Spatiotemporal 3D chromatin organization across multiple brain regions during human fetal development

Cell Discovery, 16 May, 2025, DOI：https://doi.org/10.1038/s41421-025-00798-w

Spatiotemporal 3D chromatin organization across multiple brain regions during human fetal development

Yaoyu Sun, Min Li, Chao Ning, Lei Gao, Zhenbo Liu, Suijuan Zhong, Junjie Lv, Yuwen Ke, Xinxin Wang, Qiang Ma, Zeyuan Liu, Shuaishuai Wu, Hao Yu, Fangqi Zhao, Jun Zhang, Qian Gong, Jiang Liu, Qian Wu, Xiaoqun Wang & Xuepeng Chen

Abstract

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.

文章链接：https://www.nature.com/articles/s41421-025-00798-w