Comprehensive m6A landscape from direct RNA sequencing reveals SYNPO2L RNA isoform regulation mechanisms in heart failure

Accumulating evidence suggests that epitranscriptomic regulation, particularly the m6A modification, contributes to heart failure progression. However, modification dynamics are not yet mapped and studied at base resolution and transcript isoform level. Here we use Nanopore direct RNA sequencing to profile m6A remodeling at transcriptome-wide and site-specific resolution in a mouse heart failure model. We identify thousands of differentially methylated sites with distinct sequence motifs and associations with RNA regulatory and cardiac function processes. Cross-species comparison reveals conserved m6A regulatory features in mouse and human heart failure. Isoform-resolved analysis further uncovers co/posttranscriptional regulation events involving isoform switching and m6A regulation in the SYNPO2L transcript. Mechanistically, m6A modification, alternative promoter usage and associated regulatory elements collectively explain this observation. Overall, our study provides a comprehensive, high-resolution characterization of m6A landscape and its remodeling in heart failure. Isoform-level regulation exemplifies an underappreciated shaping of RNA expression and modification. Xu et al. use nanopore direct RNA sequencing to map heart failure-associated m6A RNA modifications at transcriptome-wide and single-site resolution. Their findings reveal conserved m6A remodeling patterns and isoform-specific regulation of SYNPO2L, highlighting complex epitranscriptomic mechanisms that influence cardiac gene expression and contribute to heart failure progression.