Computational analysis of regulation and expression of plant DNA repair genes under various abiotic stresses reveals a stochastic correlation

Abstract

Biotic/abiotic stresses are known to induce genome instability in all organisms. Plants being sessile, are more vulnerable to stresses. Thus, they have evolved mechanisms to protect their genome from the unpredictably changing environment. DNA repair genes play a critical role in preserving genome integrity. Plants have about 15 different DNA repair pathways comprising more than 100 genes. To gain a better understanding of how plant DNA repair genes perceive stress and regulate their expression, we performed a computational analysis of the putative binding sites of different abiotic stress-responsive transcription factors (ASRTFs) on their promoters, in the model plant Arabidopsis thaliana. Of the 12 different ASRTFs that we analysed, MYC2 had the highest number of 1876 putative binding sites. Diversity study in 135 DNA repair gene promoters revealed that these had about 6 to 12 types of putative binding sites for the ASRTFs. While RAD51 promoter had the highest number of 207 putative binding sites, RECQ4B had only 11. Comparison of the Arabidopsis eFP browser-based temporal/spatial expression profiles of these genes under nine different abiotic stresses revealed that all of these genes had altered expression under various stresses. Some genes exhibited similar expression profiles. To identify the reasons for their similar expression pattern, we compared the promoter sequences and putative cis-regulatory elements such as binding sites for ASRTFs and methylation-prone nucleotide repeats. Our analysis indicated that the gene expression and gene regulation mediated by ASRTFs, and DNA methylation have a stochastic correlation