Coordinated series of large-scale transcriptional changes and chromatin reorganization drive cell type specification and differentiation during embryogenesis. In this process, pioneer transcription factors play key roles in programming the epigenome and facilitating recruitment of additional regulatory factors. Isl1, a LIM-homeodomain transcription factor, marks the second heart field and plays a key role in early cardiac development. However, the early embryonic lethality of Isl1 knockout mouse makes it impossible to study the role of Isl1 at later stages of mouse heart development. The role of Isl1 in epigenetic regulation during second heart field development and the mechanisms behind are still not clear. In this study, using an Isl1 hypomorphic mouse model, we found Isl1 is critical for cardiac development even at the later stages of embryonic development. To search for the downstream targets of Isl1 during cardiogenesis, we performed RNA-Sequencing with an Isl1 knockout mouse model and the Isl1 hypomorphic mouse model, together with a mESC-based directed cardiac differentiation system. In combination with ChIP in mESC-derived cardiac progenitor cells and in mouse embryos followed by high-throughput sequencing, we identified a regulatory gene network in cardiac progenitor cells and their derivatives organizing by Isl1. To investigate the molecular mechanism underlying the role of Isl1 in second heart field development, we firstly revealed that Isl1 interacts with Brg1 and Baf60c in cardiac progenitor cells by co-immunoprecipitation. We further performed ATAC-sequencing in mESC-derived cardiac progenitor cells and in mouse embryos. Analysis of ATAC-sequencing data, combined with genome-wide profiling of Isl1 binding in mESC-derived cardiac progenitor cells and in mouse embryos, we identified that Isl1 acts as a pioneer factor during cardiogenesis. Moreover, we found Isl1 might recruit Brg1 to its target sites and works cooperatively with the Brg1-Baf60c-based SWI/SNF complex to reorganize the chromatin landscape of target genes with critical functions in cardiac development, thus inducing gene expression programs in cardiac progenitors and promoting cardiac cell fate specification.In conclusion, our study highlights a pioneering function of Isl1 in cardiac lineage commitment and provides exciting novel insights into the molecular machinery orchestrating cardiogenesis.
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