Genome-wide identification of mis-spliced/intron-retained transcripts in Arabidopsis thaliana rcf1-1 mutant plants under cold stress as determined by tiling array analysis.
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE41378 | GEO | 2013/02/25
SECONDARY ACCESSION(S): PRJNA176718
REPOSITORIES: GEO
Similar Datasets
Project description:Cold stress is one of the most severe environmental conditions which cause huge losses in crop production worldwide. We identified a DEAD box RNA helicase, RCF1 (Regulator of CBF gene expression 1) that controls pre-mRNA splicing of cold-stress-responsive genes including positive and negative regulators of CBF genes. We used whole genome tiling array analysis under normal growth conditions to identify transcripts which are mis-spliced/intron-retained in rcf1-1.
2013-02-25 | GSE41377 | GEO
Project description:Cold stress is one of the most severe environmental conditions which cause huge losses in crop production worldwide. We identified a DEAD box RNA helicase, RCF1 (Regulator of CBF gene expression 1) that controls pre-mRNA splicing of cold-stress-responsive genes including positive and negative regulators of CBF genes. We used whole genome tiling array analysis under cold stress to identify transcripts which are mis-spliced/intron-retained in rcf1-1. Fourteen-day-old wild type and rcf1-1 seedlings grown on MS agar medium (1x MS salts, 2% sucrose, 0.6% agar, pH 5.7) were subjected to cold stress at 4M-BM-0C for 12 h. Total RNA was extracted with Trizol reagent (Invitrogen) and synthesized into double-stranded DNA that was hybridized to whole genome tiling arrays (Affymetrix Arabidopsis Tiling1.0R). All hybridizations were performed with 3 biological replicates.
2013-02-25 | E-GEOD-41378 | biostudies-arrayexpress
Project description:Cold stress is one of the most severe environmental conditions which cause huge losses in crop production worldwide. We identified a DEAD box RNA helicase, RCF1 (Regulator of CBF gene expression 1) that controls pre-mRNA splicing of cold-stress-responsive genes including positive and negative regulators of CBF genes. We used whole genome tiling array analysis under normal growth conditions to identify transcripts which are mis-spliced/intron-retained in rcf1-1. Fourteen-day-old wild type and rcf1-1 seedlings grown on MS agar medium (1x MS salts, 2% sucrose, 0.6% agar, pH 5.7) under normal conditions were harvested for total RNA isolation. RNA was extracted with Trizol reagent (Invitrogen) and synthesized into double-stranded DNA that was hybridized to whole genome tiling arrays (Affymetrix Arabidopsis Tiling1.0R). All hybridizations were performed with 3 biological replicates.
2013-02-25 | E-GEOD-41377 | biostudies-arrayexpress
Project description:The C-REPEAT-BINDING FACTOR (CBF) pathway has important roles in plant responses to cold stress. Previous research documented that constitutively expressed upstream transcription factors are activated by cold stress to induce the expression of CBF genes and the resulting CBF proteins trigger the expression of downstream cold responsive genes that confer freezing tolerance. In the present study, we found that dysfunction of RNA-DIRECTED DNA METHYLATION 4 (RDM4), which encodes a protein that associates with RNA polymerases Pol IV and Pol V as well as Pol II, and is required for RNA-directed DNA methylation (RdDM) and proper plant development in Arabidopsis, reduced chilling and freezing tolerance in Arabidopsis as evidenced by decreased survival and increased electrolyte leakage under cold stress conditions. CBFs and CBF regulon genes were down-regulated in rdm4 but not nrpe1 (the largest subunit of PolV) mutant plants, suggesting that the role of RDM4 in cold stress responses is independent of the RdDM pathway. Overexpression of RDM4 increased the expression of CBFs and CBF regulon genes and decreased cold-induced membrane injury. The rdm4 mutants exhibited decreased antioxidant enzyme activities and increased accumulation of reactive oxygen species. Microarray analysis indicated that a great proportion of genes affected by rdm4 overlapped with those affected by CBF2 and CBF3 in Arabidopsis. Chromatin immunoprecipitation (ChIP) results suggested that RDM4 is important for Pol II occupancy at the promoters of CBF genes but not the promoters of up-stream regulators of CBFs. Together, these data indicate that RDM4 acts as a component of a Pol II transcription complex that regulates CBF gene expression and cold stress resistance in Arabidopsis.
2016-06-30 | GSE63184 | GEO
Project description:The C-REPEAT-BINDING FACTOR (CBF) pathway has important roles in plant responses to cold stress. Previous research documented that constitutively expressed upstream transcription factors are activated by cold stress to induce the expression of CBF genes and the resulting CBF proteins trigger the expression of downstream cold responsive genes that confer freezing tolerance. In the present study, we found that dysfunction of RNA-DIRECTED DNA METHYLATION 4 (RDM4), which encodes a protein that associates with RNA polymerases Pol IV and Pol V as well as Pol II, and is required for RNA-directed DNA methylation (RdDM) and proper plant development in Arabidopsis, reduced chilling and freezing tolerance in Arabidopsis as evidenced by decreased survival and increased electrolyte leakage under cold stress conditions. CBFs and CBF regulon genes were down-regulated in rdm4 but not nrpe1 (the largest subunit of PolV) mutant plants, suggesting that the role of RDM4 in cold stress responses is independent of the RdDM pathway. Overexpression of RDM4 increased the expression of CBFs and CBF regulon genes and decreased cold-induced membrane injury. The rdm4 mutants exhibited decreased antioxidant enzyme activities and increased accumulation of reactive oxygen species. Microarray analysis indicated that a great proportion of genes affected by rdm4 overlapped with those affected by CBF2 and CBF3 in Arabidopsis. Chromatin immunoprecipitation (ChIP) results suggested that RDM4 is important for Pol II occupancy at the promoters of CBF genes but not the promoters of up-stream regulators of CBFs. Together, these data indicate that RDM4 acts as a component of a Pol II transcription complex that regulates CBF gene expression and cold stress resistance in Arabidopsis.
2016-06-30 | GSE63185 | GEO
Project description:The C-REPEAT-BINDING FACTOR (CBF) pathway has important roles in plant responses to cold stress. Previous research documented that constitutively expressed upstream transcription factors are activated by cold stress to induce the expression of CBF genes and the resulting CBF proteins trigger the expression of downstream cold responsive genes that confer freezing tolerance. In the present study, we found that dysfunction of RNA-DIRECTED DNA METHYLATION 4 (RDM4), which encodes a protein that associates with RNA polymerases Pol IV and Pol V as well as Pol II, and is required for RNA-directed DNA methylation (RdDM) and proper plant development in Arabidopsis, reduced chilling and freezing tolerance in Arabidopsis as evidenced by decreased survival and increased electrolyte leakage under cold stress conditions. CBFs and CBF regulon genes were down-regulated in rdm4 but not nrpe1 (the largest subunit of PolV) mutant plants, suggesting that the role of RDM4 in cold stress responses is independent of the RdDM pathway. Overexpression of RDM4 increased the expression of CBFs and CBF regulon genes and decreased cold-induced membrane injury. The rdm4 mutants exhibited decreased antioxidant enzyme activities and increased accumulation of reactive oxygen species. Microarray analysis indicated that a great proportion of genes affected by rdm4 overlapped with those affected by CBF2 and CBF3 in Arabidopsis. Chromatin immunoprecipitation (ChIP) results suggested that RDM4 is important for Pol II occupancy at the promoters of CBF genes but not the promoters of up-stream regulators of CBFs. Together, these data indicate that RDM4 acts as a component of a Pol II transcription complex that regulates CBF gene expression and cold stress resistance in Arabidopsis. Two-week-old seedlings of rdm4 and C24 WT plant were subjected to chilling treatment for 0, 3, and 48 h treatments.Plant materials were then collected for RNA extraction.
2016-06-30 | E-GEOD-63185 | biostudies-arrayexpress
Project description:The C-REPEAT-BINDING FACTOR (CBF) pathway has important roles in plant responses to cold stress. Previous research documented that constitutively expressed upstream transcription factors are activated by cold stress to induce the expression of CBF genes and the resulting CBF proteins trigger the expression of downstream cold responsive genes that confer freezing tolerance. In the present study, we found that dysfunction of RNA-DIRECTED DNA METHYLATION 4 (RDM4), which encodes a protein that associates with RNA polymerases Pol IV and Pol V as well as Pol II, and is required for RNA-directed DNA methylation (RdDM) and proper plant development in Arabidopsis, reduced chilling and freezing tolerance in Arabidopsis as evidenced by decreased survival and increased electrolyte leakage under cold stress conditions. CBFs and CBF regulon genes were down-regulated in rdm4 but not nrpe1 (the largest subunit of PolV) mutant plants, suggesting that the role of RDM4 in cold stress responses is independent of the RdDM pathway. Overexpression of RDM4 increased the expression of CBFs and CBF regulon genes and decreased cold-induced membrane injury. The rdm4 mutants exhibited decreased antioxidant enzyme activities and increased accumulation of reactive oxygen species. Microarray analysis indicated that a great proportion of genes affected by rdm4 overlapped with those affected by CBF2 and CBF3 in Arabidopsis. Chromatin immunoprecipitation (ChIP) results suggested that RDM4 is important for Pol II occupancy at the promoters of CBF genes but not the promoters of up-stream regulators of CBFs. Together, these data indicate that RDM4 acts as a component of a Pol II transcription complex that regulates CBF gene expression and cold stress resistance in Arabidopsis. Two-week-old seedlings of 35S::RDM4 and Col WT plant were subjected to chilling treatment for 0, 3, and 48 h treatments.Plant materials were then collected for RNA extraction.
2016-06-30 | E-GEOD-63184 | biostudies-arrayexpress
Project description:Cold temperatures are a threat to temperate plants, and Arabidopsis thaliana has acquired an adaptive gene expression network controlled by CBF transcription factors. The CBFs are sufficient to enable plants to survive otherwise lethal subzero temperatures. Constitutive CBF expression causes delayed flowering and stunted growth, and plants have evolved the ability to restrict CBF expression to occur only in the cold. This allows plants to anticipate likely freezing events and selectively deploy cold tolerance. The mechanism by which cold stress is sensed is however unknown. Here we show that protein translation rates in plants are proportional to temperature, and reduced translation rates trigger a rise in intracellular free calcium that activates the CAMTA transcription factors, and these directly activate cold-induced gene expression.
2021-02-11 | GSE166543 | GEO
Project description:Cold stress is one of the most severe environmental conditions which cause huge losses in crop production worldwide. We identified an essential regulator of cold-responsive genes and used the Affymetrix whole-genome arrays to define downstream targets of this important protein. We used the microarrays to reveal the effect of rcf1-1 mutation on global gene expression with or without cold stress at 4°C. A set of genes differentially expressed in rcf1-1 with or without cold stress are identified.
2013-02-25 | GSE39090 | GEO
Project description:<p>Cold stress negatively affects maize (<em>Zea mays</em> L.) growth, development and yield. Metabolic adjustments contribute to the adaptation of maize under cold stress. We show here that the transcription factor INDUCER OF CBF EXPRESSION 1 (ZmICE1) plays a prominent role in reprogramming amino acid metabolome and <em>COLD-RESPONSIVE</em> (<em>COR</em>) genes during cold stress in maize. Derivatives of amino acids glutamate/asparagine (Glu/Asn) induce a burst of mitochondrial reactive oxygen species, which suppress the cold-mediated induction of <em>DEHYDRATION RESPONSE ELEMENT-BINDING PROTEIN 1</em> (<em>ZmDREB1</em>) genes and impair cold tolerance. ZmICE1 blocks this negative regulation of cold tolerance by directly repressing the expression of the key Glu/Asn biosynthesis genes, <em>ASPARAGINE SYNTHETASEs</em>. Moreover, ZmICE1 directly regulates the expression of <em>DREB1s</em>. Natural variation at the <em>ZmICE1</em> promoter determines the binding affinity of the transcriptional activator ZmMYB39, a positive regulator of cold tolerance in maize, resulting in different degrees of <em>ZmICE1</em> transcription and cold tolerance across inbred lines. This study thus unravels a mechanism of cold tolerance in maize and provides potential targets for engineering cold-tolerant varieties.</p>
2022-10-31 | MTBLS4404 | MetaboLights