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Genome-wide identification of mis-spliced/intron-retained transcripts in Arabidopsis thaliana rcf1-1 mutant plants under normal growth conditions as determined by tiling array analysis.

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE41377 | GEO | 2013/02/25

SECONDARY ACCESSION(S): PRJNA176717

REPOSITORIES: GEO

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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.

2013-02-25 | GSE41378 | GEO

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.

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

Genome-wide identification of mis-spliced/intron-retained transcripts in Arabidopsis thaliana rcf1-1 mutant plants under normal growth conditions as determined by tiling array analysis.

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

RNA-DIRECTED DNA METHYLATION 4 modulates cold stress resistance in Arabidopsis through the C-REPEAT-BINDING FACTOR-mediated pathway [Agilent]

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

RNA-DIRECTED DNA METHYLATION 4 modulates cold stress resistance in Arabidopsis through the C-REPEAT-BINDING FACTOR-mediated pathway [Affymetrix]

2016-06-30 | GSE63185 | GEO

RNA-DIRECTED DNA METHYLATION 4 modulates cold stress resistance in Arabidopsis through the C-REPEAT-BINDING FACTOR-mediated pathway [Affymetrix]

2016-06-30 | E-GEOD-63185 | biostudies-arrayexpress

RNA-DIRECTED DNA METHYLATION 4 modulates cold stress resistance in Arabidopsis through the C-REPEAT-BINDING FACTOR-mediated pathway [Agilent]

2016-06-30 | E-GEOD-63184 | biostudies-arrayexpress

Ribosomes act as cryosensors in plants

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

The rcf1-1 mutation affects global gene expression in Arabidopsis thaliana with or without cold stress.

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

Brassinosteroids participate in the control of basal and acquired freezing tolerance of plants

Project description:Brassinosteroids (BRs) are growth-promoting plant hormones that play a role in abiotic stress responses, but molecular modes that enable this activity remain largely unknown. Here we show that BRs participate in the regulation of freezing tolerance. BR signaling-defective mutants of Arabidopsis thaliana were hypersensitive to freezing before and after cold acclimation. The constitutive activation of BR signaling, in contrast, enhanced freezing resistance. Evidence is provided that the BR-controlled basic helix–loop–helix transcription factor CESTA (CES) can contribute to the constitutive expression of the C-REPEAT/DEHYDRATION-RESPONSIVE ELEMENT BINDING FACTOR (CBF) transcriptional regulators that control cold responsive (COR) gene expression. In addition, CBF-independent classes of BR-regulated COR genes are identified that are regulated in a BR- and CES-dependent manner during cold acclimation. A model is presented in which BRs govern different cold-responsive transcriptional cascades through the posttranslational modification of CES and redundantly acting factors. This contributes to the basal resistance against freezing stress, but also to the further improvement of this resistance through cold acclimation. We used microarray data to investigate the contribution of different pathways to cold tolerance of Arabidopsis thaliana .

2016-09-10 | GSE86605 | GEO

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