CPSF30-L-mediated recognition of mRNA m6A modification controls alternative polyadenylation of nitrate signaling-related gene transcripts in Arabidopsis

N-methyladenosine (mA), a ubiquitous internal modification of eukaryotic mRNAs, plays a vital role in almost every aspect of mRNA metabolism. However, there is little evidence documenting the role of mA in regulating alternative polyadenylation (APA) in plants. APA is controlled by a large protein-RNA complex with many components, including CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR30 (CPSF30). In Arabidopsis, CPSF30 has two isoforms and the longer isoform (CPSF30-L) contains a YT512-B Homology (YTH) domain, which is unique to plants. In this study, we showed that CPSF30-L YTH domain binds to mA in vitro. In the cpsf30-2 mutant, the transcripts of many genes including several important nitrate signaling-related genes had shifts in polyadenylation sites that were correlated with mA peaks, indicating that these gene transcripts carrying mA tend to be regulated by APA. Wild-type CPSF30-L could rescue the defects in APA and nitrate metabolism in cpsf30-2, but mA-binding-defective mutants of CPSF30-L could not. Taken together, our results demonstrated that mA modification regulates APA in Arabidopsis and revealed that the mA reader CPSF30-L affects nitrate signaling by controlling APA, shedding new light on the roles of the mA modification during RNA 3′-end processing in nitrate metabolism.