Abstract
Methylation of lysine 4 on histone H3 (H3K4) is enriched on active promoters and enhancers where it promotes gene activation. Disruption of H3K4 methylation is associated with numerous neurodevelopmental diseases (NDDs) that display intellectual disability and abnormal body growth. Here, we perturb H3K4 methylation in the medial ganglionic eminence (MGE) and hypothalamus, two brain regions associated with these disease phenotypes. These mutant mice have fewer forebrain interneurons, deficient network rhythmogenesis, and increased spontaneous seizures and seizure susceptibility. Mutant mice are significantly smaller than control littermates, but they eventually became obese due to striking changes in the genetic and cellular hypothalamus environment in these mice. Perturbation of H3K4 methylation in these cells produces deficits in numerous NDD-associated behaviors, with a bias for more severe phenotypes in female mice. Single nuclei sequencing reveals transcriptional changes in the embryonic and adult brain that underlie many of these phenotypes. In sum, our findings highlight the critical role of H3K4 methylation in regulating survival and cell-specific gene regulatory mechanisms in forebrain GABAergic and hypothalamic cells during neurodevelopment to control network excitability and body size homoeostasis.
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Data availability
The single-cell sequencing data generated in this study have been deposited in the Gene Expression Omnibus (GEO) repository under Superseries accession code GSE293881, which includes our single-cell ATAC-seq (GSE293655) and single-cell RNA-seq (GSE293751) datasets, all of which are publicly available. Details on cell counts, number of animals used per experiment, and analyses of differentially expressed genes for all comparisons described in the manuscript are provided in the Supplementary Data files. Additional data & information used in this study are available at Synapse.org. For any additional inquiries about data accessibility and analysis, please email tim.petros@nih.gov.
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Acknowledgements
We thank all members of the Section on Cellular and Molecular Neurodevelopment, as well as Pedro Rocha, Ariel Levine and Kai Ge for discussion and comments on this project and manuscript. We thank Kai Ge (NIDDK) for the LSL-K4M mice. We thank the NICHD Molecular Genomics Core, specifically Fabio Faucz, Vivek Mahadevan, Tianwei Li and James Iben; the NIDDK Mouse Metabolism Core, particularly Oksana Gavrilova and Naili Liu, for assistance with measuring body composition; the NINDS and NICHD animal facility for mouse husbandry assistance. This work utilized the computational resources of the NIH HPC Biowulf cluster (http://hpc.nih.gov). This work was supported, in part, by the NIMH IRP Rodent Behavioral Core (MH002952). This project was funded by NICHD intramural projects HD008962 (T.J.P.), HD008986 (R.K.D.), HD001205 (C.J.M.); NICHD Scientific Director’s Award (T.J.P); NICHD Intramural Research Fellowship (J.L.); NICHD Career Development Award (J.L.). This research was supported by the Intramural Research Program of the National Institutes of Health (NIH). The contributions of the NIH author(s) are considered Works of the United States Government. The findings and conclusions presented in this paper are those of the author(s) and do not necessarily reflect the views of the NIH or the U.S. Department of Health and Human Services.
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Conceptualization – J.L. and T.J.P.; Investigation – J.L., A.F.T., G.P., A.C., R.C., D.A., Y.Z., and K.A.P.; Formal analysis – J.L., G.P., K.A.P., and M.S.; Software – M.S.; Supervision – R.K.D., C.J.M., and T.J.P.; Funding acquisition – J.L., R.K.D., C.J.M., and T.J.P.; Writing, original draft – J.L. and T.J.P.; Writing, review & editing – all authors.
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Li, J., Tanzillo, A.F., Pizzirusso, G. et al. Reducing methylation of histone 3.3 lysine 4 in the medial ganglionic eminence and hypothalamus recapitulates neurodevelopmental disorder phenotypes. Nat Commun (2026). https://doi.org/10.1038/s41467-026-69248-9
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DOI: https://doi.org/10.1038/s41467-026-69248-9
