The bladder cancer m ⁶ A landscape is defined by methylation dilution and 3′-UTR hypermethylation

N ⁶ -Methyladenosine (m ⁶ A) is the most abundant internal modification of eukaryotic mRNAs and regulates target transcripts throughout the mRNA life cycle. Although changes in m ⁶ A have been reported in human cancers, technical limitations have hindered a comprehensive understanding of the cancer-associated m ⁶ A landscape. Here, we used GLORI-sequencing to establish the first transcriptome-wide, single-nucleotide resolution maps of m ⁶ A in cancer. Differentially methylated transcripts were enriched in oncogenic pathways relevant to UCB. We discovered two key m ⁶ A signatures in UCB: a global loss of methylation and a local hypermethylation at 3′-UTRs. Integration of RNA-sequencing data revealed that the global loss resulted from dilution of methylation marks due to increased expression of unmethylated transcripts and decreased expression of highly methylated transcripts. In contrast, local 3′-UTR hypermethylation was associated with the overexpression of VIRMA, a component of the m ⁶ A writer complex, which was linked to UCB progression. Our study is the first to describe the m ⁶ A epitranscriptomic landscape of cancer at single-base resolution and provides first insights into the processes that generate its characteristic signatures.