N6-Methyladenine DNA Methylation in Japonica and Indica Rice Genomes and Its Association with Gene Expression, Plant Development, and Stress Responses [MeDIP-seq 93-11]

N6-Methyladenine (6mA) DNA methylation has recently been implicated as a potential new epigenetic marker in eukaryotes, including the dicot model Arabidopsis thaliana. However, the conservation and divergence of 6mA distribution patterns and functions in plants remain elusive. Here we report high-quality 6mA methylomes at single-nucleotide resolution in rice based on substantially improved genome sequences of two rice cultivars, Nipponbare (Nip; Japonica) and 93-11 (Indica). Analysis of 6mA genomic distribution and its association with transcription suggest that 6mA distribution and function is rather conserved between rice and Arabidopsis. We found that 6mA levels are positively correlated with the expression of key stress-related genes, which may be responsible for the difference in stress tolerance between Nip and 93-11. Moreover, we showed that mutations in DDM1 cause defects in plant growth and decreased 6mA level. Our results reveal that 6mA is a conserved DNA modification that is positively associated with gene expression and contributes to key agronomic traits in plants. Overall design: 6mA IP-seq in 3-week-old 93-11 wild-type with two replicates.

N6-甲基腺嘌呤（N6-Methyladenine，6mA）DNA甲基化近来被证实为真核生物中一种潜在的新型表观遗传标记，其中包括双子叶模式植物拟南芥（Arabidopsis thaliana）。然而，植物中6mA的分布模式与功能的保守性及差异性仍不甚明晰。本研究基于两个水稻品种——日本晴（Nipponbare，Nip；粳稻）与93-11（籼稻）的大幅优化基因组序列，获取了单碱基分辨率下的高质量水稻6mA甲基化组。对6mA的基因组分布及其与转录的关联分析表明，水稻与拟南芥之间的6mA分布模式与功能具有较高保守性。研究发现，6mA水平与关键胁迫相关基因的表达呈正相关，这或可解释日本晴与93-11之间胁迫耐受性的差异。此外，本研究证实DDM1基因突变会导致植物生长缺陷并降低6mA水平。本研究结果表明，6mA是一种保守的DNA修饰方式，其与基因表达呈正相关，并参与调控植物的重要农艺性状。实验整体设计：对3周龄的93-11野生型植株开展6mA免疫沉淀测序（6mA IP-seq）实验，设置两个生物学重复。