Sun Shuo, Zhu Jiamei, Guo Runze, Whelan James, Shou Huixia
State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, P.R. China.
The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, Zhejiang, 314400, P.R. China.
Plant J. 2021 Aug;107(3):727-739. doi: 10.1111/tpj.15318. Epub 2021 Jun 15.
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.
铁（Fe）是植物必需的微量营养元素，铁限制显著影响植物生长、产量和食品质量。虽然许多研究报道了转录组概况并探究了植物对铁限制的分子机制，但对于表观遗传因素在植物缺铁响应中是否发挥作用却知之甚少。在本研究中，我们对水稻幼苗在铁充足和缺铁条件下的根和地上部器官进行了全基因组亚硫酸氢盐测序分析、mRNA、小RNA和转座元件（TE）表达的高通量RNA测序。结果表明，缺铁后发生了广泛的高甲基化，尤其是在CHH序列背景下。甲基化和转录组的综合分析表明，缺铁诱导基因的转录丰度与附近的转座元件呈负相关，与24核苷酸的小干扰RNA呈正相关。我们使用外源性DNA甲基转移酶抑制剂（5-氮杂胞苷）以及通过基因手段利用缺乏CHH甲基化的结构域重排甲基转移酶2（DRM2）突变体，测试了甲基化影响植物对缺铁生理和分子响应的能力。两种方法均导致水稻植株生长和铁含量降低。因此，由小干扰RNA引导的特定甲基化模式的改变在水稻适应缺铁条件中发挥重要作用。此外，与其他报道的比较表明，这可能是植物适应有限养分供应的普遍机制。
