Phytochrome B and the methyltransferase complex coordinately regulate N6-methyladenosine RNA modifications and shade avoidance responses in Arabidopsis

Shade avoidance is a critical adaptive strategy employed by plants to respond to competition. N⁶-methyladenosine (m⁶A), the most abundant and dynamic mRNA modification, has emerged as a key epigenetic mechanism regulating adaptive responses. Here, we demonstrate that shade significantly reduces global m⁶A levels in a manner dependent on phytochrome B (phyB) and the m⁶A methyltransferase complex (MTC). Shade attenuates the interaction between phyB and the MTC, impairing the RNA-binding capacity and methyltransferase activity of the complex. Transcriptome-wide m⁶A profiling showed that shade and phyB mutation similarly reduce m⁶A modifications, particularly on transcripts involved in auxin and abscisic acid (ABA) signaling pathways. Phenotypic analysis confirmed that the MTC is essential for shade-induced hypocotyl elongation and ABA hypersensitivity. Mechanistically, shade-induced m⁶A reduction increases the stabilization of SAUR15/19/20 transcripts and decreases the translation efficiency of ABA signaling repressors SNZ, MYB20, and PROPEP3. Our findings reveal a mechanism by which phyB modulates m⁶A deposition to fine-tune plant elongation and stress adaptation under shade.