Unique features of mRNA m6A methylomes during expansion of tomato (Solanum lycopersicum) fruits

Global mRNA m6A levels increase during tomato fruit expansion from immature green to mature green stages, and expansion and ripening of tomato fruits require dynamic modification of m6A. N6-methyladenosine (m(6)A) is the most abundant internal modification in eukaryotic messenger RNA. Although the role of m(6)A has been demonstrated in many biological processes, including embryonic development, flowering time control, microspore generation, fruit ripening, and stress responses, its contribution to other aspects of plant development still needs to be explored. Herein, we show the potential link between m(6)A deposition and the expansion of tomato (Solanum lycopersicum) fruits through parallel m(6)A-immunoprecipitation-sequencing (m(6)A-seq) and RNA-seq analyses. We found that global m(6)A levels increased during tomato fruit expansion from immature green to mature green stage. m(6)A-seq revealed that thousands of protein-coding genes are m(6)A-modified mainly in the 3MODIFIER LETTER PRIME-untranslated regions. m(6)A-seq and RNA-seq analyses showed a positive association between m(6)A methylation and mRNA abundance. In particular, a large number of fruit expansion-related genes involved in hormone responses and endoreduplication were m(6)A modified and expressed more actively than the non-m(6)A-modified genes, suggesting a potential role of m(6)A modification in tomato fruit expansion. Importantly, altering m(6)A levels by direct injection of 3-deazaneplanocin A (DA; m(6)A writer inhibitor) or meclofenamic acid (MA; m(6)A eraser inhibitor) into tomato fruits suppressed fruit expansion; however, injection of exogenous DA or MA accelerated or delayed fruit ripening, respectively. Collectively, these results suggest a dynamic role of m(6)A methylation in the expansion and ripening of tomato fruits.

Automated summary

Global mRNA m6A levels increase during tomato fruit expansion, and there is a positive association between m6A methylation and the expression of expansion-related genes. Furthermore, altering m6A levels can affect both the expansion and ripening of tomato fruits.