MAPK/ERK signaling regulates H3K9me3 heterochromatin reorganization to confer mesendoderm developmental competence

During gastrulation, dynamic interplay among cell signaling pathways dictates cell fate decisions. While extensive studies have elucidated their critical roles in morphological regulation, how these signals orchestrate the epigenome to confer developmental competence remains unclear. In this study, we demonstrate that H3K9me3-marked facultative heterochromatin domains undergo global reorganization during differentiation of human pluripotent stem cells (hPSCs) into mesendoderm (ME) and definitive endoderm (DE), which arise through epithelial-mesenchymal transition (EMT), but not into early neural ectoderm (NE), which retains epithelial state. We identify the MAPK/ERK pathway, acting downstream of FGF signaling, as a key mediator of this reorganization within a critical temporal window during hPSC-to-ME differentiation. Mechanistically, phosphorylated-ERK is enriched across chromatin domains spanning key developmental gene loci and exhibits a reciprocal genomic pattern with H3K9me3, which becomes ectopically accumulated upon MAPK/ERK inhibition. Furthermore, using CRISPRi-mediated perturbation of H3K9me3 methyltransferases, we reveal that proper establishment of H3K9me3 domains plays a dual role in repressing off-target genes and enabling robust activation of lineage-specific programs. Collectively, our findings reveal a previously unrecognized role for MAPK/ERK signaling in reorganizing the H3K9me3 landscape to confer developmental competence, providing mechanistic insight into how signaling pathways shape the epigenetic landscape during development.