Heat acclimation memory: Does the de-acclimated transcriptome reveal epigenetic processes of transcriptional regulation?
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ABSTRACT:
ORGANISM(S): Rattus norvegicus
PROVIDER: GSE43404 | GEO | 2014/03/31
SECONDARY ACCESSION(S): PRJNA185993
REPOSITORIES: GEO
Similar Datasets
Project description:Heat acclimation (AC) allows its faster re-induction following its decline. Constitutively preserved euchromatin state in hsp70 promoter during acclimation decline/regain pushed forward the hypothesis that acclimation decline is a period of M-bM-^@M-^\dormant memoryM-bM-^@M-^] involving molecular program including epigenetic controlled transcriptional regulation leading to heat acclimation mediated cytoprotective memory. We used microarray to uncover hallmark pathways in the induction of heat-acclimation-mediated memory, focusing on markers of epigenetic processes. Rats subjected to heat acclimation, deacclimation, reacclimation and untreated controls were used. We showed here that (i) AC2d provides the molecular switch for acclimation (ii) AC30 heart demonstrates qualitative adaptations (iii) specific molecular program encompassing up/down regulated gene during DeAC, of which epigenetic markers such as class A histones, chromatin modifiers and microRNA suggest epigenetic transcriptional regulation linked to acclimation memory (iv) constitutive upregulation of MAPK P38 module and targets as well as jak/stat and AKT associated pathways during DeAC imply its major role in this process. Noteworthy are players such as poly-(ADP-ribose)polymerase-1 (PARP1) and linker histones (histones H1 cluster in this process).
2014-03-31 | E-GEOD-43404 | biostudies-arrayexpress
Project description:To understand faster reinduction of heat acclimation, in this investigation we studied global stress associated genomic response during acclimation, following its loss and re-induction. Nylon cDNA Atlas Array was used. Collectively, the study comprised nine experimental groups of which six characterized experimental basal conditions: Controls-untreated, Short and Long term heat acclimated groups ( exposure to environmental heat at 34oC for 2 or 30 days respectively), Deacclimated group (24oC for 1mo) and Reacclimated groups (2d at 34oC following the deacclimation protocol). Three additional experimental groups: Controls, Short and Long term and Reacclimated rats (as above) were tested for genomic responses following subjection to heat stress at 41oC. Because of a dichotomy between genomic and physiological responses we hypothesize thst rapid reacclimation is linked to reprograming of gene expression. Keywords: heart, Left ventricle
2007-12-31 | GSE8329 | GEO
Project description:Purpose: Acclimation referes to reversible responses that plants trigger under frequently and moderate changes in natural environments, mostly light intensity and temperature. To better understand acclimation in Arabidopsis thaliana, modulators and integrators for this process should be identified. To achieve this goal, a dynamic set-up was designed to systematically cultivate Arabidopsis plants under moderate high light, heat and cold and a multiple high-throughput strategy was conducted to monitor changes in transcriptome, proteome and metabolome. As part of this comprehensive characterisation, lncRNA-Seq has been carried out to investigate transcriptome changes and further integrated in conditional correlation networks. Methods: lncRNA-Seq libraries were prepared from 14-d-old plants cultivated under standard control conditions or acclimated to high light, cold or heat for 4 d and then de-acclimated under normal conditions for 4 additional days. Standard Illumina protocols were used for lncRNA-Seq sequencing. Unless some quality issue in libraries was detected, triplicates for 3 independent plants were used. Adaptor sequences were removed with Trimmomatic and resulting reads mapped to the Arabidopsis genome (Araport11) with Tophat 2.1.1. FPKM reads were quantified with Cufflinks to provide processed data files and differential expression analysis were conducted with featureCounts/DEseq2 pipeline. Results: lncRNA-Seq libraries contained 10 milion reads each. Transcript analysis for differential gene expression was conducted according to the Tophat/featureCounts/DESeq2 pipeline. To declare significant differences, a cut-off for absolute log2(FC) ≥ 1 compared to the corresponding control and FDR ≤ 0.05 was applied. Transcripts significantly different in at least one time-point were considered for subsequent analysis. Accordingly, high light treatments caused changes in 2683 transcripts, followed by 3470 under heat and 6882 under cold. Further data analysis revealed that more than 12% of all altered transcripts were commonly miss-regulated among the three treatments. From a dynamic point of view, transcriptional changes occurred from 3h to 4d of treatment in all treatments and tend to recover to the initial state after 2 and 4d of de-acclimation. Conclusions: the reversibility of the transcriptional changes during the recovery phase validated the conditions of our set-up to investigate acclimation. Moreover, the existance of a common fraction of transcripts that responded to the three conditions unveiled a central response to acclimation.
2020-06-21 | GSE125950 | GEO
Project description:We studied the global genomic response in the hypothalamus during heat acclimation, with and without combined hypohydration stress. Rats were acclimated for 2 days or for 30 days at 34°C. Hypohydration (10% decrease in body weight) was attained by water deprivation. Functional analyses demonstrated a bi-phasic acclimatory profile with a transient upregulation of genes encoding ion channels, transporters, and transmitter signaling upon 2 days acclimation, suggesting enhanced neuronal excitability at that acclimation phase. Following long acclimation most genes returned to their pre-acclimation expression levels. In both acclimation phases, genes encoding hormones and neuropeptides, linked with metabolic rate and food intake, were downregulated. The response to hypohydration was characterized by an upregulation of a large number of genes primarily associated with the regulation of ion channels and cell-volume and neuronal excitability. During 2 days acclimation, the response was transiently desensitized, recovering upon LTHA. The results suggest that hypohydration overrides the heat acclimatory status. Keywords: other
2005-10-29 | GSE2890 | GEO
Project description:The processes of adaptation to environmental heat and aerobic exercise training improve efficiency in various body systems and bring about acclimatory homeostasis. In order to examine the global genomic responses of the soleus and heart following exposure of rats to these stressors, nylon cDNA Atlas Array was used. Male rats were exposed to one of the following stressors: heat acclimation, aerobic training (treadmill), and combined heat acclimation and aerobic training for short (2, 3 days) and long (1 mo) time period. The study comprised seven experimental groups: Controls-untreated. Heat acclimated groups (2dac, Acc)– exposure to environmental heat at 34C for 2 or 30 days. Exercise groups (3dex, Ex)– graduated training protocol under normothermic conditions for 3 and 30 days at 24C. Exercise training and heat acclimation – (3dexac, ExAc)- exposed to both environmental heat and aerobic exercise as above. The Series data tables appended below: 1) Heart - normalized log2 ratio of geomeans defined as treatment/control 2) Soleus - normalized log2 ratio of geomeans defined as treatment/control Keywords: stress response
2007-12-31 | GSE7799 | GEO
Project description:Transcriptional regulation is a key aspect of environmental stress responses. Heat stress (HS) induces transcriptional memory that allows plants to respond more efficiently to a recurrent HS. In light of more frequent temperature extremes due to climate change, improving heat tolerance in crops is an important breeding goal. However, not all HS-inducible genes show sustained induction/transcriptional memory and it is unclear what distinguishes memory and non-memory genes. To address this issue and understand the (epi-) genome architecture in transcriptional memory after HS, we investigated genome-wide target genes of the two key memory heat shock transcription factors, HSFA2 and HSFA3. We determined the binding kinetics of these factors to their target genes and asked whether genes that show sustained induction of transcription carry specific features that allow prediction and potentially engineering of memory gene behaviour. HSFA2 and HSFA3 show near identical binding patterns. In vitro binding strength as determined by DAP-seq analysis correlates strongly with in vivo binding strength, confirming the importance of sequence features. However, no single distinctive sequence motif appears to be required for memory behaviour. Instead, HS memory genes are characterized by a combination of features: low expression levels in the absence of HS, chromatin environment and an enrichment of H3K4 methylation after HS. Our findings are confirmed by an orthogonal transcriptomic data set using both de novo clustering and an established definition of memory genes. In summary, our findings provide an integrated view of HSF-dependent transcriptional memory and shed light on its sequence and chromatin determinants. They will contribute to the prediction and engineering of genes with transcriptional memory.
2023-05-07 | GSE192427 | GEO
Project description:Transcriptional regulation is a key aspect of environmental stress responses. Heat stress (HS) induces transcriptional memory that allows plants to respond more efficiently to a recurrent HS. In light of more frequent temperature extremes due to climate change, improving heat tolerance in crops is an important breeding goal. However, not all HS-inducible genes show sustained induction/transcriptional memory and it is unclear what distinguishes memory and non-memory genes. To address this issue and understand the (epi-) genome architecture in transcriptional memory after HS, we investigated genome-wide target genes of the two key memory heat shock transcription factors, HSFA2 and HSFA3. We determined the binding kinetics of these factors to their target genes and asked whether genes that show sustained induction of transcription carry specific features that allow prediction and potentially engineering of memory gene behaviour. HSFA2 and HSFA3 show near identical binding patterns. In vitro binding strength as determined by DAP-seq analysis correlates strongly with in vivo binding strength, confirming the importance of sequence features. However, no single distinctive sequence motif appears to be required for memory behaviour. Instead, HS memory genes are characterized by a combination of features: low expression levels in the absence of HS, chromatin environment and an enrichment of H3K4 methylation after HS. Our findings are confirmed by an orthogonal transcriptomic data set using both de novo clustering and an established definition of memory genes. In summary, our findings provide an integrated view of HSF-dependent transcriptional memory and shed light on its sequence and chromatin determinants. They will contribute to the prediction and engineering of genes with transcriptional memory.
2023-05-07 | GSE192407 | GEO
Project description:The processes of adaptation to environmental heat and aerobic exercise training improve efficiency in various body systems and bring about acclimatory homeostasis. In order to examine the global genomic responses of the soleus and heart following exposure of rats to these stressors, nylon cDNA Atlas Array was used. Male rats were exposed to one of the following stressors: heat acclimation, aerobic training (treadmill), and combined heat acclimation and aerobic training for short (2, 3 days) and long (1 mo) time period. The study comprised seven experimental groups: Controls-untreated. Heat acclimated groups (2dac, Acc)â exposure to environmental heat at 34C for 2 or 30 days. Exercise groups (3dex, Ex)â graduated training protocol under normothermic conditions for 3 and 30 days at 24C. Exercise training and heat acclimation â (3dexac, ExAc)- exposed to both environmental heat and aerobic exercise as above. The Series data tables appended below: 1) Heart - normalized log2 ratio of geomeans defined as treatment/control 2) Soleus - normalized log2 ratio of geomeans defined as treatment/control 21 samples, 3 pool each, of: 1)Â Control untreated rats 2)Â Long-term heat acclimated rats 3)Â Long-term aerobic-exercised trained rats. 4)Â Rats exposed to long-term heat acclimation and exercise training. 5)Â Short term heat acclimated rats. 6)Â Short term aerobic exercised trained rats 7)Â Rats exposed to short-term heat acclimation and exercise training.
2010-05-27 | E-GEOD-7799 | biostudies-arrayexpress
Project description:HSFA2 and HSFA3 binding after heat acclimation
| PRJNA791393 | ENA
Project description:Heat stress is the primary obstacle for landscape application of azalea in hot-summer areas. Heat acclimation can confer acquired thermotolerance to R. hainanense even after a long recovery. The mechanisms and key factors involved in the heat acclimation memory were investigated.
2020-04-02 | PXD017005 | Pride