Differential SAGE analysis in Arabidopsis uncovers increased transcriptome complexity in response to low temperature (original) (raw)
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Gene Expression Phenotypes of Arabidopsis Associated with Sensitivity to Low Temperatures
Plant Physiology, 2003
Chilling is a common abiotic stress that leads to economic losses in agriculture. By comparing the transcriptome of Arabidopsis under normal (22°C) and chilling (13°C) conditions, we have surveyed the molecular responses of a chillingresistant plant to acclimate to a moderate reduction in temperature. The mRNA accumulation of approximately 20% of the approximately 8,000 genes analyzed was affected by chilling. In particular, a highly significant number of genes involved in protein biosynthesis displayed an increase in transcript abundance. We have analyzed the molecular phenotypes of 12 chilling-sensitive mutants exposed to 13°C before any visible phenotype could be detected. The number and pattern of expression of chilling-responsive genes in the mutants were consistent with their final degree of chilling injury. The mRNA accumulation profiles for the chilling-lethal mutants chs1, chs2, and chs3 were highly similar and included extensive chilling-induced and mutant-specific alterations in gene expression. The expression pattern of the mutants upon chilling suggests that the normal function of the mutated loci prevents a damaging widespread effect of chilling on transcriptional regulation. In addition, we have identified 634 chilling-responsive genes with aberrant expression in all of the chilling-lethal mutants. This reference gene list, including genes related to lipid metabolism, chloroplast function, carbohydrate metabolism and free radical detoxification, represents a potential source for genes with a critical role in plant acclimation to suboptimal temperatures. The comparison of transcriptome profiles after transfer of Arabidopsis plants from 22°C to 13°C versus transfer to 4°C suggests that quantitative and temporal differences exist between these molecular responses. ;fax919 -541-8585.
A global survey of gene regulation during cold acclimation in Arabidopsis thaliana
PLoS genetics, 2005
Many temperate plant species such as Arabidopsis thaliana are able to increase their freezing tolerance when exposed to low, nonfreezing temperatures in a process called cold acclimation. This process is accompanied by complex changes in gene expression. Previous studies have investigated these changes but have mainly focused on individual or small groups of genes. We present a comprehensive statistical analysis of the genome-wide changes of gene expression in response to 14 d of cold acclimation in Arabidopsis, and provide a large-scale validation of these data by comparing datasets obtained for the Affymetrix ATH1 Genechip and MWG 50-mer oligonucleotide whole-genome microarrays. We combine these datasets with existing published and publicly available data investigating Arabidopsis gene expression in response to low temperature. All data are integrated into a database detailing the cold responsiveness of 22,043 genes as a function of time of exposure at low temperature. We concentr...
Plant physiology, 2006
The whole-genome response of Arabidopsis (Arabidopsis thaliana) exposed to different types and durations of abiotic stress has now been described by a wealth of publicly available microarray data. When combined with studies of how gene expression is affected in mutant and transgenic Arabidopsis with altered ability to transduce the low temperature signal, these data can be used to test the interactions between various low temperature-associated transcription factors and their regulons. We quantized a collection of Affymetrix microarray data so that each gene in a particular regulon could vote on whether a cis-element found in its promoter conferred induction (+1), repression (-1), or no transcriptional change (0) during cold stress. By statistically comparing these election results with the voting behavior of all genes on the same gene chip, we verified the bioactivity of novel cis-elements and defined whether they were inductive or repressive. Using in silico mutagenesis we identif...
2016
Phenotypic variation in stress response has been widely observed within species. This variation is an adaptive response to local climates and is controlled by gene sequence variation and especially by variation in expression at the transcriptome level. Plants from contrasting climates are thus expected to have different patterns in gene expression. Acclimation, a pre-exposure to sub-lethal temperature before exposing to extreme high temperature, is an important adaptive mechanism of plant survival. We are interested to evaluate the gene expression difference to heat stress for plants from contrasting climates and the role of acclimation in altering their gene expression pattern. Natural Arabidopsis thaliana plants from low elevation mediterranean and high elevation montane climates were exposed to two heat treatments at the bolting stage: a) 45 oC: a direct exposure to 45oC heat; b) 38/45 oC: an exposure to 45oC heat after a 38oC acclimation treatment. Variation in overall gene expr...
Predicting transcriptional responses to cold stress across plant species
2020
ABSTRACTAlthough genome sequence assemblies are available for a growing number of plant species, gene expression responses to stimuli have been catalogued for only a subset of these species. Many genes show altered transcription patterns in response to abiotic stresses. However, orthologous genes in related species often exhibit different responses to a given stress. Accordingly, data on the regulation of gene expression in one species are not reliable predictors of orthologous gene responses in a related species. Here, we trained a supervised classification algorithm to identify genes that transcriptionally respond to cold stress. A model trained with only features calculated directly from genome assemblies exhibited only modest decreases in performance relative to models trained using genomic, chromatin, and evolution/diversity features. Models trained with data from one species successfully predicted which genes would respond to cold stress in other related species. Cross-species...
Transcriptional Regulation of Cold Stress Tolerance in Plants. Present Status and Future Prospects
Plants are often subjected to a broad range of environmental stresses such as drought, cold, salinity, heat, heavy metals, and other abiotic stresses. These stresses critically influence plant growth, development, and productivity. Among various abiotic stresses, cold (chilling or low temperature) is one of the major hindrances to crop productivity. In response to cold stress, plants have evolved various types of mechanisms that involve altered physiological, biochemical, and molecular processes to deal with cold stress. Advances in the fields of genetics and molecular biology have led to the development of various tools for the analysis of molecular networks involved in a certain trait. Nowadays, the advent of “OMICS” technology has been widely applied to understand the complex genetic nature of cold stress tolerance in plants. Being a complex trait, cold stress in plants is governed by more than one gene, including transcription factors that facilitate plants' survival in adve...
Functional & Integrative Genomics, 2006
A comparative analysis of gene expression profiles during cold acclimation and deacclimation is necessary to elucidate the molecular mechanisms of cold stress responses in higher plants. We analyzed gene expression profiles in the process of cold acclimation and deacclimation (recovery from cold stress) using two microarray systems, the 7K RAFL cDNA microarray and the Agilent 22K oligonucleotide array. By both microarray analyses, we identified 292 genes up-regulated and 320 genes down-regulated during deacclimation, and 445 cold up-regulated genes and 341 cold down-regulated genes during cold acclimation. Many genes up-regulated during deacclimation were found to be down-regulated during cold acclimation, and vice versa. The genes up-regulated during deacclimation were classified into (1) regulatory proteins involved in further regulation of signal transduction and gene expression and (2) functional proteins involved in the recovery process from cold-stress-induced damages and plant growth. We also applied expression profiling studies to identify the key genes involved in the biosynthesis of carbohydrates and amino acids that are known to play important roles in cold acclimation. We compared genes that are regulated during deacclimation with those regulated during rehydration after dehydration to discuss the similarity and difference of each recovery process.