MicroRNA Biogenesis Modulates mRNA N⁶-methyladenosine Methylation in Arabidopsis

N⁶-methyladenosine (m⁶A) is the most abundant modification observed in eukaryotic mRNAs. With the advances of transcriptome-wide m⁶A mapping and sequencing technologies, several conserved motifs, including RRACH (R = A/G and H = A/C/U) and UGUAH motifs, have been identified in plants mainly in the 3ʹ-untranslated region (UTR) and around the stop codon. However, the mechanisms underlying the deposition of the m⁶A marks at a specific position of the conserved motif in each transcript are largely known. A previous study in animals has shown that microRNAs (miRNAs) may play a role in depositing m⁶A marks at a specific site in a transcript via a base-pairing mechanism. To understand the potential involvement of miRNAs in the sequence-specific deposition of m⁶A marks in plants, in this study, we performed m⁶A-seq and RNA-seq for a mutant of dicer-like 1 (dcl1), a key component in miRNA biogenesis in Arabidopsis (Arabidopsis thaliana). The global m⁶A levels were marginally reduced in the dcl1 mutant compared to the wild type. Approximately 236 and 234 genes were m⁶A-hypomethylated and -hypermethylated in the dcl1 mutant, respectively. The DCL1-mediated m⁶A methylation contributed negatively to the global expression of genes involved in transcription regulation, phosphorylation, oxidation‒reduction, and defense/stress responses. Although not experimentally proven in this study, the prediction of potential miRNAs that could bind to m⁶A-modified transcripts suggested a possible association between miRNA and m⁶A enrichment. Collectively, these results propose a potential correlation between miRNA biogenesis and sequence-specific m⁶A methylation in Arabidopsis.