The N-Methyladenosine Methylome of Petunia mRNA.

N-methyladenosine is a unique type of base methylation in that it blocks Watson-Crick base pairing and introduces a positive charge. mA is prevalent in yeast and mammalian mRNA and plays a functional role. However, little is known about the abundance, dynamics, and topology of this modification in plant mRNA. Dot blotting and liquid chromatography tandem mass spectrometry analyses revealed a dynamic pattern of mA mRNA modification in various tissues and at different developmental stages in petunia (), a model system for plant growth and development. We performed transcriptome-wide profiling of mA in petunia mRNA by mA mRNA immunoprecipitation followed by a deep-sequencing approach (mA-seq, using an mA-specific antibody). mA-seq analysis identified 4,993 mA peaks in 3,231 genes expressed in petunia corollas; there were 251 mA peaks in which A residues were partly replaced by thymine and/or reverse transcription stopped at an adenine site. mA was enriched in coding sequences, with single peaks located immediately after start codons. Ethylene treatment upregulated 400 mA peaks in 375 mRNAs and downregulated 603 mA peaks in 530 mRNAs in petunia corollas; 975 mA peaks in mRNA were only detected in corollas treated with air and 430 were only detected in corollas treated with ethylene. Silencing of petunia () reduced the mA level in mRNA in vivo and in vitro. In addition, silencing caused abnormal leaf development, and the PhTRMT61A protein was localized to the nucleus. Thus, mA in mRNA is an important epitranscriptome marker and plays a role in plant growth and development.