Dysregulation of an H3K79me2-dependent epigenetic barrier impairs neural progenitor cell proliferation and differentiation in Fragile X syndrome

Abstract

Fragile X syndrome (FXS) is a neurodevelopmental disorder caused by silencing of the FMR1 gene, which encodes the multifunctional RNA-binding protein FMRP. While FMRP is best known for its roles in RNA metabolism, it can also associate with chromatin through recognition of histone H3 lysine 79 di-methylation (H3K79me2), an epigenetic mark linked to transcriptionally active genes. However, the functional relevance of this FMRP-H3K79me2 interaction has remained largely unexplored in the context of FXS pathophysiology. We assessed H3K79me2 levels during the differentiation of induced pluripotent stem cells (iPSCs) generated from both healthy individuals and FXS patients and discovered a global increase in H3K79me2 levels specifically in FXS neural progenitor cells (NPCs). Altered H3K79me2 landscape drives widespread transcriptional dysregulation, characterized by reduced expression of neurogenesis-associated genes alongside aberrant activation of programs promoting proliferation and glial lineage commitment. Functionally, these changes result in enhanced NPCs proliferation and a biased differentiation trajectory. Notably, pharmacological reduction of global H3K79me2 levels in FXS NPCs using DOT1L inhibitors effectively mitigates these defects, restoring proliferation rate and rebalancing lineage specification, thereby rescuing key aspects of the pathological phenotype. Collectively, our findings identify an H3K79me2-dependent epigenetic barrier regulating NPC proliferation and lineage commitment and link its dysregulation to the neurodevelopmental defects associated with FXS.