Genome-wide analysis of epigenetic and transcriptional changes in the pathogenesis of RGSV in rice.
Genome-wide analysis of epigenetic and transcriptional changes in the pathogenesis of RGSV in rice.
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水稻 RGSV 发病机制中表观遗传和转录变化的全基因组分析
DOI：
10.3389/fpls.2022.1090794
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发表时间：
2022
影响因子：
5.6
通讯作者：
Wu, Jianguo
中科院分区：
文献类型：
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作者：
Wu, Xiaoqing;Liu, Hongfei;Lian, Bi;Jiang, Xue;Chen, Cheng;Tang, Tianxin;Ding, Xinlun;Hu, Jie;Zhao, Shanshan;Zhang, Shuai;Wu, Jianguo
水稻草矮病毒(RGSV)是一种典型的负性单链RNA病毒，侵染水稻并产生矮化、分蘖和不育等症状。先前的研究表明，RGSV编码的蛋白可以迫使宿主的泛素-蛋白酶体系统利用它们来进行病毒致病。然而，大多数研究局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数据收集和相关性分析。在这里，我们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，发现在感染RGSV的水稻叶片中，所有三种胞嘧啶(CG、CHG和CHH)的水平都略低于正常水稻。大部分DMR分布在启动子和基因间隔区，并且大多数DMR在CHH环境中富含，其中CHH低DMR的数量几乎是高DMR的两倍。在下调表达和高甲基化的基因中，我们分析和鉴定了11个与育性、株高和分蘖有关的转录本，而在转录上调和高甲基化的基因中，我们挖掘到了7个与育性、株高和分蘖有关的转录本。通过分析组蛋白H3K9me3修饰在病毒侵染前后的变化，发现H3K9me3修饰在整个水稻基因组中的分布普遍，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。结合转录学数据，发现H3K9me3标记有利于靶向高表达基因。在RGSV感染后，CTK和BR激素信号相关基因的多个区域的H3K9me3修饰发生了改变，为后续的研究提供了重要的靶点。
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.
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影响因子：
16.6
作者：
Gui X;Liu C;Qi Y;Zhou X
通讯作者：
Zhou X
影响因子：
9.2
作者：
Melnyk, Charles W.;Molnar, Attila;Baulcombe, David C.
通讯作者：
Baulcombe, David C.
影响因子：
5.4
作者：
Raja, Priya;Sanville, Bradley C.;Bisaro, David M.
通讯作者：
Bisaro, David M.
CSE1L介导的核输入途径在表观遗传沉默中的作用
DOI：
10.1073/pnas.1800505115
发表时间：
2018-04-24
影响因子：
11.1
作者：
Dong, Qiang;Li, Xiang;Zhu, Bing
通讯作者：
Zhu, Bing
DOI：
10.1038/nrg2719
发表时间：
2010-03
期刊：
Nature reviews. Genetics
影响因子：
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作者：
通讯作者：
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