Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250004, UP, India.
Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland, 2074, USA.
Mol Genet Genomics. 2022 May;297(3):731-749. doi: 10.1007/s00438-022-01879-1. Epub 2022 Mar 19.
Epigenetic regulation of the activity of defense genes during onset of diseases or resistance against diseases in plants is an active area of research. In the present study, a pair of wheat NILs for leaf rust resistance gene Lr28 (R) in the background of an Indian cultivar HD2329 (S) was used for a study of DNA methylation mediated regulation of gene expression. Leaf samples were collected at 0 h before (S0 and R0) and 96 h after inoculation (S96 and R96). The DNA samples were subjected to BS-Seq and sequencing data were used for identification of differentially methylated/demethylated regions/genes (DMRs and DMGs). Following four pairs of comparisons were used for this purpose: S0 vs S96; S0 vs R0; R0 vs R96; S96 vs R96. Major role of CHH methylation relative to that of CG and CHG methylation was observed. Some important observations include the following: (i) abundance of CHH methylation among DMRs; (ii) predominance of DMRs in intergenic region, relative to other genomic regions (promoters, exons, introns, TSS and TTS); (iii) abundance of transposable elements (TEs) in DMRs with CHH context; (iv) demethylation mediated high expression of genes during susceptible reaction (S0 vs S96) and methylation mediated low expression of genes during resistant reaction (R0 vs R96 and S96 vs R96); (v) major genes under regulation encode proteins, which differ from those encoded by genes regulated during susceptible reaction and (vi) ~ 500 DMGs carried differential binding sites for H3K4/K27me3 marks suggesting joint involvement of DNA and H3 methylation. Thus, CHH methylation either alone or in combination with histone methylation plays a major role in regulating the expression of genes involved in wheat-leaf rust interaction.
植物疾病发生或抗病过程中防御基因活性的表观遗传调控是一个活跃的研究领域。本研究以印度品种 HD2329（S）背景下的小麦叶锈病抗性基因 Lr28（R）的一对近等基因系（NILs）为材料，研究了基因表达的 DNA 甲基化调控。在接种前 0 小时（S0 和 R0）和接种后 96 小时（S96 和 R96）收集叶片样本。将 DNA 样本进行 BS-Seq 测序，并使用测序数据鉴定差异甲基化/去甲基化区域/基因（DMRs 和 DMGs）。为此，进行了以下四对比较：S0 与 S96；S0 与 R0；R0 与 R96；S96 与 R96。观察到 CHH 甲基化相对于 CG 和 CHG 甲基化的主要作用。一些重要的观察结果包括以下几点：（i）DMR 中 CHH 甲基化的丰度；（ii）与其他基因组区域（启动子、外显子、内含子、TSS 和 TTS）相比，DMR 主要位于基因间区；（iii）CHH 背景下 DMR 中存在转座元件（TEs）的丰度；（iv）易感反应（S0 与 S96）过程中基因的去甲基化介导的高表达和抗性反应（R0 与 R96 和 S96 与 R96）过程中基因的甲基化介导的低表达；（v）受调控的主要基因编码的蛋白质与易感反应过程中受调控的基因编码的蛋白质不同；（vi）~500 个 DMG 携带组蛋白 H3K4/K27me3 标记的差异结合位点，表明 DNA 和 H3 甲基化的共同参与。因此，CHH 甲基化或单独或与组蛋白甲基化一起，在调节参与小麦叶锈病互作的基因表达中发挥主要作用。
