ATP-dependent chromatin remodelers utilize the energy from ATP hydrolysis to reposition or evict nucleosomes, a process essential for downstream biological events such as transcription (Clapier and Cairns, 2009). Chromatin remodelers are critical for development, and pathogenic variants in these proteins are associated with a range of developmental disorders (Ho and Crabtree, 2010; Gourisankar et al., 2024). CHARGE syndrome (MIM: 214800), a severe developmental disorder, is caused by heterozygous variants in chromodomain helicase DNA-binding protein 7 (CHD7), which encodes a chromatin remodeler (Vissers et al., 2004). In addition, CHD7 variants have been identified in patients with Idiopathic Hypogonadotropic Hypogonadism (IHH), with or without anosmia (Kim et al., 2008; Jongmans et al., 2009). Notably, in CHARGE syndrome, more than 90% of CHD7 variants, including nonsense, frameshift, and splice-site variants, lead to protein truncation (Basson and van Ravenswaaij-Arts, 2015). By contrast, over 70% of CHD7 variants in IHH are missense variants (Balasubramanian et al., 2014; Marcos et al., 2014). However, the molecular characterization of most CHD7 missense variants remains unknown because of the lack of appropriate assays.

Three CHD7 missense variants reported in CHARGE and IHH patients have been shown to impair CHD7 ATPase and nucleosome remodeling activity (Bouazoune and Kingston, 2012). Notably, a serine-to-phenylalanine substitution (S834F) in the first chromodomain of CHD7 causes a complete loss of enzymatic activity. The S834F mutation was identified in three familial CHARGE syndrome patients and in one IHH patient (Delahaye et al., 2007; Kim et al., 2008). A mouse line carrying the Chd7 S824F mutation, corresponding to the human S834F variant, has been reported (Yan et al., 2020). All Chd7S824F/S824F embryos died between embryonic day 10.5 and 12.5 (E10.5–E12.5), a phenotype comparable to, but slightly less severe than, that of Chd7-null embryos (Alavizadeh et al., 2001; Hurd et al., 2007). This finding suggests an enzymatic activity-independent role of CHD7 in development. The authors further showed that, in cardiac neural crest cells, CHD7 recruits the WDR5-containing H3K4 methyltransferase complex to activate gene expression in an ATPase-independent manner (Yan et al., 2020). However, whether similar molecular regulation occurs in the nervous system and how the Chd7 S824F mutation affects neural phenotypes remain to be determined.

In this study, we generated mouse embryonic stem cell (mESC) lines carrying either the ATPase-deficient Chd7 S824F mutation or an inducible knockout allele (RosaCT-Chd7f/f), derived from genetically modified mouse lines. Embryoid body (EB) and teratoma assays revealed defects in neural induction and differentiation in Chd7-mutant cells. Results from multiple neural differentiation assays, including cerebral organoids, retinoic acid-induced differentiation, and NGN2-induced neuronal differentiation, further demonstrated that CHD7 enzymatic activity is indispensable for maintaining neural gene expression. Transcriptomic and epigenomic analyses revealed that CHD7 chromatin remodeling activity is required for the deposition of active histone marks and the maintenance of open chromatin at neural gene loci. Together, these findings elucidate the molecular mechanisms through which CHD7 orchestrates neural differentiation and provide insights into its essential role in neurodevelopment.