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<p>Transfer RNA-derived non-coding RNAs (tncRNAs) are potential regulators of gene expression in plants, and it’s crucial to understand their diversity and functional roles in modulating plant stress responses. To expand knowledge of stress-responsive tncRNAs in agronomically important crops, we investigated rice and chickpea, two major crop species highly affected by drought and salinity, under respective stress conditions. Small RNA sequencing revealed that 70.2% of tncRNAs in rice and 45% in chickpea were commonly expressed across multiple stress conditions. qRT-PCR validation showed that most tRF-5s were upregulated in both rice and chickpea under drought and salt stress. In rice, 3′tRHs were specifically induced by drought, whereas 5′tRHs responded predominantly to salt stress. In chickpea, tRF-3s were upregulated during drought but downregulated under salt stress. Furthermore, we confirmed the mRNA targets of these stress-associated tRNA fragments using RLM-RACE, thereby verifying the cleavage of specific target mRNAs in both species. Expression profiling of target genes revealed a negative association with their corresponding tRFs in both species. Subcellular localization demonstrated that OsGEM and OsPPR were primarily localized in the nucleus, while CaMIZ1 and CaSKP1 were detected at the plasma membrane. Overall, we identified abiotic stress-responsive tncRNAs in rice and chickpea, suggesting their potential contribution to plant resilience under changing environmental conditions.</p>

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Abiotic Stress-Mediated Modulation of the tncRNome: Unraveling tRNA-Derived RNA Networks in Plant Adaptive Responses

  • 期刊论文

  • 发表日期：

    2026年6月22日

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  • Shafaque Zahra,
  • Rashmi Gangwar,
  • Sneha Tiwari,
  • Dipul Kumar Biswas,
  • Amarjeet Singh,
  • Shailesh Kumar

摘要

Transfer RNA-derived non-coding RNAs (tncRNAs) are potential regulators of gene expression in plants, and it’s crucial to understand their diversity and functional roles in modulating plant stress responses. To expand knowledge of stress-responsive tncRNAs in agronomically important crops, we investigated rice and chickpea, two major crop species highly affected by drought and salinity, under respective stress conditions. Small RNA sequencing revealed that 70.2% of tncRNAs in rice and 45% in chickpea were commonly expressed across multiple stress conditions. qRT-PCR validation showed that most tRF-5s were upregulated in both rice and chickpea under drought and salt stress. In rice, 3′tRHs were specifically induced by drought, whereas 5′tRHs responded predominantly to salt stress. In chickpea, tRF-3s were upregulated during drought but downregulated under salt stress. Furthermore, we confirmed the mRNA targets of these stress-associated tRNA fragments using RLM-RACE, thereby verifying the cleavage of specific target mRNAs in both species. Expression profiling of target genes revealed a negative association with their corresponding tRFs in both species. Subcellular localization demonstrated that OsGEM and OsPPR were primarily localized in the nucleus, while CaMIZ1 and CaSKP1 were detected at the plasma membrane. Overall, we identified abiotic stress-responsive tncRNAs in rice and chickpea, suggesting their potential contribution to plant resilience under changing environmental conditions.