A Global Survey of Gene Regulation during Cold Acclimation in Arabidopsis thaliana

Abstract

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 concentrate our functional analysis on global changes marking relevant pathways or functional groups of genes. These analyses provide a statistical basis for many previously reported changes, identify so far unreported changes, and show which processes predominate during different times of cold acclimation. This approach offers the fullest characterization of global changes in gene expression in response to low temperature available to date.

Synopsis

Freezing tolerance is an important determinant of geographical distribution of plant species, and freezing damage in crop plants leads to severe losses in agriculture. Many temperate plants increase their freezing tolerance during exposure to low, but nonfreezing temperatures, a process known as cold acclimation. Freezing tolerance and cold acclimation are complex, quantitative genetic traits. The number and functional roles of the responsible genes are not known for any plant species. Using the model plant Arabidopsis thaliana, which is moderately freezing tolerant and able to cold acclimate, the global regulation of gene expression during exposure to 4 °C for 14 d was analyzed by microarray hybridization. For validation of gene expression data, triplicate biological samples were hybridized to two different oligonucleotide arrays. Results from the two platforms showed good agreement, indicating the reliability of the measurements. The authors combined their data with all publicly available data on cold-regulated gene expression in A. thaliana to compile a database detailing the cold responsiveness of 22,043 genes as a function of exposure time. In addition, thorough statistical analysis was used to identify metabolic pathways and physiological processes that are predominantly involved in the plant cold-acclimation process.