MSL2 disruption leads to autism-like behaviors, impairs neurogenesis, and alters histone H4K16 acetylation.

Neurodevelopmental disorders (NDDs) are frequently associated with dysregulation of epigenetic mechanisms. Recent studies have implicated variants in components of the Male-Specific Lethal (MSL) complex, including MSL2, in NDD pathogenesis. However, the pathogenic mechanisms underlying MSL2-related neurodevelopmental disorders remain poorly defined. Here, we elucidate the role of MSL2 in neurodevelopment and NDDs through comprehensive analysis of conditional knockout mice and multi-omics profiling. Aggregation of published and unpublished genomic data and case series revealed that pathogenic variants in MSL complex components, including MSL2, presented with shared phenotypes. Using a nervous system-specific Msl2 conditional knockout mouse model, we demonstrate that Msl2 deficiency leads to impaired social novelty recognition, learning deficits, and spatial memory impairments. These behavioral abnormalities are characterized by disrupted neocortical lamination, compromised proliferation capacity and differentiative ability of neural progenitor cells, and reduced neuronal migration. Mechanistically, Msl2-deficient brains exhibit significantly reduced levels of histone H4 lysine 16 acetylation (H4K16ac), particularly at promoter regions. Integrated RNA-seq, ChIP-seq, and ATAC-seq analyses revealed widespread transcriptional downregulation and loss of chromatin accessibility at NDD-related genes. Variants in the MSL2 DNA-binding domain disrupted its ability to target key regulatory genes including FMR1, confirming direct epigenetic regulation. Together, these findings demonstrate that MSL2 promotes neurodevelopment primarily by maintaining chromatin accessibility through H4K16ac deposition, and its disruption underlies the molecular and behavioral hallmarks of NDDs.