Year: 2026
Type: preprint
Abstract: Background Autism spectrum disorder (ASD) shows a strong male bias (∼4:1). CHD8, a frequently mutated ASD gene, regulates neuronal development and Xist regulation in X-chromosome inactivation (XCI). However, its role in female neurodevelopment remains poorly understood due to the predominance of male-derived or sex-agnostic models. Methods We performed integrated multi-omics analysis of female mouse embryonic stem cells (ES) differentiating to neuronal progenitor cells (NPCs) using wild-type, CHD8 knockdown (KD), knockout (KO), and domain-specific rescue lines (full-length, ΔChromo, ΔHelicase). RNA-seq, CHD8 and H3K4me3 ChIP-seq, and ATAC-seq datasets were integrated to assess transcriptional, chromatin-binding and -accessibility changes during differentiation. Results CHD8 occupancy was substantially remodelled during female neuronal differentiation, with 3,754 genes gaining NPCs-specific CHD8 binding predominantly at distal regulatory elements. CHD8 loss dysregulated 2,752 genes (1,134 upregulated and 1,618 downregulated), in NPCs. Differential accessibility analysis identified 4,486 chromatin regions with significant CHD8-dependent changes. Domain-specific rescue experiments showed that chromodomain and helicase activity makes distinct, non-redundant contributions to transcriptional recovery: ΔChromo-rescued only ∼ 1.0% of CHD8-dependent transcriptional changes, ΔHelicase rescued ∼ 41.1%, and full-length CHD8 rescued ∼ 70%. Integration of binding, expression, and accessibility data identified 8 high-confidence direct CHD8 target genes, and cross-referencing with the SFARI Autism Risk Gene database revealed that CHD8-dependent transcriptional changes converge on autism-related pathways. Conclusions CHD8 acts as a key regulator of female-derived neuronal differentiation, recruited to H3K4me3-marked promoters in a chromodomain-dependent manner, with helicase activity providing non-redundant regulatory capacity at a subset of targets. These findings provide a molecular framework for CHD8-dependent transcriptional regulation in female NPCs and underscore the importance of including female-derived systems in neurodevelopmental disorder research. Graphical Abstract
Institutions: National Institute of Immunology, Saint Camillus International University of Health and Medical Sciences, Università degli Studi del Piemonte Orientale “Amedeo Avogadro”, Casa Sollievo della Sofferenza, Queen Mary University of London, King's College London, Blizard Institute, University of Pisa, Ostim Technical University, Italian Institute of Technology, Egyptian Russian University, European Molecular Biology Laboratory
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7212157044