NERD-dependent m⁶A modification of the nascent FLC transcript regulates flowering time in Arabidopsis

N⁶-methyladenosine (m⁶A) is the most prevalent internal modification on messenger RNA. Although recent studies have shown m⁶A effects on determining the fate of mRNA through modulating various aspects of plant mRNA metabolism, whether and how m⁶A affects gene transcription in plants remains elusive. Here we show that NEEDED FOR RDR2-INDEPENDENT DNA METHYLATION (NERD), a plant-specific protein, is an essential component of the m⁶A methyltransferase complex required for regulating the transcription of a central floral repressor FLOWERING LOCUS C (FLC) in Arabidopsis. NERD interacts with and stabilizes the two core methyltransferases, mRNA adenosine methylases A and B, to promote m⁶A modification of nascent RNA, conferring an overall negative effect on gene transcription. At the FLC locus, NERD-mediated m⁶A modification on the nascent transcript negatively affects H3K36me3 deposition and FLC transcription through NERD interaction with the H3K36me3 methyltransferase SET DOMAIN GROUP 8. Collectively, our findings reveal that NERD mediates the crosstalk between epitranscriptomic and epigenetic regulation of FLC to modulate flowering in Arabidopsis.