Plant J: 浙江大学生科院寿惠霞团队揭示 DNA 甲基化参与了水稻缺铁适应过程
铁是植物必需的微量营养元素，铁限制严重影响植物的生长、产量和食品品质。虽然许多研究报道了铁限制的转录调控和分子机制，但是表观遗传因子是否在铁缺乏的反应中发挥作用尚不清楚。本研究以水稻幼苗为材料，在铁充足和铁缺乏条件下，对其根、茎器官进行了全基因组亚硫酸盐定序分析、 mRNA 高通量 RNA 表达、小 RNA 和转座子(TE)表达。结果表明，铁缺乏后发生了广泛的甲基化，尤其是在 CHH 环境下。甲基化和转录组的综合分析表明，缺铁诱导的基因转录丰度与附近 TEs 呈负相关，与24核苷酸 siRNAs 呈正相关。使用外源性 DNA甲基转移酶抑制剂(5-氮杂胞苷)检测甲基化影响缺铁生理和分子反应的能力，并从遗传学上使用缺乏 CHH 甲基化的甲基转移酶2(DRM2)域的突变体。这两种方法都导致水稻植株生长和铁含量下降。因此，在缺铁条件下水稻特定甲基化模式的改变，在缺铁条件下水稻的适应中起着重要作用。此外，与其他报告的比较表明，这可能是一个普遍的机制，以适应有限的营养可用性。
Iron (Fe) is an essential micronutrient in plants, and Fe limitation significantly affects plant growth, yield and food quality. While many studies have reported the transcriptomic profile and pursue molecular mechanism in response to Fe limitation, little is known if epigenetic factors play a role in response to Fe-deficiency. In this study, whole-genome bisulfite sequencing analysis, high-throughput RNA-Seq of mRNA, small RNA and transposable element (TE) expression with root and shoot organs of rice seedlings under Fe-sufficient and Fe-deficient conditions were performed. The results showed that widespread hypermethylation, especially for the CHH context, occurred after Fe-deficiency. Integrative analysis of methylation and transcriptome revealed that the transcript abundance of Fe-deficiency-induced genes was negatively correlated with nearby TEs and positively with the 24-nucleotide siRNAs. The ability of methylation to affect the physiology and molecular response to Fe-deficiency was tested using an exogenous DNA methyltransferase inhibitor (5-azacytidine), and genetically using a mutant for domains rearranged methyltransferase 2 (DRM2), that lacks CHH methylation. Both approaches resulted in decreased growth and Fe content in rice plants. Thus, alterations in specific methylation patterns, directed by siRNAs, play an important role in acclimation of rice to Fe-deficient conditions. Furthermore, comparison with other reports suggests this may be a universal mechanism to acclimate to limited nutrient availability.
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