Blanes, N. R. | Search bioRxiv

bioRxiv2026

CHD8 orchestrates chromatin landscapes during early female neuronal differentiation

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, {Delta}Chromo, {Delta}Helicase). 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: {Delta}Chromo-rescued only ~ 1.0% of CHD8-dependent transcriptional changes, {Delta}Helicase 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.

neuroscience↗

bioRxiv2026

LBR nucleoplasmic domains regulate X-chromosome solubility and nuclear organization

The nuclear lamina plays a central role in genome organization, yet how specific lamina-associated proteins regulate chromosome architecture during development remains unclear. Here, we show that the nucleoplasmic domains of the Lamin B Receptor (LBR) are essential for X-chromosome localization at the nuclear periphery and chromatin architecture during neural differentiation. Using genetic dissection of LBR function, combined with genome-wide chromatin solubility profiling and transcriptional analyses, we demonstrate that loss of LBR N-terminal domains impairs proper cell differentiation and X chromosome inactivation (XCI), selectively disrupting chromatin structure in neural progenitors but not in pluripotent cells. Strikingly, these effects are disproportionately concentrated - but not limited to - on the inactive X chromosome, which undergoes a pronounced shift toward a more soluble chromatin state. Our findings establish the nucleoplasmic function of LBR as a key determinant of X-chromosome functionality and identify chromatin solubility and accessibility as a previously underappreciated layer of genome regulation by the nuclear lamina in XCI. Finally, our work provides definitive genetic evidence that LBRs nuclear architectural functions are molecularly separable from its metabolic sterol reductase activity, which is preserved in our model, and are critically necessary for XCI in differentiating mouse female XX ESCs models.

genetics↗