Piya Sarbottam, Lopes-Caitar Valeria S, Kim Won-Seok, Pantalone Vince, Krishnan Hari B, Hewezi Tarek
Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States.
Plant Science Division, University of Missouri, Columbia, MO, United States.
Front Mol Biosci. 2021 Apr 13;8:616623. doi: 10.3389/fmolb.2021.616623. eCollection 2021.
DNA methylation has recently emerged as a powerful regulatory mechanism controlling the expression of key regulators of various developmental processes, including nodulation. However, the functional role of DNA methylation in regulating the expression of microRNA (miRNA) genes during the formation and development of nitrogen-fixing nodules remains largely unknown. In this study, we profiled DNA methylation patterns of miRNA genes during nodule formation, development, and early senescence stages in soybean () through the analysis of methylC-seq data. Absolute DNA methylation levels in the CG, CHH, and CHH sequence contexts over the promoter and primary transcript regions of miRNA genes were significantly higher in the nodules compared with the corresponding root tissues at these three distinct nodule developmental stages. We identified a total of 82 differentially methylated miRNAs in the nodules compared with roots. Differential DNA methylation of these 82 miRNAs was detected only in the promoter (69), primary transcript region (3), and both in the promoter and primary transcript regions (10). The large majority of these differentially methylated miRNAs were hypermethylated in nodules compared with the corresponding root tissues and were found mainly in the CHH context and showed stage-specific methylation patterns. Differentially methylated regions in the promoters of 25 miRNAs overlapped with transposable elements, a finding that may explain the vulnerability of miRNAs to DNA methylation changes during nodule development. Gene expression analysis of a set of promoter-differentially methylated miRNAs pointed to a negative association between DNA methylation and miRNA expression. Gene Ontology and pathways analyses indicate that changes in DNA methylation of miRNA genes are reprogrammed and contribute to nodule development through indirect regulation of genes involved in cellular processes and pathways with well-established roles in nodulation.
DNA甲基化最近已成为一种强大的调控机制，可控制包括结瘤在内的各种发育过程关键调节因子的表达。然而，在固氮根瘤的形成和发育过程中，DNA甲基化在调控微小RNA（miRNA）基因表达方面的功能作用仍 largely未知。在本研究中，我们通过分析甲基C测序数据，描绘了大豆根瘤形成、发育和早期衰老阶段miRNA基因的DNA甲基化模式。在这三个不同的根瘤发育阶段，与相应的根组织相比，miRNA基因启动子和初级转录本区域的CG、CHH和CHH序列背景中的绝对DNA甲基化水平在根瘤中显著更高。与根相比，我们在根瘤中总共鉴定出82个差异甲基化的miRNA。仅在启动子（69个）、初级转录本区域（3个）以及启动子和初级转录本区域均有差异（10个）检测到这82个miRNA的差异DNA甲基化。与相应的根组织相比，这些差异甲基化的miRNA中的绝大多数在根瘤中发生了高甲基化，并且主要在CHH背景中发现，并呈现出阶段特异性的甲基化模式。25个miRNA启动子中的差异甲基化区域与转座元件重叠，这一发现可能解释了miRNA在根瘤发育过程中对DNA甲基化变化的易感性。一组启动子差异甲基化miRNA的基因表达分析表明DNA甲基化与miRNA表达之间存在负相关。基因本体和通路分析表明，miRNA基因的DNA甲基化变化被重新编程，并通过间接调控参与细胞过程和在结瘤中具有既定作用的通路的基因来促进根瘤发育。
