In Silico Analysis of miRNA-mRNA Binding Sites in <i>Arabidopsis thaliana</i> as a Model for Drought-Tolerant Plants
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 <i>Arabidopsis thaliana</i> as a model to perform an in silico analysis of miRNA–mRNA interactions linked to post...
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2025-06-01
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| Online Access: | https://www.mdpi.com/2223-7747/14/12/1800 |
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| author | Yryszhan Zhakypbek Aizhan Rakhmetullina Zhigerbek Kamarkhan Serik Tursbekov Qingdong Shi Fei Xing Anna Pyrkova Anatoliy Ivashchenko Bekzhan D. Kossalbayev Ayaz M. Belkozhayev |
| author_facet | Yryszhan Zhakypbek Aizhan Rakhmetullina Zhigerbek Kamarkhan Serik Tursbekov Qingdong Shi Fei Xing Anna Pyrkova Anatoliy Ivashchenko Bekzhan D. Kossalbayev Ayaz M. Belkozhayev |
| author_sort | Yryszhan Zhakypbek |
| collection | DOAJ |
| description | 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 <i>Arabidopsis thaliana</i> 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 (<i>CSD1</i>, <i>FSD1</i>); ath-miR393a/b-5p and ath-miR167a-c-5p targeting hormonal signaling genes (<i>TIR1</i>, <i>ARF6</i>); 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 <i>Arabidopsis thaliana</i> 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. |
| format | Article |
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| institution | OA Journals |
| issn | 2223-7747 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | MDPI AG |
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| series | Plants |
| spelling | doaj-art-d3c1fabca0634995b08ba73f4c3334a82025-08-20T02:21:46ZengMDPI AGPlants2223-77472025-06-011412180010.3390/plants14121800In Silico Analysis of miRNA-mRNA Binding Sites in <i>Arabidopsis thaliana</i> as a Model for Drought-Tolerant PlantsYryszhan Zhakypbek0Aizhan Rakhmetullina1Zhigerbek Kamarkhan2Serik Tursbekov3Qingdong Shi4Fei Xing5Anna Pyrkova6Anatoliy Ivashchenko7Bekzhan D. Kossalbayev8Ayaz M. Belkozhayev9Department of Mine Surveying and Geodesy, Institute Mining and Metallurgical Institute Named After O.A. Baikonurov, Satbayev University, Almaty 050043, KazakhstanInstitute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, PolandDepartment of Mechanical Engineering, Institute of Energy and Mechanical Engineering Named After A. Burkitbayev, Satbayev University, Almaty 050013, KazakhstanDepartment of Mine Surveying and Geodesy, Institute Mining and Metallurgical Institute Named After O.A. Baikonurov, Satbayev University, Almaty 050043, KazakhstanCollege of Ecology and Environment, Xinjiang University, Urumqi 830017, ChinaCollege of Geography and Remote Sensing Sciences, Xinjiang University, Urumqi 830017, ChinaDepartment of Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, KazakhstanDepartment of Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, KazakhstanDepartment of Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, KazakhstanDepartment of Chemical and Biochemical Engineering, Geology and Oil-Gas Business Institute Named After K. Turyssov, Satbayev University, Almaty 050043, KazakhstanDrought 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 <i>Arabidopsis thaliana</i> 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 (<i>CSD1</i>, <i>FSD1</i>); ath-miR393a/b-5p and ath-miR167a-c-5p targeting hormonal signaling genes (<i>TIR1</i>, <i>ARF6</i>); 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 <i>Arabidopsis thaliana</i> 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.https://www.mdpi.com/2223-7747/14/12/1800<i>Arabidopsis thaliana</i>miRNAmRNAdrought tolerancebinding sites |
| spellingShingle | Yryszhan Zhakypbek Aizhan Rakhmetullina Zhigerbek Kamarkhan Serik Tursbekov Qingdong Shi Fei Xing Anna Pyrkova Anatoliy Ivashchenko Bekzhan D. Kossalbayev Ayaz M. Belkozhayev In Silico Analysis of miRNA-mRNA Binding Sites in <i>Arabidopsis thaliana</i> as a Model for Drought-Tolerant Plants Plants <i>Arabidopsis thaliana</i> miRNA mRNA drought tolerance binding sites |
| title | In Silico Analysis of miRNA-mRNA Binding Sites in <i>Arabidopsis thaliana</i> as a Model for Drought-Tolerant Plants |
| title_full | In Silico Analysis of miRNA-mRNA Binding Sites in <i>Arabidopsis thaliana</i> as a Model for Drought-Tolerant Plants |
| title_fullStr | In Silico Analysis of miRNA-mRNA Binding Sites in <i>Arabidopsis thaliana</i> as a Model for Drought-Tolerant Plants |
| title_full_unstemmed | In Silico Analysis of miRNA-mRNA Binding Sites in <i>Arabidopsis thaliana</i> as a Model for Drought-Tolerant Plants |
| title_short | In Silico Analysis of miRNA-mRNA Binding Sites in <i>Arabidopsis thaliana</i> as a Model for Drought-Tolerant Plants |
| title_sort | in silico analysis of mirna mrna binding sites in i arabidopsis thaliana i as a model for drought tolerant plants |
| topic | <i>Arabidopsis thaliana</i> miRNA mRNA drought tolerance binding sites |
| url | https://www.mdpi.com/2223-7747/14/12/1800 |
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