Isoform-Resolved Post-Transcriptional Regulation in Human Skin Wound Healing

Tissue repair requires rapid changes in cell state and gene function, yet most studies have focused on gene abundance and overlooked how transcript isoforms shape gene output during repair. Here, we built a cell-type-specific, isoform-resolved atlas of human skin wound repair by integrating PacBio Iso-Seq, deep short-read RNA-seq, and single-cell transcriptomics from a longitudinal human in vivo wound model with donor-matched intact skin and wound tissues. PacBio Iso-Seq defined a high-confidence full-length transcriptome reference for fibroblasts and keratinocytes, revealing marked cell-type specificity among previously unannotated transcripts. Quantitative profiling of day-7 wound cells uncovered extensive isoform-level reprogramming, including differential isoform abundance and isoform-switching events beyond total gene-expression changes. Alternative splicing was dominated by skipped-exon events in both fibroblasts and keratinocytes, with FN1 emerging as a major wound-regulated splicing target in fibroblasts. Single-cell exon-skipping analysis further refined wound cell-state classification and linked injury-associated exon usage to chromatin organization and stress responses. Alternative promoter usage revealed widespread 5' initiation diversity affecting 18% of fibroblast genes and 12% of keratinocyte genes, while single-cell alternative polyadenylation identified dynamic 3' end regulation, including pronounced 3' UTR shortening in proliferative-phase fibroblasts. Together with an interactive public browser, our study establishes transcript isoform remodeling as a key regulatory dimension of human skin wound healing and provides a foundation for future isoform-aware studies of tissue repair.