Transcriptome-wide changes in HeLa cell line investigated in response to Heat-shock stress
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: mitali mukerji
PROVIDER: E-GEOD-26776 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:The heat-shock stress response was studied at the level of exons using Affymetrix Exon-array profiling for both sense and anti-sense transcripts. Sense transcript profiling was done as per the protocol of Affymetrix Exon 1.0 ST array and anti-sense transcript array profiling was done using a modified protocol (Xijin Ge et al., BMC Genomics. 2008 Jan 22;9:27). In short, for profiling antisense transcripts, first cycle cDNA synthesis and IVT step is skipped. This modified protocol starts directly from the second cycle cDNA synthesis step. The labelled target DNA fragments are in reverse orientation of original mRNAs. Thus the hybridization signals will represent transcripts from the same exonic regions but from the opposite DNA strand. Study was undertaken with 2 biological replicates each for - a) Heat-shock treated Sense b) Heat-shock treated Anti-sense c) Untreated control Sense d) Untreated control Anti-Sense
2011-07-31 | E-GEOD-27127 | biostudies-arrayexpress
Project description:Exiqon miRNA array contains LNA-modified oligos which minimizes the Tm-range within which probe hybridizes with the transcript in query, thus minimizing the mis-match. Taking advantage of this, we used the miRCURY LNA array to investigate genome wide signatures for miRNA expression in response to heat shock stress. We also did mRNA expression profiling using the same RNA to look for possible miRNA-mRNA interaction in response to heat shock stress. For the differentially expressed miRNAs, target predictions were done using both miRanda and TargetScan. The consensus set was used for subsequent experimental validation. In total, 6 comparative hybridizations of heat-shock treated versus control were profiled using the Exiqon arrays. These consisted of 3 biological replicates, each with its dye-swap pair.
2015-01-01 | E-GEOD-60472 | biostudies-arrayexpress
Project description:High-temperature stress is a critical environmental parameter for all organisms and induces a cellular heat shock response, characterized by an upregulation of heat shock proteins. For Crenarchaeota, it is unknown how this response is regulated, given the lack of conservation of known prokaryotic or eukaryotic heat shock-regulating transcription factors and how cellular processes are affected. To this end, we studied the heat shock response of the thermoacidophilic Sulfolobus acidocaldarius, thriving in volcanic hot springs at 75°C, upon shift to 86°C, at the transcriptome and proteome level. By pulse-labeling of neosynthesized RNA and proteins upon heat shock, we show a drastic reduction of the cell’s major transcriptional activity immediately after shift and neosynthesis of certain abundant (heat shock) proteins, including the thermosome. By combining RNA-sequencing and mass spectrometry, we show that RNA levels of half of the genes are affected immediately after temperature shift and that reprogramming of the protein landscape takes at least one hour and changes are more subtle. Correlation analysis provides evidence that considerable post-transcriptional and post-translational regulation is occurring upon heat shock. Functional enrichment analysis indicates that nearly all biological processes are affected by heat shock. An overall downregulation is observed for transcription, translation, DNA replication and cell division. However, quality control of translation and of the protein landscape is increased. Many DNA repair pathways are differentially expressed, accompanied with an increase in a DNA import system. Furthermore, expression of DNA topoisomerases is investigated, coinciding with a significant differential expression of nucleoid-associated proteins. Based on these findings and considering the absence of a conserved DNA-binding motif, we propose that regulation of the heat shock response in Sulfolobales is most likely not established by a classical transcription factor, but is rather caused by changes in chromosome organization or established at the post-transcriptional level.
2023-08-07 | PXD038744 | Pride
Project description:Heat shock induces rapid modification of proteins with SUMO2/3. This study concentrated in charaterizing how these changes are reflected on SUMOylation of chromatin bound proteins, trancsription, and chromatin binding of SUMO ligase PIAS1. Comparison of chromatin SUMO2/3 modification pattern in non-stressed and heat shocked K562 and VCaP cells. All samples were done as biological replicates. In K562 cells, SUMO2/3 ChIP-seq was done in non-stressed (37C) and heat shocked (30min at 43C) cells. The effect of heat shock factor 1 (HSF1) to chromatin SUMOylation in HS was studied in HSF1 silenced (shHSF1) K562 cells (non-stressed vs. heat shocked) using scramble shRNA transfected cells as control (shSCR). SUMO2/3, SUMO ligase PIAS1,and RNA polymerase II binding in HS (30 min at 43C) and recovery from HS (1h at 37C after HS) was studied using ChIP-seq. Effect of PIAS1 for chromatin SUMOylation was studied in PIAS1 silenced (siRNA for PIAS1, siPIAS1) cells (non-stressed or heat shocked) using non-targeting siRNA transfected cells as a control (siNON). Effect of SUMOylation to chromatin binding of RNA polymerase II was studied in UBE2I silenced (siRNA for UBE2I) and control (non-targeting siRNA transfected, siNON) VCaP cells (non-stressed or heat shocked). Effect of transtription inhibition for chromatin SUMOylation was studied in TRP (triptolide; 1 micromolar, 3h) and DRB (5,6-Dichlorobenzimidazole 1-beta-D-ribofuranosidase; 100 micromolar, 3h) treated VCaP cells. GRO-seq was used to determine HS-induced changes in nascent transcription in K562 cells.
2015-07-02 | E-GEOD-66448 | biostudies-arrayexpress
Project description:Sinorhizobium meliloti can live as a soil saprophyte, and can engage in a nitrogen fixing symbiosis with plant roots. To succeed in such diverse environments, the bacteria must continually adjust gene expression. Transcriptional plasticity in eubacteria is often mediated by alternative sigma factors interacting with core RNA polymerase. The S. meliloti genome encodes 14 of these alternative sigmas, including two putative RpoH (heat shock) sigmas. We used custom Affymetrix Symbiosis Chips to characterize the global transcriptional response of S. meliloti rpoH1, rpoH2 and rpoH1 rpoH2 mutants during heat shock and stationary phase growth. Under these conditions, expression of over 300 genes is dependent on rpoH1 and rpoH2. Gene expression profiling of Sinorhizobium meliloti Rm1021 and its isogenic rpoH1, rpoH2, and rpoH1rpoH2 mutants, subjected to heat shock or stationary phase growth, was performed using custom Affymetrix GeneChips
2012-10-02 | E-GEOD-36186 | biostudies-arrayexpress
Project description:Increased exposure to heat-stress leads to an increasingly altered transcriptome in Caenorhabditis elegans. It is however unclear how the recovery from heat-stress progresses after increased heat-stress exposures. Hence, we exposed populations of the N2 strain to a 2, 3, 4, or 6 hour heat-shock of 35 degrees Celsius and took samples from 1 - 4 hours after termination of stress. This experiment was conduced in three biological replicates.
2019-11-12 | E-MTAB-7948 | biostudies-arrayexpress
Project description:After measuring the transcriptional response to increasing exposure of Caenorhabditis elegans N2 to 35 degrees Celsius, we wondered how recovery from heat-stress would progress. Hence, we exposed populations of the N2 strain to a 2 hour heat-shock of 35 degrees Celsius and took samples from 0 - 7 hours after termination of stress. This experiment was conduced in three biological replicates.
2023-05-30 | E-MTAB-7947 | biostudies-arrayexpress
Project description:Environmental conditions are quite effective during propagation and industrial application of Baker’s yeast (Saccharomyces cerevisiae). The change of temperature is one of the most important conditions which affects the dough-leaving capacity of yeast cells. Accordingly, heat changes play an essential role in the commercial and economic impact of the yeast. Recent technologies in genomics have been used for analysis of global gene expression profiles such as microarray and RNA sequencing to solve the problems related with industrial application of yeast. Hereby, the aim of this study is to explore the effects of heat stresses on global gene expression profiles and to identify the candidate genes for the heat stress response in commercial baker’s yeast by using microarray technology and comparative statistical data analyses. Data from all hybridizations and array normalization were analyzed using the GeneSpringGX 12.1 (Agilent) and the R 2.15.2 program language. In the analysis of this dataset, all required statistical methods are performed comparatively in each step and the best performed ones are used in further computations. Hence, as the first step of the analyses, different background normalization algorithms such as MAS5.0, RMA, MBEI and GC-RMA were applied and the algorithm which gives the most accurate findings was chosen for the normalization procedure. As a result, expression values, computed from CEL files, were processed by Robust Multiarray Analysis (RMA) which is the selected procedure for the normalization of the systematic differences between samples. In order to determine differentially expressed genes under heat stress treatments, two different methods, namely, the fold-change and the hypothesis testing approaches are executed. In the fold-change method, various cut-off values are implemented while different multiple testing procedures are performed for the hypothesis testing. Under the heat shock and temperature-shift stress conditions, up/down regulated differentially expressed probes were functionally categorized into the different groups via the cluster analyses. Transcriptome changes under the heat shock and temperature-shift stress treatments show that the number of differentially up-regulated genes among the heat shock proteins (HSPs) and transcription factors (TFs) changed significantly. Consequently, the identification of thousands of genes related with heat stress treatments via microarray technology and comparative statistical analysis resulted in the creation of big picture which provides the understanding of the importance for the baker’s yeast industrial applications.
2017-01-30 | E-MTAB-3459 | biostudies-arrayexpress
Project description:aThese experiments address the effects of depleting Hsp90 upon the transcriptome of the major fungal pathogen, Candida albicans, during the heat shock response. The data show that key virulence factors are regulated in response to heat shock, and that Hsp90 exerts major effects on the heat shock transcriptome.a
2016-05-16 | E-MTAB-4075 | biostudies-arrayexpress
Project description:To understand how microRNAs are involved in stress response, we examined their expression changes in C. elegans animals that were exposed to stress conditions, including heat shock, oxidation, hypoxia and starvation. Total RNAs were purified from young adult animals that were exposed to each stress, and used for cDNA library preparation for small RNAs. In this experiment, spe-9(hc88), a temperature sensitive sterile mutant, that were cultured at 23dC, was used in order to avoid the effect from developing embryos. Stress conditions we examined include: Heat shock (32M-BM-0C, 6 hrs), Recovery from heat shock (6 hrs recovery at 23M-BM-0C after heat shock treatment at 32M-BM-0C for 6 hrs), Hypoxia (0.01%, 6 hrs), Oxidation (Juglone 750 M-NM-<M, 6 hrs), Starvation (complete food deprivation, 12 hrs). In addition to these stress conditions, RNAs were prepared from normally cultured, untreated animals at three time points, 0 hr (baseline), 6 hrs (as controls for heat shock, hypoxia and oxidation) and 12 hrs (as controls for heat shock recovery and starvation) after starting stress exposure. These cDNA libraries established were sequenced with Illumina Genome Analyzer II.
2012-02-04 | E-GEOD-35529 | biostudies-arrayexpress