Transcriptome-wide isoform and promoter remodeling in DM1 fibroblasts uncovered by long-read RNA sequencing

Myotonic dystrophy type 1 (DM1) is characterized by sequestration of RNA-binding proteins and widespread transcriptomic dysregulation, yet isoform-level transcriptomic landscapes remain incompletely defined. Here, we performed integrated long-read (PacBio Iso-Seq) and short-read (Illumina RNA-seq) profiling of primary fibroblasts from DM1 patients and healthy controls. Long-read sequencing identified >15,000 transcript isoforms in DM1 fibroblasts, revealing extensive alternative splicing and novel transcript discovery beyond short-read resolution. Isoform-switching analysis uncovered 104 significant events, particularly affecting signaling and cytoskeletal pathways, independent of gene-level expression changes. Differential promoter usage further highlighted transcriptional rewiring, with 106 dysregulated promoters, over two-thirds of which were previously unannotated. Moreover, systematic splicing analysis detected >1200 significantly altered events, predominantly alternative first exons, converging on extracellular matrix remodeling and muscle contractility pathways. Together, these data provide an isoform-resolved landscape of DM1 fibroblasts, demonstrating that transcript-level remodeling-including alternative splicing, isoform switching, and promoter dysregulation-constitutes a critical regulatory layer underlying DM1 pathogenesis.