Target mimicry: The interplay of LncRNAs and MiRNAs in the complex network of abiotic stress responses in Oryza sativa

Abstract

Initially dismissed as ‘junk DNA’, genomic progress highlights the essential role of non-coding regulatory RNAs (ncRNAs) in gene expression. Long non-coding RNA (lncRNAs) and microRNA (miRNAs) play a vital role in regulating diverse plant biological processes. Despite extensive identification and characterization through bioinformatics and RNA-seq, only a limited subset of lncRNAs has been functionally studied. In this particular research, a total of twenty-six drought induced lncRNAs were selected from RNA-seq dataset of Oryza sativa for in depth analysis including in silico promoter analysis and the examination of their expression patterns under abiotic stress conditions, with the aim of unravelling their intricate regulatory mechanisms. Promoter analysis revealed their responsiveness to both ABA-independent and dependent pathways, indicating potential roles in pathway-regulated responses. Notably, three lncRNAs- OsDlnc12, OsDlnc22, and OsDlnc24 found to act as ceRNA (competing endogenous RNAs) for Osa-miR169 family members, Osa-miR2864.2, and Osa-miR1437b-3p respectively. Subsequent target prediction revealed that Osa-miR169 family members target OsNF-YA3, OsNF-YA7, and HAP2, Osa-miR2864.2 targets OsERD-15, and Osa-miR1437b-3p targets OsCYP450, OsAQP, and OsPRX precursor genes. Furthermore, qRT-PCR was employed to investigate the expression patterns and target mimicry mechanisms of selected lncRNAs under various abiotic stresses, revealing temporally regulated expressions. This finding provides insights into plant regulatory mechanisms under environmental stress, emphasizing the potential importance of lncRNAs in these processes.