In Silico Analysis of miRNA-mRNA Binding Sites in Arabidopsis thaliana as a Model for Drought-Tolerant Plants

Zhakypbek Y. Rakhmetullina A. Kamarkhan Z. Tursbekov S. Shi Q. Xing F. Pyrkova A. Ivashchenko A. Kossalbayev B.D. Belkozhayev A.M.
June 2025 Multidisciplinary Digital Publishing Institute (MDPI)

Plants
2025 #14 Issue 12

Drought stress limits plant survival and yield in arid regions. Uncovering the molecular mechanisms of drought tolerance is key to developing resilient crops. This study used Arabidopsis thaliana as a model to perform an in silico analysis of miRNA–mRNA interactions linked to post-transcriptional drought response. Using the MirTarget program, 274 miRNAs and 48,143 gene transcripts were analyzed to predict high-confidence miRNA–mRNA interactions based on binding free energies (−79 to −129 kJ/mole). Predicted binding sites were located in the CDS, 5′UTR, and 3′UTR regions of target mRNAs. Key regulatory interactions included ath-miR398a-c and ath-miR829-5p targeting ROS detoxification genes (CSD1, FSD1); ath-miR393a/b-5p and ath-miR167a-c-5p targeting hormonal signaling genes (TIR1, ARF6); and the miR169 family, ath-miR414, and ath-miR838 targeting drought-related transcription factors (NF-YA5, DREB1A, WRKY40). Notably, ath-miR414, ath-miR838, and the miR854 family showed broad regulatory potential, targeting thousands of genes. These findings suggest the presence of conserved regulatory modules with potential roles in abiotic stress tolerance. While no direct experimental validation was performed, the results from Arabidopsis thaliana provide a useful genomic framework for hypothesis generation and future functional studies in non-model plant species. This work provides a molecular foundation for improving drought and salt stress tolerance through bioinformatics-assisted breeding and genetic research.

Arabidopsis thaliana , binding sites , drought tolerance , miRNA , mRNA

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Department of Mine Surveying and Geodesy, Institute Mining and Metallurgical Institute Named After O.A. Baikonurov, Satbayev University, Almaty, 050043, Kazakhstan
Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, 02-106, Poland
Department of Mechanical Engineering, Institute of Energy and Mechanical Engineering Named After A. Burkitbayev, Satbayev University, Almaty, 050013, Kazakhstan
College of Ecology and Environment, Xinjiang University, Urumqi, 830017, China
Key Laboratory of Oasis Ecology, Xinjiang University, Urumqi, 830017, China
College of Geography and Remote Sensing Sciences, Xinjiang University, Urumqi, 830017, China
Department of Biotechnology, Al-Farabi Kazakh National University, Almaty, 050040, Kazakhstan
Center for Bioinformatics and Nanomedicine, Almaty, 050060, Kazakhstan
Ecology Research Institute, Khoja Akhmet Yassawi International Kazakh Turkish University, Turkistan, 161200, Kazakhstan
Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
Department of Chemical and Biochemical Engineering, Geology and Oil-Gas Business Institute Named After K. Turyssov, Satbayev University, Almaty, 050043, Kazakhstan
M.A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, 050000, Kazakhstan

Department of Mine Surveying and Geodesy
Institute of Biochemistry and Biophysics
Department of Mechanical Engineering
College of Ecology and Environment
Key Laboratory of Oasis Ecology
College of Geography and Remote Sensing Sciences
Department of Biotechnology
Center for Bioinformatics and Nanomedicine
Ecology Research Institute
Tianjin Institute of Industrial Biotechnology
Department of Chemical and Biochemical Engineering
M.A. Aitkhozhin Institute of Molecular Biology and Biochemistry

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