RT Journal
A1 Delimata-Raczek, Joanna
A1 Koralewska, Natalia
A1 Krist, Bart
A1 Rakoczy, Magdalena
A1 Figlerowicz, Marek
A1 Stolarek, Ireneusz
T1 Dynamics and consequences of differential RNA isoform production during cardiomyocyte fate determination and early-stage maturation
JF Genome Research 
JO Genome Research 
YR 2026 
FD April 03 
DO 10.1101/gr.281150.125 
SP gr.281150.125 
UL http://genome.cshlp.org/content/early/2026/04/03/gr.281150.125.abstract 
AB 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.