Abstract

N6-methyladenosine (m6A) is a pervasive RNA modification with critical roles in post-transcriptional regulation, yet accurate transcriptome-wide identification of functional m6A sites remains challenging. Here, we present M6AFormer, a hybrid deep-learning framework that combines convolutional feature extraction with a lightweight Transformer to capture both local sequence motifs and broader contextual dependencies. M6AFormer consistently outperformed representative m6A predictors, including MST-M6A, CLSM6A and deepSRAMP. Transcriptome-wide scanning revealed a large repertoire of previously unannotated candidate m6A sites that retained hallmark m6A features, including canonical motif enrichment, characteristic spatial distribution and preferential overlap with m6A writer and reader binding regions. Importantly, M6AFormer-predicted sites were broadly associated with genetic and disease-relevant features, including SNPs, sequence variants and GWAS-linked loci, suggesting their potential contribution to human disease mechanisms. Finally, experimental validation confirmed a previously unreported m6A site in NEU4 mRNA and demonstrated its functional impact on cancer cell migration. Together, M6AFormer provides an accurate, interpretable and biologically informative framework for m6A site discovery.