The dynamic N¹-methyladenosine RNA methylation provides insights into the tomato fruit ripening

N¹-methyladenosine (m¹A) methylation is an essential mechanism of gene regulation known to impact several biological processes in living organisms. However, little is known about the abundance, distribution, and functional significance of mRNA m¹A modification during fruit ripening of tomato the main model species for fleshy fruits. Our study shows that m¹A modifications are prevalent in tomato mRNA and are detected in lncRNA and circRNA. The distribution of m¹A peaks in mRNA segments indicates that m¹A is mainly enriched at the start codon and CDS regions. Assessing changes in global RNA methylation during fruit ripening in wild-type tomatoes and in the ripening-impaired Nr mutant affected in the ethylene receptor gene (SlETR3) revealed a decrease in the overall methylation levels from mature green (MG) stage to 6 days postbreaker (Br + 6). Nr mutant fruits show significantly lower methylation levels than Ailsa Craig (AC) fruits. Notably, differences in m¹A methylation are well correlated to the expression levels of a number of key ripening-related genes. The integration of RNA-seq and MeRIP-seq data suggests a potential positive impact of m¹A modifications on gene expression. In comparison to the AC fruits, the hypomethylation and reduced expression of ethylene-related genes, ACO3, EBF1, and ERF.D6, in the Nr mutants likely underpin the distinct phenotypic traits observed between the two fruit genotypes at the Br6 stage. Overall, our study brings further arguments supporting the potential significance of m¹A methylation modifications in fruit ripening, a developmental process that is instrumental to plant reproduction and to fruit sensory and nutritional qualities.