RNA methylomes reveal the m6A-mediated regulation of DNA demethylase gene SlDML2 in tomato fruit ripening.
BACKGROUND
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.


RESULTS
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.


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 m6A methylation during fruit ripening.
['Zhou|Leilei|L|', 'Tian|Shiping|S|', 'Qin|Guozheng|G|0000-0003-3046-1177']
D000241:Adenosine D019175:DNA Methylation D004721:Endoplasmic Reticulum D005638:Fruit D015971:Gene Expression Regulation, Enzymologic D018506:Gene Expression Regulation, Plant D018551:Lycopersicon esculentum D008745:Methylation D009154:Mutation D059372:Nucleotide Motifs D010940:Plant Proteins D020871:RNA Stability D012333:RNA, Messenger
Tomato Fruit ripening mRNA m6A methylation DNA methylation Colorless non-ripening DNA demethylase SlDML2 RNA demethylase SlALKBH2 m6A RNA methylome