Identification and analysis of adenine N⁶-methylation sites in the rice genome

First author: Chao Zhou; Affiliations: Huazhong Agricultural University (华中农业大学): Wuhan, China

Corresponding author: Dao-Xiu Zhou

DNA N⁶-methyladenine (6mA; 甲基腺嘌呤) is a non-canonical DNA modification that is present at low levels in different eukaryotes, but its prevalence and genomic function in higher plants are unclear. Using mass spectrometry (质谱分析), immunoprecipitation (免疫沉淀) and validation with analysis of single-molecule real-time sequencing, we observed that about 0.2% of all adenines (腺嘌呤) are 6mA methylated in the rice genome. 6mA occurs most frequently at GAGG motifs and is mapped to about 20% of genes and 14% of transposable elements. In promoters, 6mA marks silent genes, but in bodies correlates with gene activity. 6mA overlaps with 5-methylcytosine (5mC; 甲基胞嘧啶) at CG sites in gene bodies and is complementary to 5mC at CHH sites in transposable elements. We show that OsALKBH1 may be potentially involved in 6mA demethylation in rice. The results suggest that 6mA is complementary to 5mC as an epigenomic mark in rice and reinforce a distinct role for 6mA as a gene expression-associated epigenomic mark in eukaryotes.

DNA N6甲基腺嘌呤是一类非常规DNA甲基化，在不同真核生物中水平非常低，但其在高等植物基因组上的分布及功能还不是很清楚。本文通过质谱分析、免疫沉淀及随后的单分子实时定量测序进行验证，作者发现水稻基因组上约有0.2%的腺嘌呤被6mA甲基化。在GAGG基序上6mA发生最频繁，并且约在20%的基因区及14%转座子元件上分布。在启动子区，6mA标志着基因沉默，但在基因区6mA与基因的活性相关。在基因区，6mA与5mC（甲基胞嘧啶）在CG位点存在重叠，但在转座元件上的CHH位点与5mC互补。本文的研究显示OsALKBH1可能与水稻6mA去甲基化相关。6mA作为水稻5mC互补的表观标记，并且6mA可以用作于真核生物中基因表达相关的表观标记。

通讯：周道绣 (http://lst.hzau.edu.cn/info/1028/1788.htm)

个人简介：1979-1983年，华中农业大学，农学学士；1984-1985年，法国GRENOBLE大学，理学硕士；1985-1988年，法国GRENOBLE大学，理学博士；1988-1990年，美国加利福尼亚大学，博士后研究员。

研究方向：以粮食作物水稻为研究对象，从染色质和组蛋白修饰识别因子出发，系统地研究植物组蛋白修饰、染色质变构因子的调控与识别机制，解析组蛋白和染色质修饰的表观基因组；探讨植物对环境适应的表观遗传机制；同时研究植物顶端发育基因的表观调控网络。

doi: https://doi.org/10.1038/s41477-018-0212-z

Journal: Nature Plants

Published date: 30 July, 2018

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