Stage-specific epigenetic priming amplifies gene activation during lineage commitment

Neural progenitor cells exhibit developmental plasticity as they can commit to distinct developmental trajectories. The male-specific lethal complex (MSLc) is linked to multiple developmental disorders, suggesting a role in neural fate commitment. To dissect MSLc function, we used a multipronged approach combining chronic and acute depletion models. Knockout of the MSLc scaffolding component MSL1 caused embryonic lethality by E10.5 (embryonic day 10.5), and single-cell multiomics revealed altered cell population composition across multiple germ layer–derived lineages, including neuroectoderm. Two-dimensional directed differentiation models showed that the MSLc facilitates accessibility at regulatory elements during early stages of neurogenesis. Neurodevelop-mental genes displayed reduced enhancer-promoter contacts and failed to reach appropriate expression levels when the MSLc was absent early in neural differentiation. In contrast, MSLc loss at later stages did not recapitulate this phenotype, indicating that MSLc-mediated gene priming is a key mechanism enabling timely activation of lineage-specifying transcriptional programs.