Beyond gene expression: Single-cell transcriptomics at isoform resolution

Single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of cellular heterogeneity, yet traditional scRNA-seq methods primarily capture transcript ends, limiting analyses to total gene expression. Advances in isoform-resolved scRNA-seq, including short-read technologies that span full-length transcripts and long-read technologies that directly sequence full-length transcripts end-to-end, have enabled the characterization of alternative splicing variation and transcript isoform diversity at single-cell resolution. These advances fill critical knowledge gaps about cell-type-specific transcript isoform usage and its regulation in single cells. Here, we review the evolution of isoform-resolved single-cell transcriptomics, highlighting experimental and computational innovations. We discuss its broad applications in characterizing transcriptome variation and RNA processing, and explore its emerging impact across new dimensions of single-cell biology.