Chen Xiufei, Cheng Jingfei, Kong Linzhen, Shu Xiao, Xu Haiqi, Inoue Masato, Fernández-Berrocal Marion Silvana, Døskeland Dagny Sanden, Bjørås Magnar, Sivakumar Shivan, Liu Yibin, Ye Jing, Song Chun-Xiao
Department of Central Laboratory, The First Affiliated Hospital of Ningbo University, Ningbo, 315010, China.
Nuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, OX3 7FZ, UK.
Genome Biol. 2025 Aug 18;26(1):244. doi: 10.1186/s13059-025-03708-1.
We present direct sequencing methodologies, scTAPS for 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) and scCAPS + specifically for 5hmC, enabling quantitative detection of 5mC and 5hmC at single-base resolution and single-cell level. Achieving approximately 90% mapping efficiency, our plate-based methods accurately recover 5mC and 5hmC profiles in CD8 + T and mouse embryonic stem cells. Notably, scCAPS + reveals a global increase in 5hmC across neuronal and non-neuronal cells in the hippocampus of aging mice. Our methods offer strong potential for seamless integration into high-throughput single-cell multi-omics, facilitating future investigations of epigenomic dynamics in specific biological processes.
我们展示了直接测序方法，即用于5-甲基胞嘧啶（5mC）和5-羟甲基胞嘧啶（5hmC）的scTAPS以及专门用于5hmC的scCAPS +，能够在单碱基分辨率和单细胞水平上对5mC和5hmC进行定量检测。我们基于平板的方法实现了约90%的映射效率，可准确恢复CD8 + T细胞和小鼠胚胎干细胞中的5mC和5hmC图谱。值得注意的是，scCAPS +揭示了衰老小鼠海马体中神经元和非神经元细胞中5hmC的整体增加。我们的方法具有无缝整合到高通量单细胞多组学中的强大潜力，有助于未来对特定生物学过程中表观基因组动态的研究。
