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.

Advances in physiological and molecular aspects of plant cold tolerance

“…Cold acclimation affects the expression of a huge number of genes by either up-or down-regulations (Hannah et al 2005). Furthermore, there is crosstalk between the response of different abiotic stresses and some of the genes up-regulated by drought or salt stress (Thomashow 1999;Seki et al 2003;Zhao & Zhu 2016).…”

Comparative analysis of seed transcriptomes of ambient ozone-fumigated 2 different rice cultivars

“…43 One upregulated gene bHLH (LOC_Os11 g25560) in Takanari is similar to AtbHLH62 in Arabidopsis, which is induced by low temperature. 44 Moreover, our microarray data released that OsNAC8 (ONAC074, LOC_Os01 g15640) homologous (71%) to wheat TaNAC8 was upregulated in Takanari. 45 TaNAC8 is expressed significantly in developing wheat seeds, by pathogen infection, JA treatment, and ET but not in stems and flowers, by SA and abscisic acid (ABA).…”

Cold tolerance in cypress (Cupressus sempervirens L.): a physiological and molecular study

“…Low-temperature resistance in plants is a very complex trait, involving many different metabolic pathways and cell compartments (Hannah et al 2005). The main effect of cold damage in plants is the disruption of cellular membranes and structures due to the formation of extracellular ice crystals which induce a rapid loss of water and consequent desiccation (Pearce 2001;Larcher 2003).…”