Xiaoqing Wu, Hongfei Liu, Bi Lian, Xue Jiang, Cheng Chen, Tianxin Tang, Xinlun Ding, Jie Hu, Shanshan Zhao, Shuai Zhang, Jianguo Wu

Front Plant Sci.; 2023 Jan 11; 13:1090794. doi: 10.3389/fpls.2022.1090794.

Abstract

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.

See https://pubmed.ncbi.nlm.nih.gov/36714706/

Figure 1 Characteristics of methylation genomics of rice infected with RGSV. (A) The signs of the disease induced by RGSV on rice plants. (B) The expression of the RGSV coat protein (CP) gene was measured using qRT-PCR. (C) The viral content in rice leaves infected with RGSV was detected using western blotting with anti-RGSV CP and anti-RGSV PC5 polyclonal antibody. Rice actin was used as the loading control. (D) The frequency histogram of methylation of CG, CHG and CHH types in RGSV infected and uninfected rice. (E–J) Visualization of DNA methylation profiles of mCG, mCHG and mCHH peripheral genes and transposable elements (TE_S, within 1.5 kb) in RGSV-infected and uninfected rice.