N 6-methyladenosine modifications stabilize phosphate starvation response–related mRNAs in plant adaptation to nutrient-deficient stress

N6-methyladenosine (m6A), an abundant internal mRNA modification, is induced by various stress conditions and post-transcriptionally regulates gene expression. However, how m6A modifications help plants respond to nutrient-deficiency stress remains unclear. Here, we profile high-confidence m6A modifications in Arabidopsis transcriptome-wide under normal and inorganic orthophosphate (Pi)–deficient conditions (−P). High-confidence m6A modifications are identified using synthetic modification-free RNA libraries for systematic calibration. Pi starvation induces widespread m6A modifications, mediated by the Pi starvation response (PSR) master regulator PHOSPHATE STARVATION RESPONSE1 (PHR1) and its family members. Many Pi starvation–induced (PSI) m6A modifications occur on PSR-related mRNAs, including PHR1. In addition, PHR1 proteins interact with the m6A writers MRNA ADENOSINE METHYLASE (MTA) and METHYLTRANSFERASE B (MTB) in nuclei under −P conditions. m6A modifications facilitate systemic PSR signaling, as reflected by the reduced Pi content and PSR signaling in a knockdown artificial miRNA line targeting MTA, which shows a global decrease in m6A. Transcriptome-wide mRNA decay analysis reveals that PSI-m6A increases the stability of PSR-related mRNAs, but not through alternative polyadenylation site shifts. Analysis of transgenic plants with mutations in m6A loci demonstrates that m6A stabilizes PHR1 transcripts via a positive feedback loop. Our findings indicate that PSI-m6A modifications facilitate PSR signaling by enhancing the stability of certain mRNAs, shedding light on the role of m6A modifications in nutrient stress responses in plants.