Phosphate Starvation Shapes M⁶A Modification and Poly(A) Tails to Regulate mRNA Decay in Rice

Phosphorus is essential for plant growth and reproduction. Plants have evolved diverse strategies to adapt to fluctuations in inorganic phosphate (Pi) availability by reprogramming gene expression. In addition to transcriptional regulation, RNA decay plays a crucial role in mRNA metabolism. In this study, we investigated whether RNA decay influences mRNA stability and whether m⁶A and m⁵C modifications and poly(A) tails are involved in this process, using Direct RNA sequencing for detection. We successfully established a genome-wide mRNA decay assay in rice and found that mRNA decay rates are primarily determined by G/C content in the 5' UTR, G/C content and RNA secondary structures in the CDS, m⁶A and m⁵C modifications in the 3' UTR, as well as the number of introns and the length of poly(A) tails. Both phosphate-starvation-induced (PSI) and phosphate-starvation-downregulated (PSD) genes decay faster than non-responsive genes, likely due to their higher CDS G/C content, fewer introns, and lower m⁶A modification rates. Pi starvation accelerated the decay of PSI genes but slowed the decay of PSD genes. Nanopore Direct RNA sequencing revealed that m⁶A modification and poly(A) tail length, rather than m⁵C modification, play central roles in regulating mRNA decay under Pi starvation. Furthermore, overexpression of the m⁶A reader OsYTH10 protected m⁶A-modified transcripts of OsPT2 and OsPAP21b from degradation, thereby enhancing Pi accumulation in rice. Collectively, our findings demonstrate that phosphate starvation remodels m⁶A methylations and poly(A) tails to modulate mRNA stability and shape the gene expression landscape in rice.