Chithung Tonu Angaila, Kansal Shivani, Jajo Ringyao, Balyan Sonia, Raghuvanshi Saurabh
Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Marg, New Delhi, 110021, India.
Funct Integr Genomics. 2023 Jan 6;23(1):30. doi: 10.1007/s10142-022-00958-1.
miRNA biogenesis process is an intricate and complex event consisting of many proteins working in a highly coordinated fashion. Most of these proteins have been studied in Arabidopsis; however, their orthologs and functions have not been explored in other plant species. In the present study, we have manually curated all the experimentally verified information present in the literature regarding these proteins and found a total of 98 genes involved in miRNA biogenesis in Arabidopsis. The conservation pattern of these proteins was identified in other plant species ranging from dicots to lower organisms, and we found that a major proportion of proteins involved in the pri-miRNA processing are conserved. However, nearly 20% of the genes, mostly involved in either transcription or functioning of the miRNAs, were absent in the lower organisms. Further, we manually curated a regulatory network of the core components of the biogenesis process and found that nearly half (46%) of the proteins interact with them, indicating that the processing step is perhaps the most under surveillance/regulation. We have subsequently attempted to characterize the orthologs identified in Oryza sativa, on the basis of transcriptome and epigenetic modifications under field drought conditions in order to assess the impact of drought on the process. We found several participating genes to be differentially expressed and/or epigenetically methylated under drought, although the core components like DCL1, SE, and HYL1 remain unaffected by the stress itself. The study enhances our present understanding of the biogenesis process and its regulation.
微小RNA（miRNA）的生物合成过程是一个复杂且精密的事件，由许多蛋白质以高度协调的方式共同发挥作用。这些蛋白质中的大多数已在拟南芥中得到研究；然而，它们在其他植物物种中的直系同源物及其功能尚未得到探索。在本研究中，我们手动整理了文献中所有关于这些蛋白质的经过实验验证的信息，发现拟南芥中共有98个基因参与miRNA的生物合成。在从双子叶植物到低等生物的其他植物物种中鉴定了这些蛋白质的保守模式，我们发现参与初级miRNA（pri-miRNA）加工的大部分蛋白质是保守的。然而，近20%的基因，主要参与miRNA的转录或功能，在低等生物中不存在。此外，我们手动构建了生物合成过程核心成分的调控网络，发现近一半（46%）的蛋白质与它们相互作用，这表明加工步骤可能是最受监测/调控的。随后，我们试图根据田间干旱条件下的转录组和表观遗传修饰来表征在水稻中鉴定出的直系同源物，以评估干旱对该过程的影响。我们发现尽管像DCL1、SE和HYL1等核心成分不受胁迫本身的影响，但在干旱条件下有几个参与基因发生了差异表达和/或表观遗传甲基化。该研究增进了我们目前对生物合成过程及其调控的理解。
