Identification of oxidative stress responsive hub genes and their related miRNAs in Arabidopsis thaliana based on integrated bioinformatics meta-analysis

Oxidative stress is an integral component of various stress conditions in plants, and determines the substantialoverlap in physiological and molecular responses to biotic and abiotic environmental challenges. To betterunderstand plants how to adapt environmental stress, we retrieved the oxidative-responsive genes ofArabidopsis thaliana, the main model plant for the experimental analysis. The purpose of our study was theidentification of oxidative-responsive genes and their related miRNAs and associated pathways in A. thalianaunder stress conditions using a high-throughput in silico meta-analysis. In this study we integrate threemicroarray datasets (GSE۲۰۰۰۹, GSE۴۰۵۷۴ and GSE۵۷۲۸۶) in the Gene Expression Omnibus (GEO)database. Normalization and processing of raw data performed by (SVA) and (limma) packages of R (version۱.۴.۱). The DEGs were identified by the thresholds of p-value < ۰.۰۵, and |log۲fold change (FC)| > ۱. Theanalysis of gene ontology enrichment (GO), protein-protein interaction (PPI), pathway analysis, and potentialmiRNAs for hub genes, were performed using bioinformatics online tools DAVID, STRING, KEGG,psRNATarget and RNAhybrid. The result ۹۰ DEGs, including ۴۶ up-regulated and ۴۴ down-regulated genes,were analyzed by integrated bioinformatics approaches enriched in glutathione metabolism, flavonoidbiosynthesis, oxidation-reduction process, and response to stress. DFR, GSTU۵, PGDH, GSTF۶, GSTF۱۲,PYD۴, APL۳, CYP۸۱D۱ and F۳H was hub genes in oxidative stress. All hub genes except GSTF۶, APL۳and F۳H were target genes of ۱۱ miRNAs. This research indicated that two hub genes DFR and GSTU۵ andtheir related miRNAs: ath-miR۴۱۸ and ath-miR۳۹۱ have effect on flavonoid biosynthesis and glutathionemetabolism pathways respectively in oxidative response adaptation. They also can be considered in breedingprograms and genetic engineering for the production of tolerant plants.

کلیدواژه ها:

Oxidative stress ، Arabidopsis thaliana ، miRNA ، integrated bioinformatics meta-analysis