Plant microRNA networks in abiotic stress pathways: Meta-analyses of sRNA data associated with drought, heat and salt stress responses in Arabidopsis thaliana

MicroRNAs (miRNAs) are a diverse group of small regulatory RNAs in plants that modulate gene expression at the post-transcriptional or translational level. This study focuses on identifying novel miRNAs and their target pathways involved in responses to drought, salt, and heat stress. A small RNA (sRNA) sequencing dataset was analysed to identify mature miRNAs expressed in 15-day-old Arabidopsis thaliana seedlings subjected to abiotic stress conditions. Differential expression analysis was performed using log ₂ FC-based filtering (stress vs. control), which led to the identification of significantly upregulated and downregulated miRNAs, including novel families such as miR3932b, miR5630b, and miR169j. Target genes of these miRNAs were predicted using the psRNA target tool (pmiREN), and protein-protein interaction (PPI) analysis was conducted using STRING. Additionally, analyses with the Find Individual Motif Sites (FIM) algorithm showed significant enrichment of crucial transcription factor families, including AP2 (APETALA2), WRKY, BBR (BARLEY B RECOMBINANT), etc. The identified miRNA targets were also found to be involved in signal transduction pathways other than stress, including most significant developmental and growth processes. Our findings therefore offer meaningful insights into the intricacies of miRNA–target networks and their modulation of transcriptional pathways during plant acclimation to abiotic stresses.