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Direct and bisulfite-free 5-methylcytosine and 5-hydroxymethylcytosine sequencing at single-cell resolution with scTAPS and scCAPS +

Year: 2025
Type: article
Abstract: 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.
DOI: 10.1186/s13059-025-03708-1
Authors: Xiufei Chen, Jingfei Cheng, Linzhen Kong, Xiao Shu, Haiqi Xu, Masato Inoue, Marion Silvana Fernández-Berrocal, Dagny Sanden Døskeland, Magnar Bjørås, Shivan Sivakumar, Yibin Liu, Jing Ye, Chun-Xiao Song
Institutions: Ningbo University, University of Oxford, Ludwig Cancer Research, Norwegian University of Science and Technology, Oslo University Hospital, University of Oslo, Kennedy Institute of Rheumatology, University of Birmingham, Wuhan University
Language: English
Open Access status: gold
Estimated APC paid: $5,490
Funders: Ludwig Institute for Cancer Research, Cancer Research UK, National Institute for Health and Care Research, National Natural Science Foundation of China, China Scholarship Council, Norges Forskningsråd, NIHR Oxford Biomedical Research Centre
OpenAlex ID: W4413273545
FWCI: 0.765
Cites: 43
Cited by: 3
Related to: 10