Zhao Lin, Zhang Mengyan, Wu Qi, Wu Xi, Yun Zhenyu
Sub-Institute of Agriculture and Food Standardization, China National Institute of Standardization, Beijing, China.
Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
PLoS One. 2025 Aug 28;20(8):e0329456. doi: 10.1371/journal.pone.0329456. eCollection 2025.
DNA methylation plays a crucial role in plants' adaptation to environmental stresses. However, the precise role of DNA methylation in regulating the response of maize (Zea mays L.) to copper stress remains incompletely understood. In this study, an integrated analysis of DNA methylome and transcriptome of the hybrid variety "Zhengdan 958" exposed to 1mM Cu stress at seedling stage was conducted using whole genome bisulfite sequencing (WGBS) and RNA-sequencing (RNA-seq). In the comparison between the control and copper stress sample, 3364 differentially expressed genes (DEGs) were detected (1637 upregulated and 1727 downregulated). The WGBS analysis revealed a genome-wide decrease in methylation levels across all cytosine contexts (CG, CHG, and CHH) under copper stress, with 1545 gene body hypomethylated differentially methylated genes (DMGs) and 1806 promoter hypomethylated DMGs. By integrating the analysis of DEGs and hypomethylated DMGs, we identified two predominant patterns of epigenetic regulation: (1) gene body CHG/CHH hypomethylation associated with transcriptional activation of metabolic and stress-response genes, and (2) promoter CHH hypomethylation linked to repression of developmental regulators and signaling components. This study provides valuable data for the epigenetic regulation of copper stress responses and identifies potential targets for developing stress-tolerant maize varieties through epigenetic breeding approaches.
DNA甲基化在植物适应环境胁迫中起着至关重要的作用。然而，DNA甲基化在调节玉米（Zea mays L.）对铜胁迫反应中的精确作用仍未完全了解。在本研究中，利用全基因组亚硫酸氢盐测序（WGBS）和RNA测序（RNA-seq）对杂交品种“郑单958”在苗期暴露于1mM铜胁迫下的DNA甲基化组和转录组进行了综合分析。在对照和铜胁迫样品的比较中，检测到3364个差异表达基因（DEG）（1637个上调和1727个下调）。WGBS分析显示，在铜胁迫下，所有胞嘧啶背景（CG、CHG和CHH）的甲基化水平在全基因组范围内下降，有1545个基因体低甲基化差异甲基化基因（DMG）和1806个启动子低甲基化DMG。通过整合DEG和低甲基化DMG的分析，我们确定了两种主要的表观遗传调控模式：（1）基因体CHG/CHH低甲基化与代谢和应激反应基因的转录激活相关，（2）启动子CHH低甲基化与发育调节因子和信号成分的抑制相关。本研究为铜胁迫反应的表观遗传调控提供了有价值的数据，并确定了通过表观遗传育种方法培育耐胁迫玉米品种的潜在靶点。
