Li Wen, Lu Jiansen, Lu Ping, Gao Yun, Bai Yichen, Chen Kexuan, Su Xinjie, Li Mengyao, Liu Jun'e, Chen Yijun, Wen Lu, Tang Fuchou
School of Life Sciences, Biomedical Pioneering Innovative Center, Peking University, Beijing, China.
Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
Nat Methods. 2023 Oct;20(10):1493-1505. doi: 10.1038/s41592-023-01978-w. Epub 2023 Aug 28.
The high-order three-dimensional (3D) organization of regulatory genomic elements provides a topological basis for gene regulation, but it remains unclear how multiple regulatory elements across the mammalian genome interact within an individual cell. To address this, herein, we developed scNanoHi-C, which applies Nanopore long-read sequencing to explore genome-wide proximal high-order chromatin contacts within individual cells. We show that scNanoHi-C can reliably and effectively profile 3D chromatin structures and distinguish structure subtypes among individual cells. This method could also be used to detect genomic variations, including copy-number variations and structural variations, as well as to scaffold the de novo assembly of single-cell genomes. Notably, our results suggest that extensive high-order chromatin structures exist in active chromatin regions across the genome, and multiway interactions between enhancers and their target promoters were systematically identified within individual cells. Altogether, scNanoHi-C offers new opportunities to investigate high-order 3D genome structures at the single-cell level.
调控基因组元件的高阶三维（3D）组织为基因调控提供了拓扑学基础，但目前尚不清楚哺乳动物基因组中的多个调控元件如何在单个细胞内相互作用。为了解决这一问题，我们在此开发了scNanoHi-C，它应用纳米孔长读长测序技术来探索单个细胞内全基因组范围的近端高阶染色质接触。我们表明，scNanoHi-C能够可靠且有效地描绘3D染色质结构，并区分单个细胞之间的结构亚型。该方法还可用于检测基因组变异，包括拷贝数变异和结构变异，以及用于构建单细胞基因组的从头组装。值得注意的是，我们的结果表明，全基因组活跃染色质区域中存在广泛的高阶染色质结构，并且在单个细胞内系统地鉴定了增强子与其靶启动子之间的多路相互作用。总之，scNanoHi-C为在单细胞水平研究高阶3D基因组结构提供了新机会。
