MEK/ERK signaling blocks H3K9me3 heterochromatin formation to potentiate human mesoderm and endoderm differentiation. [ChIP-Seq]

Pluripotent cells differentiate into the three definitive germ layers – ectoderm, mesoderm, and endoderm, thereby establishing the foundation of the body plan. Mesoderm and endoderm arise through epithelial-to-mesenchymal transition (EMT), a critical process that occurs during gastrulation in early embryogenesis. While these differentiation processes are driven by BMP, WNT, NODAL, and FGF signaling, the functional mechanisms underlying FGF signaling remain the least understood. In this study, we demonstrate that the H3K9me3-marked facultative heterochromatin domains undergo global reorganization during the differentiation of human pluripotent stem cells into mesoderm and endoderm but not ectoderm. We reveal that the MEK/ERK pathway, critical downstream of FGF signaling during gastrulation, mediates this heterochromatin reorganization. Specifically, MEK/ERK blocks the establishment of H3K9me3 domains at EMT- and lineage-specific gene loci necessary for mesoderm and endoderm differentiation. Collectively, our findings uncover the critical role of the MEK/ERK signaling pathway in reshaping the lineage-specific H3K9me3 landscape, addressing a key gap in our knowledge of the interplay between cell singling and epigenetics in cell differentiation. Overall design: ChIP-seq data of H3K9me3 in human pluripotent stem cells (hPSCs), neuroectoderm (NE), paraxial mesoderm (PM), and definitive endoderm (DE), with or without 1 µM MEK/ERK inhibitor (PD0325901) treatment.