Surprisingly, we find that the HSF1 targets most affected upon stress are not directly associated with proteostasis, but with cytoskeletal binding, focal adhesion and GTPase activity. Our data raise the intriguing hypothesis that the accumulated damage from life-long impairment in these stress responses may contribute significantly to the etiology of Huntington's disease. Affymetrix MG430 2.0 expression levels of wild-type (STHdhQ7/Q7) and mutant (STHdhQ111/Q111) striatal cells under growth condition (33 C) and upon heat shock (42 C for six hours)
2012-06-18 | E-GEOD-38001 | biostudies-arrayexpress
Project description:Elevated temperature occurring at reproductive stage has great impact on gametophyte development and therefore ultimate fruit or seed set in plants, the underlying molecular mechanisms are less understood. We investigated the effect of elevated temperature stress on reproductive development in Arabidopsis with tissue-specific transcriptome profiling and observed distinct response patterns between vegetative and reproductive tissues. Heat stress exposure affected reproductive developmental programs including early phases of anther/ovule development and meiosis process, and genes participating in the unfolded protein response (UPR) were enriched among the heat up-regulated reproductive tissue-specific genes. We found that the bzip28bzip60 double mutant defective in UPR were sensitive to elevated temperature stress in terms of reduced silique length and fertility comparing to the wild-type plants. Comparison of heat responsiveness between the wild-type and bzip28zip60 plants identified 521 genes that were regulated by bZIP28 and bZIP60 upon heat stress at reproductive stage, most of which were non-canonical UPR genes. Further ChIP-Seq data revealed 133 direct targets of bZIP28 in Arabidopsis seedlings subjected to heat stress, of which 39 target genes were up-regulated by heat stress at reproductive stage. Our results provide novel insights into heat responsiveness in reproductive tissues and demonstrate the protective roles of UPR for maintaining fertility upon heat stress in plants.
2017-03-15 | GSE94146 | GEO