RNA m6A regulates the transcription and heterochromatin state of retrotransposons in Arabidopsis

Chromatin and transcription states are crucial for establishing and maintaining gene regulation and genome integrity, governed by a complex network of epigenetic modifications. Despite significant advancements, the interplay between epitranscriptomic and epigenetic modifications in transcriptional regulation and chromatin state remains elusive in plants. Here we profile a comprehensive spectrum of N⁶-methyladenosine (m⁶A) on chromatin-associated RNAs, especially retrotransposon transcripts, in Arabidopsis. We show that m⁶A writer subunits FIP37 and VIR mediate the methylation of retrotransposon RNAs, which are recognized by the nuclear m⁶A reader proteins CPSF30-L and ECT12, leading to a closed heterochromatin state and transcription suppression of m⁶A retrotransposon RNAs. Through monitoring nuclear RNA stability and transcription rate upon the depletion of either writer or reader, we provide evidence consistent with a model in which CPSF30-L associates with SUVH4/5/6 and ATXR5/6 and contributes to histone H3 K9 dimethylation and H3 K27 monomethylation at m⁶A-marked retrotransposons. Our findings elucidate a regulatory mechanism involving RNA m⁶A formation and recognition, coupled with histone modifications, thereby highlighting the intricate epitranscriptomic and epigenetic interplay in plant physiological and biological processes.