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<p><i>Conocarpus erectus L.</i>, a traditionally important medicinal plant, is increasingly recognized as a potential source of bioactive small RNAs with therapeutic relevance. Leveraging a cross- and intra-kingdom computational framework, we identified and characterized 30 novel microRNAs (miRNAs) from the <i>C. erectus</i> transcriptome. These plant-derived miRNAs were predicted to target genes in both <i>Homo sapiens</i> and <i>Arabidopsis thaliana</i>, thereby offering a unique opportunity to explore conserved and species-specific molecular mechanisms. Functional enrichment of human and <i>A. thaliana</i> gene targets revealed significant involvement in regulatory networks controlling genome integrity, including pathways related to MAPK signaling, PI3K-Akt, insulin, and neurotrophin signaling, as well as cellular senescence. In humans, top-ranked hub genes such as <i>CDC42, MAPK14, PIK3R1, AR,</i> and <i>NTRK2</i> were implicated in genome instability-associated conditions, including neurodegeneration and metabolic diseases. In parallel, the <i>A. thaliana</i> targets provided insights into conserved post-transcriptional regulatory networks and stress adaptation pathways. Notably, both organisms demonstrated miRNA influence over genes involved in DNA repair, epigenetic modulation, and signal transduction. Molecular dynamics simulations validated the structural stability of the <i>CDC42</i>–cer-miR1134-5p complex over a 300&#xa0;ns trajectory, suggesting stable and functional RNA-RNA interactions. Collectively, our findings propose that <i>C. erectus</i> miRNAs act as interspecies epigenetic regulators with the potential to impact genome stability, offering promising leads for novel RNA-based therapeutics in neurodegenerative and genome instability-linked diseases.</p>

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Cross- and intra-kingdom miRNA-mediated transcriptomic regulation by Conocarpus erectus L.: a novel insight into genome stability, epigenetic control, and neurodegenerative pathways

  • 期刊论文

  • 发表日期：

    2025年7月22日

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  • Poojaben Prajapati,
  • Tithi S. Trivedi,
  • Bharat B. Maitreya,
  • Rakesh M. Rawal,
  • Saumya K. Patel

摘要

Conocarpus erectus L., a traditionally important medicinal plant, is increasingly recognized as a potential source of bioactive small RNAs with therapeutic relevance. Leveraging a cross- and intra-kingdom computational framework, we identified and characterized 30 novel microRNAs (miRNAs) from the C. erectus transcriptome. These plant-derived miRNAs were predicted to target genes in both Homo sapiens and Arabidopsis thaliana, thereby offering a unique opportunity to explore conserved and species-specific molecular mechanisms. Functional enrichment of human and A. thaliana gene targets revealed significant involvement in regulatory networks controlling genome integrity, including pathways related to MAPK signaling, PI3K-Akt, insulin, and neurotrophin signaling, as well as cellular senescence. In humans, top-ranked hub genes such as CDC42, MAPK14, PIK3R1, AR, and NTRK2 were implicated in genome instability-associated conditions, including neurodegeneration and metabolic diseases. In parallel, the A. thaliana targets provided insights into conserved post-transcriptional regulatory networks and stress adaptation pathways. Notably, both organisms demonstrated miRNA influence over genes involved in DNA repair, epigenetic modulation, and signal transduction. Molecular dynamics simulations validated the structural stability of the CDC42–cer-miR1134-5p complex over a 300 ns trajectory, suggesting stable and functional RNA-RNA interactions. Collectively, our findings propose that C. erectus miRNAs act as interspecies epigenetic regulators with the potential to impact genome stability, offering promising leads for novel RNA-based therapeutics in neurodegenerative and genome instability-linked diseases.