Wu Xiaoqing, Liu Hongfei, Lian Bi, Jiang Xue, Chen Cheng, Tang Tianxin, Ding Xinlun, Hu Jie, Zhao Shanshan, Zhang Shuai, Wu Jianguo
Vector-borne Virus Research Center, Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China.
Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China.
Front Plant Sci. 2023 Jan 11;13:1090794. doi: 10.3389/fpls.2022.1090794. eCollection 2022.
Rice grassy stunt virus (RGSV), a typical negative single-stranded RNA virus, invades rice and generates several disease signs, including dwarfing, tillering, and sterility. Previous research has revealed that RGSV-encoded proteins can force the host's ubiquitin-proteasome system to utilize them for viral pathogenesis. However, most of the studies were limited to a single omics level and lacked multidimensional data collection and correlation analysis on the mechanisms of RGSV-rice interactions. Here, we performed a comprehensive association analysis of genome-wide methylation sequencing, transcriptome sequencing, and histone H3K9me3 modification in RGSV-infested as well as non-infested rice leaves, and the levels of all three cytosine contexts (CG, CHG and CHH) were found to be slightly lower in RGSV-infected rice leaves than in normal rice. Large proportions of DMRs were distributed in the promoter and intergenic regions, and most DMRs were enriched in the CHH context, where the number of CHH hypo-DMRs was almost twice as high as that of hyper-DMRs. Among the genes with down-regulated expression and hypermethylation, we analyzed and identified 11 transcripts involved in fertility, plant height and tillering, and among the transcribed up-regulated and hypermethylated genes, we excavated 7 transcripts related to fertility, plant height and tillering. By analyzing the changes of histone H3K9me3 modification before and after virus infestation, we found that the distribution of H3K9me3 modification in the whole rice genome was prevalent, mainly concentrated in the gene promoter and gene body regions, which was distinctly different from the characteristics of animals. Combined with transcriptomic data, H3K9me3 mark was found to favor targeting highly expressed genes. After RGSV infection, H3K9me3 modifications in several regions of CTK and BR hormone signaling-related genes were altered, providing important targets for subsequent studies.
水稻草状矮化病毒（RGSV）是一种典型的负链单链RNA病毒，侵染水稻并产生多种病害症状，包括矮化、分蘖和不育。先前的研究表明，RGSV编码的蛋白可迫使宿主的泛素-蛋白酶体系统将其用于病毒致病过程。然而，大多数研究仅限于单一的组学水平，缺乏对RGSV与水稻相互作用机制的多维度数据收集和相关性分析。在此，我们对受RGSV侵染和未受侵染的水稻叶片进行了全基因组甲基化测序、转录组测序和组蛋白H3K9me3修饰的综合关联分析，发现RGSV感染的水稻叶片中所有三种胞嘧啶背景（CG、CHG和CHH）的水平均略低于正常水稻。大部分差异甲基化区域（DMR）分布在启动子和基因间区域，且大多数DMR在CHH背景中富集，其中CHH低甲基化DMR的数量几乎是高甲基化DMR的两倍。在表达下调且发生高甲基化的基因中，我们分析并鉴定出11个与育性、株高和分蘖相关的转录本，在表达上调且发生高甲基化的基因中，我们挖掘出7个与育性、株高和分蘖相关的转录本。通过分析病毒侵染前后组蛋白H3K9me3修饰的变化，我们发现H3K9me3修饰在整个水稻基因组中普遍存在，主要集中在基因启动子和基因体区域，这与动物的特征明显不同。结合转录组数据，发现H3K9me3标记倾向于靶向高表达基因。RGSV感染后，细胞分裂素（CTK）和油菜素内酯（BR）激素信号相关基因的几个区域的H3K9me3修饰发生改变，为后续研究提供了重要靶点。
