The m(6)A pathway protects the transcriptome integrity by restricting RNA chimera formation in plants

Global, segmental, and gene duplication–related processes are driving genome size and complexity in plants. Despite their evolutionary potentials, those processes can also have adverse effects on genome regulation, thus implying the existence of specialized corrective mechanisms. Here, we report that an N6-methyladenosine (m(6)A)–assisted polyadenylation (m-ASP) pathway ensures transcriptome integrity in Arabidopsis thaliana. Efficient m-ASP pathway activity requires the m(6)A methyltransferase-associated factor FIP37 and CPSF30L, an m(6)A reader corresponding to an YT512-B Homology Domain-containing protein (YTHDC)-type domain containing isoform of the 30-kD subunit of cleavage and polyadenylation specificity factor. Targets of the m-ASP pathway are enriched in recently rearranged gene pairs, displayed an atypical chromatin signature, and showed transcriptional readthrough and mRNA chimera formation in FIP37- and CPSF30L-deficient plants. Furthermore, we showed that the m-ASP pathway can also restrict the formation of chimeric gene/transposable-element transcript, suggesting a possible implication of this pathway in the control of transposable elements at specific locus. Taken together, our results point to selective recognition of 3′-UTR m(6)A as a safeguard mechanism ensuring transcriptome integrity at rearranged genomic loci in plants.