ABSTRACT: HeLa cells were treated with 100 mM NaCl during 2h versus untreated. HeLa cells treated with 100 mM NaCl during 2h versus HeLa cells treated with 100 mM NaCl during 2h after pre-treatment with 10 μM SB203580 for 30 min. Alternative splicing is a crucial mechanism for gene regulation that is modulated in response to a wide range of extracellular stimuli. Stress-activated protein kinases (SAPKs) play a key role in controlling several steps of mRNA biogenesis. Here, we show that osmostress has a major impact on the regulation of alternative splicing (AS), which is partly mediated through the action of the p38 SAPK.
Project description:Cells have the ability to respond and adapt to environmental changes through the activation of stress-activated protein kinases (SAPKs). Although it has been shown that p38 SAPK signalling participates in the regulation of gene transcription, there is not a comprehensive genome-wide transcription study reported to date describing neither the role of the p38 SAPK on the immediate response to stress and its kinetics nor a comparative vision of the genes that respond to different stimuli that activate the p38 SAPK. Here, we report a whole genome microarray analyses on wild type mouse embryonic fibroblasts (MEFs) treated with different p38 SAPK activators, namely the physiological cytokine TNF alpha, the protein synthesis inhibitor antibiotic anisomycin and osmostress. In addition, we have analysed the contribution of p38 alpha the major isoform of p38 present in MEF cells, in the overall transcription in response to those stimuli by both, the inhibition of p38 SAPK by using a chemical inhibitor (SB203580) and the use of p38 alpha knock out MEFs. Furthermore, we have analysed the kinetics of the gene expression response to osmostress by the p38 SAPK. Two samples have been analysed; wild type Mouse embryonic fibroblast (WT-MEFs) and MAPK p38alfa knock out MEFs (KO-MEFs) respectively treated with 11 and 4 different treatments. Each experiment was performed in duplicate and referenced to a pool of two non-treated WT MEFs.
Project description:Alternative splicing is a crucial mechanism for gene regulation that is modulated in response to a wide range of extracellular stimuli. Stress-activated protein kinases (SAPKs) play a key role in controlling several steps of mRNA biogenesis. Here, we show that osmostress has a major impact on the regulation of alternative splicing (AS), which is partly mediated through the action of the p38 SAPK. Remarkably, a splicing network analysis revealed a functional connection between p38 and the spliceosome component SKIIP. Depletion of SKIIP abolished a significant part of the p38-mediated alternative splicing.
Project description:Cells have the ability to respond and adapt to environmental changes through the activation of stress-activated protein kinases (SAPKs). Although it has been shown that p38 SAPK signalling participates in the regulation of gene transcription, there is not a comprehensive genome-wide transcription study reported to date describing neither the role of the p38 SAPK on the immediate response to stress and its kinetics nor a comparative vision of the genes that respond to different stimuli that activate the p38 SAPK. Here, we report a whole genome microarray analyses on wild type mouse embryonic fibroblasts (MEFs) treated with different p38 SAPK activators, namely the physiological cytokine TNF alpha, the protein synthesis inhibitor antibiotic anisomycin and osmostress. In addition, we have analysed the contribution of p38 alpha the major isoform of p38 present in MEF cells, in the overall transcription in response to those stimuli by both, the inhibition of p38 SAPK by using a chemical inhibitor (SB203580) and the use of p38 alpha knock out MEFs. Furthermore, we have analysed the kinetics of the gene expression response to osmostress by the p38 SAPK.
Project description:Salt responsive genes were identified in chinese willow (Salix matsudana) after the plants were treated with 100 mM NaCl. for 48 hours We used microarrays to identify genes responsible for combating salt stress. Those up-regulated during the NaCl treatment may protect the plants from damages caused by salt stress.
Project description:Using data from microarray experiments, we investigated the transcriptional changes in evolved and ancestor D. vulgaris strains. gene expression changes in evolved salt-stressed DvH strain (ES, evolved in LS4D + 100 mM NaCl for 1200 generations), evolved control DvH strain (EC, evolved in LS4D for 1200 generations) and ancestor DvH strain grown in non-stress (LS4D), low salt stress (LS4D + 100 mM NaCl) or high salt stress (LS4D + 250 mM NaCl) conditions
Project description:To analyze the molecular function of ethanol in salt stress responses in Arabidopsis, we conducted microarray analysis using 4-day-old plants, which were treated with 0.3 % ethanol or water for 24 h, and then treated with or without 100 mM NaCl for 2 h
Project description:A comparative transcriptomic study of the impact of salt toxicity on rice plant (Oryza sativa L.; cv 'I Kong Pao') after short term (48 hours) exposure to NaCl (200 mM) or Na2SO4 (100 mM). Twenty five days old rice seedlings were exposed to 0, 200 mM NaCl or 100 mM Na2SO4 for 48 hours in hydroponic culture. Comparison between control and salt-stressed plants were done at the shoot and the root levels. The essays were replicated twice on two independent plant cultures.
Project description:To analyze the molecular function of HDAC inhibitors in salt stress responses in Arabidopsis, we conducted microarray analysis using 4-day-old plants, which were treated with 1 μM Ky-9 or Ky-72 or water for 24 h, and then treated with or without 100 mM NaCl for 2 h
Project description:We will use high-throughput sequencing technology to study gene expression under NaCl treatment, screen for differential expressed genes, and then analyze the gene regulation features. Nitraria sibirica Pall. seedlings were treated by 0, 100 and 400 mM NaCl with 3 replicates,and the leaves were harvested after treated 3 days. Extracting total RNA of leaves and then sequencing by Illumina HiSeq 2000 sequencing platform. Our study provides a basis for the study of salt-tolerant gene resources in Nitraria sibirica Pall.
Project description:A549 cells were transfected with 100 pmol DNA probes complementary to the back-splice site of circITGB6 or PDPN 3’UTR region. 24 h later, cells were washed with PBS and lysed with the lysis buffer (150 mM NaCl, 20 mM Tris-HCl, pH 7.5, 1.5 mM MgCl2, 0.5% NP-40, 0.5% Triton X-100, 10% glycerol, RNase inhibitors (Thermo Scientific), protease and phosphatase inhibitor cocktails). Pre-treated streptavidin magnetic beads were incubated with cell lysates at 4°C for 1 h, followed by washing five times with the washing buffer (20 mM Tri-HCl, pH7.5, 1 mM EDTA and 450 mM NaCl) and elution with Laemmli sample buffer. The circITGB6- or PDPN mRNA- interacting proteins were subjected to SDS-PAGE and visualized by coomassie blue staining or immunoblot analysis. Protein bands were excised and identified by LC-MS/MS mass spectrometry and Proteome Discoverer software (version 1.4; Thermo Scientific).