RNA methylomes reveal the m6A-mediated regulation of DNA demethylase gene SlDML in tomato fruit ripening

First author: Leilei Zhou; Affiliations: CAS Institute of Botany (中科院植物所): Beijing, China

Corresponding author: Guozheng Qin

Methylation of nucleotides, notably in the forms of 5-methylcytosine (5mC) in DNA and N6-methyladenosine (m6A) in mRNA, carries important information for gene regulation. 5mC has been elucidated to participate in the regulation of fruit ripening, whereas the function of m6A in this process and the interplay between 5mC and m6A remain uncharacterized. Here, we show that mRNA m6A methylation exhibits dynamic changes similar to DNA methylation during tomato fruit ripening. RNA methylome analysis reveals that m6A methylation is a prevalent modification in the mRNA of tomato fruit, and the m6A sites are enriched around the stop codons and within the 3′ untranslated regions. In the fruit of the ripening-deficient epimutant Colorless non-ripening (Cnr) which harbors DNA hypermethylation, over 1100 transcripts display increased m6A levels, while only 134 transcripts show decreased m6A enrichment, suggesting a global increase in m6A. The m6A deposition is generally negatively correlated with transcript abundance. Further analysis demonstrates that the overall increase in m6A methylation in Cnr mutant fruit is associated with the decreased expression of RNA demethylase gene SlALKBH2, which is regulated by DNA methylation. Interestingly, SlALKBH2 has the ability to bind the transcript of SlDML2, a DNA demethylase gene required for tomato fruit ripening, and modulates its stability via m6A demethylation. Mutation of SlALKBH2 decreases the abundance of SlDML2 mRNA and delays fruit ripening. Our study identifies a novel layer of gene regulation for key ripening genes and establishes an essential molecular link between DNA methylation and mRNA m6A methylation during fruit ripening.

核苷酸上的甲基化，尤其是DNA上的5mC和mRNA上的m6A对于基因的调控都具有非常重要的作用。已经有研究报道了5mC参与果实的成熟过程，而m6A及其与5mC之间的互作在果实成熟过程中的作用还不清楚。本文的研究揭示了在番茄果实成熟过程中，mRNA上m6A甲基化与DNA甲基化有着类似的动态改变。RNA甲基化组分析显示m6A甲基化是番茄果实mRNA上一个比较普遍的甲基化修饰，并且m6A甲基化的位点比较富集在终止密码子和3’端未翻译区域。在番茄的果实成熟缺陷表观突变体Cnr中，DNA存在超甲基化，其超过1100个转录本都显示出m6A的水平增加，而仅仅只有134个转录本显示m6A的富集降低，说明整体水平上m6A的增加。m6A的沉积通常与转录本的富集呈负相关的关系。进一步的分析显示Cnr突变体果实中m6A整体水平的增加与RNA去甲基化酶SlALKBH2基因表达的降低有关，该基因的表达受到DNA甲基化的影响。有趣的是，SlALKBH2能够结合到SlDML2基因的转录本上并且能够通过m6A去甲基化调控其稳定性，而SlDML2基因是一个DNA去甲基化酶，其对于番茄果实的成熟是必须的。SlALKBH2基因的突变能够降低SlDML2基因mRNA的丰度，延迟果实成熟。本文的研究鉴定了番茄果实成熟新的基因调控层级，并且新建立了果实成熟过程中DNA甲基化和mRNA甲基化之间的关联。

通讯：秦国政  (http://sourcedb.ib.cas.cn/cn/expert/201809/t20180930_5125842.html)

个人简介：2000年，四川大学，学士；2004年，中国科学院植物研究所，博士；2006-2007年，美国亚利桑那州立大学，博士后。

研究方向：以番茄为主要研究材料，解析果实成熟和衰老过程中色泽、风味等品质形成的分子机制及其调控基础。

doi: https://doi.org/10.1186/s13059-019-1771-7

Journal: Genome Biology

Published date: August 06, 2019