Spatiotemporal 3D chromatin organization across multiple brain regions during human fetal development
Elucidating the regulatory mechanisms underlying the development of different brain regions in humans is essential for understanding advanced cognition and neuropsychiatric disorders. However, the spatiotemporal organization of three-dimensional (3D) chromatin structure and its regulatory functions across different brain regions remain poorly understood. Here, we generated an atlas of high-resolution 3D chromatin structure across six developing human brain regions, including the prefrontal cortex (PFC), primary visual cortex (V1), cerebellum (CB), subcortical corpus striatum (CS), thalamus (TL), and hippocampus (HP), spanning gestational weeks 11-26. We found that the spatial and temporal dynamics of 3D chromatin organization play a key role in regulating brain region development. We also identified H3K27ac-marked super-enhancers as key contributors to shaping brain region-specific 3D chromatin structures and gene expression patterns. Finally, we uncovered hundreds of neuropsychiatric GWAS SNP-linked genes, shedding light on critical molecules in various neuropsychiatric disorders. In summary, our findings provide important insights into the 3D chromatin regulatory mechanisms governing brain region-specific development and can serve as a valuable resource for advancing our understanding of neuropsychiatric disorders.
Authors
- Qian Wu (ORCID: https://orcid.org/0000-0002-7469-1583)
- Shuaishuai Wu
- Qian Gong
- Fangqi Zhao (ORCID: https://orcid.org/0000-0001-8692-9424)
- Yaoyu Sun
- Jiang Liu (ORCID: https://orcid.org/0000-0002-5687-5047)
- Xin Wang (ORCID: https://orcid.org/0000-0002-5122-2418)
- Haoyong Yu (ORCID: https://orcid.org/0000-0002-9876-4863)
- Jun Zhang (ORCID: https://orcid.org/0000-0001-5411-1273)
- Zeyuan Liu (ORCID: https://orcid.org/0000-0003-0007-9874)
- Min Li (ORCID: https://orcid.org/0000-0002-0188-1394)
- Yuwen Ke
- Qiang Ma (ORCID: https://orcid.org/0000-0002-8352-228X)
- Xiaoqun Wang (ORCID: https://orcid.org/0000-0003-3440-2617)
- Lei Gao (ORCID: https://orcid.org/0000-0002-0882-7518)
- Zhenbo Liu (ORCID: https://orcid.org/0000-0002-3944-2557)
- Xuepeng Chen (ORCID: https://orcid.org/0000-0001-7316-6894)
- Chao Ning (ORCID: https://orcid.org/0000-0001-9621-3147)
- Suijuan Zhong (ORCID: https://orcid.org/0000-0003-4382-6577)
- Junjie Lv
Institutions
- McGovern Institute for Brain Research (US)
- Chinese Academy of Sciences (CN)
- Beijing Normal University (CN)
- Guangdong-Hongkong-Macau Joint Laboratory of Collaborative Innovation for Environmental Quality (CN)
- Institute of Biophysics (CN)
- Chinese Institute for Brain Research (CN)
- Beijing Anzhen Hospital (CN)
- University of Chinese Academy of Sciences (CN)
- State Key Laboratory of Brain and Cognitive Science
- China Agricultural University (CN)
- Guangzhou Medical University (CN)
- China National Petroleum Corporation (China) (CN)
Publication Details
- Journal
- Cell Discovery
- Published
- 2025-05-16
- DOI
- https://doi.org/10.1038/s41421-025-00798-w
- Citations
- 3
- Primary Topic
- Genomics and Chromatin Dynamics
- Type
- article
- Field-Weighted Citation Impact
- 2.42
Funders
- National Natural Science Foundation of China
- Chinese Academy of Sciences
- Ministry of Science and Technology of the People's Republic of China
- National Key Research and Development Program of China
- Fundamental Research Funds for the Central Universities