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 4M-BM-0C. A set of genes differentially expressed in rcf1-1 with or without cold stress are identified. Fourteen-day-old seedlings of Arabidopsis thaliana wild type (Columbia gl1 expressing CBF2::LUC transgene) and rcf1-1 mutant seedlings subjected to cold stress at 4M-BM-0C for 0, 12, and 24 h were used for total RNA extraction and hybridizations with Affymetrix ATH1 GeneChips. There are two biological replicate per genotype.
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.
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.
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.
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.
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.
Project description:Biotic and abiotic stresses limit agricultural yields, and plants are often simultaneously exposed to multiple stresses. Combinations of stresses such as heat and drought or cold and high light intensity, have profound effects on crop performance and yeilds To analyze such responses, we initially compared transcriptome changes in ten Arabidopsis thaliana ecotypes using cold, heat, high light, salt and flagellin treatments as single stress factors or their double combinations. Arabidopsis thaliana plants of ecotypes (Col, Ler, C24, Cvi, Kas1, An1, Sha, Kyo2, Eri and Kond) were subjected to the following stress treatments: Salt, Cold, Heat, High Light (HL), Salt+Heat, Salt+HL, Cold+HL, Heat+HL, as well as FLG (Flagellin, flg22 peptide), Cold+FLG, Heat+FLG
Project description:To understand the role of GCN2 in stress response, the total transcript and translation state were compared between Arabidopsis thaliana wild type (ecotype Landsberg erecta) and gcn2 (Genetrap line GT8359, Cold Spring Harbor Laboratory) seedlings with or without herbicide chlorosufuron treatment RNA was fractionated using sucrose gradients into polysomal and nonpolysomal RNAs. We also determined overall total transcript levels. We used Affymetrix ATH1 microarrays.
