ArticleNucleic acids research2023
Lineage specific 3D genome structure in the adult human brain and neurodevelopmental changes in the chromatin interactome.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed, 25 citations in OpenAlex.
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- Multi-omic data integration improves the resolution of the molecular etiology of autism in a mouse model.Molecular psychiatry · 2026Article
- Non-coding structural variants disrupt FOXG1 transcriptional regulation in early neurodevelopment.Nature communications · 2026Article
- Chromatin-associated intronic RNAs from long genes form introsomes that shape nuclear architecture in neuronal cells.bioRxiv : the preprint server for biology · 2026Article
- CITED2 is a druggable epigenetic switch coupling neuronal maturation to regenerative decline.EMBO molecular medicine · 2026Article
- A Single-Cell and Spatial 3D Multi-omic Atlas of Developing Human Basal Ganglia and Inhibitory Neurons.bioRxiv : the preprint server for biology · 2026Article
- Immune signaling as a determinant of cellular identity and tissue function.Frontiers in immunology · 2026Review
- The neuronal chromatin landscape in brains from individuals with schizophrenia is linked to early fetal development.Nature neuroscience · 2025Article
- Hi-GDT: A Hi-C-based 3D gene domain analysis tool for analyzing local chromatin contacts in plants.GigaScience · 2025Article
- Epigenetics and the timing of neuronal differentiation.Current opinion in neurobiology · 2024Review
- A multi-regional human brain atlas of chromatin accessibility and gene expression facilitates promoter-isoform resolution genetic fine-mapping.Nature communications · 2024Article
- The chromatin tapestry as a framework for neurodevelopment.Genome research · 2024Review
- Unraveling the three-dimensional (3D) genome architecture in Neurodevelopmental Disorders (NDDs).Neurogenetics · 2024Review
- Three-dimensional chromatin mapping of sensory neurons reveals that promoter-enhancer looping is required for axonal regeneration.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Extensive long-range polycomb interactions and weak compartmentalization are hallmarks of human neuronal 3D genome.Nucleic acids research · 2024Article
- Three-dimensional chromatin mapping of sensory neurons reveals that cohesin-dependent genomic domains are required for axonal regeneration.bioRxiv : the preprint server for biology · 2024Article
- From compartments to loops: understanding the unique chromatin organization in neuronal cells.Epigenetics & chromatin · 2024Review
- The 3D Genome in Brain Development: An Exploration of Molecular Mechanisms and Experimental Methods.Neuroscience insights · 2024Review
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Authors and funding
15 authors at 3 institutions in 1 country.
Funding
Abstract
The human brain is a complex organ comprised of distinct cell types, and the contribution of the 3D genome to lineage specific gene expression remains poorly understood. To decipher cell type specific genome architecture, and characterize fine scale changes in the chromatin interactome across neural development, we compared the 3D genome of the human fetal cortical plate to that of neurons and glia isolated from the adult prefrontal cortex. We found that neurons have weaker genome compartmentalization compared to glia, but stronger TADs, which emerge during fetal development. Furthermore, relative to glia, the neuronal genome shifts more strongly towards repressive compartments. Neurons have differential TAD boundaries that are proximal to active promoters involved in neurodevelopmental processes. CRISPRi on CNTNAP2 in hIPSC-derived neurons reveals that transcriptional inactivation correlates with loss of insulation at the differential boundary. Finally, re-wiring of chromatin loops during neural development is associated with transcriptional and functional changes. Importantly, differential loops in the fetal cortex are associated with autism GWAS loci, suggesting a neuropsychiatric disease mechanism affecting the chromatin interactome. Furthermore, neural development involves gaining enhancer-promoter loops that upregulate genes that control synaptic activity. Altogether, our study provides multi-scale insights on the 3D genome in the human brain.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.