m6A-mediated epi-transcriptomic dysregulation underlies synaptic dysfunction in fragile X syndrome [MeRIP-seq]

N6-methyladenosine (m6A) is a prevalent mRNA modification essential for post-transcriptional regulation. Fragile X syndrome (FXS), the leading genetic cause of intellectual disability, arises from FMR1 gene silencing and loss of FMRP, which has been shown to antagonize m6A readers. However, the impact of FMRP loss on transcriptome-wide m6A modifications in human FXS remains unknown. Using cortical neurons derived from healthy subjects and FXS patient-induced pluripotent stem cells, we found that FXS neurons exhibited synaptic and neuronal network defects, mirroring clinical EEG data from the same FXS patients. FMRP deficiency led to increased translation of m6A writers, resulting in transcriptome-wide hypermethylation, primarily affecting synapse-associated transcripts and increasing mRNA decay. Treatment with an m6A writer inhibitor rescued synaptic defects in FXS neurons, highlighting its therapeutic potential. Our findings uncover an epi-transcriptomic mechanism by which FMRP deficiency disrupts m6A modifications in FXS, contributing to FXS pathogenesis, and suggest a promising avenue for m6A-targeted therapies. To unravel the transcriptome-wide m6A landscape in FXS, we employed methylated RNA immunoprecipitation sequencing (MeRIP-Seq) on FXS neurons derived from six FXS patients and compared the results with seven control samples. Additionally, MeRIP-seq was performed on postmortem cortex tissues obtained from three FXS patients and healthy control subjects.