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

N6-methyladenosine (mA) 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 mA in plants, our knowledge and comprehension of this process in cotton is still significantly limited. In this study, we identified the cotton mA 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 mA writer gene, achieved through virus-induced gene silencing, resulted in decreased mRNA mA 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 mA writers mediate mA modification and transcripts of mRNAs in cotton MSA by recognizing the motif GGACH and/or GAAGM. Furthermore, mA writers install mA 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 mA posttranscriptional regulation and offers valuable insights into the roles of mA writers in controlling MSA development.