Abstract
Cellular identity is dictated by precise transcriptomic programs; however, the mechanisms that dynamically shape the transcriptome by producing diverse RNA isoforms remain incompletely understood. Here, through longitudinal transcriptomic profiling of cardiomyogenesis, we delineate pervasive RNA isoform switching across the developmental trajectory of cardiac differentiation. We show that the changes in isoform accumulation are largely decoupled from shifts in overall gene expression levels and arise predominantly from alternative transcription start and termination rather than splicing. This regulatory layer preferentially targets genes essential for cardiac function, specifically those encoding contractile machinery and ion channel complexes. We demonstrate that genes undergoing isoform switching without changing overall expression constitute a functionally distinct cohort, establishing isoform switching as an independent layer of gene regulation. Furthermore, we characterize stage-specific expression dynamics for numerous RNA-binding proteins and link their expression to specific isoform switching events. Our findings support a coordinated mechanism for the targeted regulation of RNA diversity, positioning isoform switching as a primary driver of transcriptomic maturation during lineage commitment.