Background: Methylation of nucleotides, notably in the forms of 5-methylcytosine (5mC) in DNA and N6 - methyladenosine (m6 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 m6 A in this process and the interplay between 5mC and m6 A remain uncharacterized.

Results: Here, we show that mRNA m6 A methylation exhibits dynamic changes similar to DNA methylation during tomato fruit ripening. RNA methylome analysis reveals that m6 A methylation is a prevalent modification in the mRNA of tomato fruit, and the m6 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 m6 A levels, while only 134 transcripts show decreased m6 A enrichment, suggesting a global increase in m6 A. The m6 A deposition is generally negatively correlated with transcript abundance. Further analysis demonstrates that the overall increase in m6 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 m6 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 m6 A methylation during fruit ripening.