Zhu Huihui, Han Guanghao, Wang Jiayi, Xu Jiming, Hong Yiguo, Huang Li, Zheng Shaojian, Yang Jianli, Chen Weiwei
State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China.
Hortic Res. 2023 May 12;10(7):uhad104. doi: 10.1093/hr/uhad104. eCollection 2023 Jul.
Iron (Fe) is an essential micronutrient for all organisms, including plants, whose limited bioavailability restricts plant growth, yield, and nutritional quality. While the transcriptional regulation of plant responses to Fe deficiency have been extensively studied, the contribution of epigenetic modulations, such as DNA methylation, remains poorly understood. Here, we report that treatment with a DNA methylase inhibitor repressed Fe deficiency-induced responses in tomato () roots, suggesting the importance of DNA methylation in regulating Fe deficiency responses. Dynamic changes in the DNA methylome in tomato roots responding to short-term (12 hours) and long-term (72 hours) Fe deficiency identified many differentially methylated regions (DMRs) and DMR-associated genes. Most DMRs occurred at CHH sites under short-term Fe deficiency, whereas they were predominant at CG sites following long-term Fe deficiency. Furthermore, no correlation was detected between the changes in DNA methylation levels and the changes in transcript levels of the affected genes under either short-term or long-term treatments. Notably, one exception was CG hypermethylation at the promoter, which was positively correlated with its transcriptional induction. In agreement, we detected lower CG methylation at the promoter and lower expression in -RNA interference lines compared with wild-type seedlings. Virus-induced gene silencing of and luciferase reporter assays revealed that is positively involved in the modulation of Fe homeostasis. Altogether, we propose that dynamic epigenetic DNA methylation in the CG context at the promoter is involved in its transcriptional regulation, thus contributing to the Fe deficiency response of tomato.
铁（Fe）是包括植物在内的所有生物体必需的微量营养素，其生物有效性有限会限制植物的生长、产量和营养品质。虽然植物对缺铁反应的转录调控已得到广泛研究，但诸如DNA甲基化等表观遗传调控的作用仍知之甚少。在此，我们报道用DNA甲基化酶抑制剂处理可抑制番茄根中缺铁诱导的反应，这表明DNA甲基化在调节缺铁反应中具有重要作用。番茄根中响应短期（12小时）和长期（72小时）缺铁时DNA甲基化组的动态变化鉴定出许多差异甲基化区域（DMR）和与DMR相关的基因。大多数DMR在短期缺铁时出现在CHH位点，而在长期缺铁后它们在CG位点占主导地位。此外，在短期或长期处理下，未检测到DNA甲基化水平的变化与受影响基因转录水平的变化之间存在相关性。值得注意的是，一个例外是在启动子处的CG高甲基化，这与其转录诱导呈正相关。与此一致，与野生型幼苗相比，我们在启动子处检测到较低的CG甲基化和在RNA干扰系中较低的表达。病毒诱导的基因沉默和荧光素酶报告基因检测表明，正向参与铁稳态的调节。总之，我们提出在启动子处CG背景下的动态表观遗传DNA甲基化参与其转录调控，从而有助于番茄的缺铁反应。
