RNA m6A modification co-transcriptionally facilitates DNA methylation in maize

N6-methyladenosine (m6A) in mRNA and 5-methylcytosine (5mC) in DNA act critical functions on regulating gene expression and modulating plant growth and development. However, the interplay between m6A and 5mC is an unexplored territory and remains uncharacterized mechanistically. Here we report an occurrence of crosstalk between m6A and 5mC in maize via the physical interaction between ZmMTA, the core component of the m6A methyltransferase complex, and ZmDDM1, a key chromatin-remodeling factor regulating DNA methylation. Genes with m6A modification coordinated with much higher level of DNA methylation compared to genes without m6A modification. Dysfunction of ZmMTA caused severe arrect in maize embryogenesis and endosperm development, leading to a significant decrease of CHH methylation in 5- regions of m6A-modified genes. Instead, loss-of-function of ZmDDM1 had no noteworthy effects on ZmMTA-related activity. This study establishes a direct link between m6A and 5mC during maize kernel development, and provides moonlighting insight into the co-transcriptional interplay between RNA modification and DNA methylation.