Genome-wide transcriptional profiles during temperature and oxidative stress reveal coordinated expression patterns and overlapping regulons in rice

Abstract

Genome wide transcriptional changes by cold stress, heat stress and oxidative stress in rice seedlings were analyzed. Heat stress resulted in predominant changes in transcripts of heat shock protein and heat shock transcription factor genes, as well as genes associated with synthesis of scavengers of reactive oxygen species and genes that control the level of sugars, metabolites and auxins. Cold stress treatment caused differential expression of transcripts of various transcription factors including desiccation response element binding proteins and different kinases. Transcripts of genes that are part of calcium signaling, reactive oxygen scavenging and diverse metabolic reactions were differentially expressed during cold stress. Oxidative stress induced by hydrogen peroxide treatment, resulted in significant up-regulation in transcript levels of genes related to redox homeostasis and down-regulation of transporter proteins. ROS homeostasis appeared to play central role in response to temperature extremes. The key transcription factors that may underlie the concerted transcriptional changes of specific components in various signal transduction networks involved are highlighted. Co-ordinated expression pattern and promoter architectures based analysis (promoter models and overrepresented transcription factor binding sites) suggested potential regulons involved in stress responses. A considerable overlap was noted at the level of transcription as well as in regulatory modules of differentially expressed genes.

Figure 1. Global gene expression pattern in response to CS, HS and OS.

A. Representation of the number of differentially regulated genes following CS (CS1 h and CS5 h), HS (HS10 min and HS30 min) and OS (OS1 h and OS4 h). Numbers given in brackets represent the total number of differentially expressed genes in CS1 h, CS5 h, HS10 min, HS30 min, OS1 h and OS4 h respectively. B. Differentially expressed genes for a stress condition (i.e. the data from the two time points for one stress is considered as a condition). C. Hierarchical cluster image showing differentially expressed genes for stress conditions depicted in 1B. Detailed gene lists are provided in Data S1.

Figure 2. Functional classification of up-regulated genes.

Significant GO/functional categories enriched for the up-regulated genes during CS, HS and OS are shown in the form of a pie chart. For details refer to the Data S2.

Figure 3. Functional classification of down-regulated genes.

Significant GO/functional categories enriched for the down-regulated genes during CS, HS and OS are shown in the form of a pie chart. For details refer to the Data S2.

Figure 4. Network analysis.

Clusters enriched for DEGs during CS, HS and OS. Hit molecules – red color, Inter connecting molecules - grey color. Red and Green Box – level of expressions during stress treatments respectively. Details of the genes shown in the clusters are provided in Table S1.

Figure 5. Specific gene expression pattern in response to CS, HS and OS.

Representation of the number of DEGs based on the time points of stress treatments is depicted classifying the number of genes in early or late responsive genes. Early refers to time points: CS1 h, HS10 min and OS1 h of CS, HS and OS stress condition. Late refers to time points: CS5 h, HS30 min and OS4 h of CS, HS and OS stress condition. Detailed gene lists are provided in Data S1.

Figure 6. Hierarchical clustering of the differentially expressed transcription factors (TFs).

Detailed gene lists (with fold changes, GO, gene descriptions, Gramene pathways and other relevant information) are provided in the Data S3.