The m6A writer complex function in main stem apex development by promoting mRNA stability of GIF3, HDA6, and KNAT2/6 in Gossypium hirsutum

N6-methyladenosine (m⁶A) is the most abundant internal posttranscriptional modification of eukaryotic messenger RNA (mRNA), which can be involved in the regulation of mRNA metabolism and processing. Although some progress has been made in understanding the methylation mechanism of mRNA m⁶A in plants, our knowledge and comprehension of this process in cotton is still significantly limited. In this study, we identified the cotton m⁶A writers, namely GhMTA-A/D, GhMTB-A/D, and GhFIP37-A/D. These writers are localized within the nucleus. Notably, GhMTA-D has been found to interact with both GhMTB-A and GhFIP37-A. The knockdown of each cotton m⁶A writer gene, achieved through virus-induced gene silencing, resulted in decreased mRNA m⁶A levels in cotton main stem apex (MSA). This led to a thicker shoot apical meristem, the formation of an abnormal MSA, and dwarf plants. MeRIP-seq and RNA-seq analyses showed that m⁶A writers mediate m⁶A modification and transcripts of mRNAs in cotton MSA by recognizing the motif GGACH and/or GAAGM. Furthermore, m⁶A writers install m⁶A in GhGIF3, GhHDA6, and GhKNAT2/6 transcripts, thereby affecting their mRNA stability and regulating MSA development. In summary, our research elucidates a novel mechanism for m⁶A posttranscriptional regulation and offers valuable insights into the roles of m⁶A writers in controlling MSA development.