Elektra-Qki and Alien-Wt1 lncRNA-protein interaction controls myocardial ion channel expression and epicardial EMT during heart development

Background The heart is the first organ to develop during embryogenesis, reflecting its vital role maintaining oxygen and nutrient delivery to the developing embryo. Initially, the heart forms as a linear tube composed of two distinct layers: the myocardium and the endocardium. A third layer, the embryonic epicardium (EE), originates soon thereafter from a transient structure called the proepicardium (PE). PE cells migrate over the myocardial surface to generate the EE, and, in subsequent stages, a subset of these epicardial cells undergoes an epithelial-to-mesenchymal transition (EMT), invades the subepicardial space and leads to epicardial-derived cells (EPDCs) colonizing the embryonic myocardium and differentiating into multiple cardiac lineages. In recent years, long non-coding RNAs (lncRNAs) have emerged as key regulators of cardiac development. Previous data from our laboratory identified two murine lncRNAs, Elektra and Alien , with differential expression between the PE and the EE. Methods In this study, we performed a comprehensive characterization of both lncRNAs, analyzing their expression in embryonic and adult tissues with a focus on the three main cardiac cell types. We evaluated their transcriptional regulation by cardiogenic transcription factors and identified lncRNA-binding proteins via RNA pull-down (PD) and mass spectrometry (MS) assays, followed by validation using RNA immunoprecipitation (RIP). Functional analyses through loss-of-function experiments, qPCR, cell migration and EMT assays revealed distinct roles for each lncRNA. Results Elektra regulated the expression of ion channel genes in the myocardium through interaction with Qki protein, while Alien modulates the epicardial EMT process by interacting with Wt1 and controlling EMT-related genes, including Snai1 , Snai2 , Cdh1 and Cdh2 . Conclusion Altogether, our findings reveal that Elektra and Alien exert important roles in cardiac development by regulating myocardial ion channel expression and epicardial EMT, respectively, supporting new insights into lncRNA-mediated regulation of heart morphogenesis.