Transcription factor NFYA3_0 promotes MTA-mediated m6A modification of PVY genomic RNA to confer antiviral resistance in Nicotiana benthamiana

N⁶-methyladenosine (m⁶A), a reversible epigenetic modification, is ubiquitously present across diverse RNA species, including viral RNA. This modification plays a pivotal role in orchestrating RNA metabolism. Nevertheless, the mechanisms by which plants utilize m⁶A modifications to fine-tune antiviral immunity remain largely unknown. In this study, we systematically examined the dynamic changes and biological significance of m⁶A modifications throughout potato virus Y (PVY) infection in host plants. Methylated RNA immunoprecipitation sequencing reveals a conserved m⁶A distribution pattern in Nicotiana benthamiana, predominantly enriched in 3' untranslated regions of transcripts. The nuclear transcription factor NFYA3_0 exhibits robust hypermethylation accompanied by transcriptional upregulation during PVY infection. NFYA3_0 knockdown promotes PVY accumulation and reduces global m⁶A modification levels in the host. NFYA3_0 positively regulates transcription of the m⁶A methyltransferase gene NbMTA, whose loss of function similarly compromises viral resistance while diminishing m⁶A abundance. Moreover, NbMTA anchors and methylates the PVY coat protein-coding region, thereby facilitating viral RNA degradation and effectively restricting infection. These findings indicate that the core antiviral mechanism of the nuclear transcription factor NFYA3_0 enables targeted degradation of viral RNA by activating methyltransferase NbMTA-mediated m⁶A epitranscriptome regulation. This work provides a new strategy for developing green virus-resistant crop lines based on epigenetic editing.