Methods paperIdentification of cis-regulatory elements specific for different types of reactive oxygen species in Arabidopsis thaliana

The type of reactive oxygen species (ROS) is a major factor that determines the specificity of biological responses. These responses may be elicited by activation of transcription factors that recognize ROS-specific cis-regulatory elements in target genes. In search for Arabidopsis promoter motifs specific for particular types of ROS, genome-wide microarray expression profiles for 283 abiotic stress-related conditions were subjected to cluster analysis to identify gene groups induced by singlet oxygen, superoxide radicals, and H2O2. Promoters of these gene groups were analyzed to identify cis-regulatory elements that are associated with specific types of ROS. Eleven ROS-specific de novo identified elements, seven known promoter motifs and several sequences enriched in ROS-responsive clusters but lacking in specificity are reported. The conservation of the identified motifs was determined in orthologous genes in C. papaya, V. vinifera and P. trichocarpa. Finally, biological functions were attributed to the motifs by calculation of GO-term enrichment for genes with conserved ROS-responsive elements.

► Clusters enriched in genes responsive to a single type of ROS were obtained. ► ROS-specific clusters were subjected to 3 motif finding algorithms. ► Cis-regulatory elements enriched in the ROS-specific clusters were reported. ► The conservation of the reported motifs was studied by phylogenetic footprinting. ► Genes with conserved ROS-responsive elements were analyzed for GO-term enrichment.