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. This study reports that m6A on retrotransposon RNAs is recognized by nuclear readers CPSF30-L and ECT12, which associate with SUVH4/5/6 and ATXR5/6 to enhance H3 K9 dimethylation and H3 K27 monomethylation at specific sites, thereby leading to closed heterochromatin states and transcriptional silencing.