Identification of tissue-specific RBFOX1 alternative promoters in the developing brain, heart and muscle

The precise regulation of cell type- and time-specific gene expression is highly dependent on the use of alternative promoters, enhancers and silencers. The recent advancement of genomic technologies has driven the identification of potential promoter regions for a large number of genes. Nevertheless, comprehensive analyses of alternative promoter usage across diverse tissues and developmental stages remain limited for the majority of human genes. In this study, we identified putative promoter regions located upstream of the alternative first exons of RBFOX1 using publicly available databases and functionally validated them in vivo via reporter gene expression assays in transgenic zebrafish. We uncovered both tissue-restricted and ubiquitously active promoters that collectively shape the complex regulatory expression profile of this essential developmental gene. We also mapped the core promoter of RBFOX1 -E1B, defining its minimal functional unit and demonstrating that endogenous minimal promoters confer tissue-specific enhancer responsiveness that generic heterologous promoters lack. Together, these findings shed light on the complex cis -regulatory machinery driving the precise spatiotemporal expression of this key gene in neurodevelopment and muscle differentiation, and provide a foundation for the development of more specific reporter systems and gene therapy tools targeting neurological diseases.