Exploring the Dynamics and Consequences of Differential Transcript Usage in Cardiomyocyte Fate Specification

Cardiovascular research often relies on in vitro models using induced pluripotent stem cells (iPSCs) differentiating into induced cardiomyocytes (iCM). Little is known about the changes in transcript variants, termed differential transcript usage (DTU), which greatly influence cellular programs. In this study, we explored the DTU landscape during the iPSC-to-iCM differentiation and its relation to iCM fate. We found that DTU is consistently displayed by a subset of genes during iCM differentiation. DTU largely operates on a distinct set of genes than DGE, and both impact different biological processes. The DTU is used more often by protein coding in the late stage of iCM differentiation. The DTU-displaying genes are linked with functions specific to CMs, including ion signaling and cell junction organization, and their expression is cell-type specific. The RNA binding proteins (RBPs) involved in shaping the alternative splicing during the iCM differentiation experience early directed gene expression changes in their expression. Our research emphasizes that analyzing transcript variant expression levels is crucial for uncovering novel genes and functions, and for mapping fine-tuning gene expression and cardiomyocyte-specific functions during cell differentiation. Overall design: To investigate the DTU in iCM differentiation we have establlished iPSC-to-iCM differentiation and sampled the cells at subsequent stages of differentiation.