Definition of germ cell lineage alternative splicing programs reveals a critical role for Quaking in specifying cardiac cell fate

Abstract

SummaryAlternative splicing is critical for animal ontogeny; however, its role in the earliest developmental decision, the specification of the three embryonic germ layers, is poorly understood. By performing RNA-Seq on human embryonic stem cells (hESCs) and derived definitive endoderm, cardiac mesoderm, and ectoderm cell lineages, we detect distinct alternative splicing programs associated with each lineage, with the largest splicing differences observed between definitive endoderm and cardiac mesoderm. Integrative multiomics analyses predict lineage-specific RNA binding protein regulators, including a prominent role for Quaking (QKI) in the specification of cardiac mesoderm. Remarkably, knockout of QKI in hESCs disrupts the cardiac mesoderm-associated alternative splicing program and formation of myocytes, likely in part through reduced expression of BIN1 splice variants linked to cardiac development. Our results thus uncover alternative splicing programs associated with the three germ lineages and highlight an important role for QKI and its target transcripts in the formation of cardiac mesoderm.