Background Methylation of nucleotides, notably in the forms of 5-methylcytosine (5mC) in DNA and N 6 -methyladenosine (m 6 A) in mRNA, carries important information for gene regulation. 5mC has been elucidated to participate in the regulation of fruit ripening, whereas the function of m 6 A in this process and the interplay between 5mC and m 6 A remain uncharacterized. Results Here, we show that mRNA m 6 A methylation exhibits dynamic changes similar to DNA methylation during tomato fruit ripening. RNA methylome analysis reveals that m 6 A methylation is a prevalent modification in the mRNA of tomato fruit, and the m 6 A 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 m 6 A levels, while only 134 transcripts show decreased m 6 A enrichment, suggesting a global increase in m 6 A. The m 6 A deposition is generally negatively correlated with transcript abundance. Further analysis demonstrates that the overall increase in m 6 A 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 m 6 A demethylation. Mutation of SlALKBH2 decreases the abundance of SlDML2 mRNA and delays fruit ripening. Conclusions Our study identifies a novel layer of gene regulation for key ripening genes and establishes an essential molecular link between DNA methylation and mRNA m 6 A methylation during fruit ripening. Electronic supplementary material The online version of this article (10.1186/s13059-019-1771-7) contains supplementary material, which is available to authorized users.

Background Epigenetic mark such as DNA methylation plays pivotal roles in regulating ripening of both climacteric and non-climacteric fruits. However, it remains unclear whether mRNA m6A methylation, which has been shown to regulate ripening of the tomato, a typical climacteric fruit, is functionally conserved for ripening control among different types of fruits. Results Here we show that m6A methylation displays a dramatic change at ripening onset of strawberry, a classical non-climacteric fruit. The m6A modification in coding sequence (CDS) regions appears to be ripening-specific and tends to stabilize the mRNAs, whereas m6A around the stop codons and within the 3′ untranslated regions is generally negatively correlated with the abundance of associated mRNAs. We identified thousands of transcripts with m6A hypermethylation in the CDS regions, including those of NCED5, ABAR, and AREB1 in the abscisic acid (ABA) biosynthesis and signaling pathway. We demonstrate that the methyltransferases MTA and MTB are indispensable for normal ripening of strawberry fruit, and MTA-mediated m6A modification promotes mRNA stability of NCED5 and AREB1, while facilitating translation of ABAR. Conclusion Our findings uncover that m6A methylation regulates ripening of the non-climacteric strawberry fruit by targeting the ABA pathway, which is distinct from that in the climacteric tomato fruit.