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RNA methylomes reveal the m6A-mediated regulation of DNA demethylase gene SlDML2 in tomato fruit ripening
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RNA methylomes reveal the m6A-mediated regulation of DNA demethylase gene SlDML2 in tomato fruit ripening
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Journal Article
RNA methylomes reveal the m6A-mediated regulation of DNA demethylase gene SlDML2 in tomato fruit ripening
2019
Overview
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.
Publisher
BioMed Central,Springer Nature B.V,BMC
Subject
/ Animal Genetics and Genomics
/ Biomedical and Life Sciences
/ Codons
/ DNA
/ Fruits
/ Genes
/ Genomes
/ Microbial Genetics and Genomics
/ mutants
/ Mutation
/ Proteins
/ Ripening
/ RNA
/ tomatoes
