FPU2025 - Productividad transcripcional de los contactos entre enhancers y promotores

We previously implemented a synthetic engineering approach to systematically compare the regulatory properties of different types of enhancers (Pachano et al., Nat Genet, 2021). Using this synthetic engineering approach, we recently uncovered that the strong regulatory activity of enhancers clusters (i.e. super-enhancers) can not be explained by changes in enhancer-promoter contact frequency or the formation of transcriptional condensates. Instead, our data suggest that the emergent regulatory properties of enhancer clustering might preferentially entail an increase in the fraction of transcriptionally productive enhancer-promoter contacts (Haro et al., bioRxiv, 2025). We now aim at systematically evaluating whether different types of enhancers control target gene expression by preferentially increasing either enhancer–promoter contact frequency and/or the productivity of such contacts. To do so, we will (1) engineer mESC lines containing different types of synthetic enhancers (i.e. “core” enhancer alone, 4x ”core” enhancer cluster, “core” enhancer + CpG island, “core” enhancer + 3xCTCF) and reporter systems (i.e. MS2-MCP, ANCHOR); (2) use these systems to simultaneously measure enhancer–promoter distances (ANCHOR system) and nascent transcription (MS2-MCP system) using super-resolution live imaging upon neural differentiation; (3) reconcile conflicting observations regarding the importance of enhancer–promoter