Direct and bisulfite-free 5-methylcytosine and 5-hydroxymethylcytosine sequencing at single-cell resolution with scTAPS and scCAPS +
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.
Authors
- Xiufei Chen
- Masato Inoue (ORCID: https://orcid.org/0000-0001-7412-0505)
- Magnar Bjørås (ORCID: https://orcid.org/0000-0001-8759-1170)
- Xiao Ou Shu (ORCID: https://orcid.org/0000-0002-1053-1353)
- Haiqi Xu (ORCID: https://orcid.org/0009-0006-4486-5075)
- Jingfei Cheng (ORCID: https://orcid.org/0000-0001-9615-2719)
- Chun‐Xiao Song (ORCID: https://orcid.org/0000-0002-7781-6521)
- Marion Silvana Fernández-Berrocal (ORCID: https://orcid.org/0000-0002-5839-9355)
- Shivan Sivakumar (ORCID: https://orcid.org/0000-0002-5175-2697)
- Linzhen Kong
- Dagny Sanden Døskeland
- Jing Ye (ORCID: https://orcid.org/0009-0008-9262-4916)
- Yibin Liu (ORCID: https://orcid.org/0009-0003-7775-0221)
Institutions
- Oslo University Hospital (NO)
- University of Oslo (NO)
- Norwegian University of Science and Technology (NO)
- Nuffield Orthopaedic Centre (GB)
- Wuhan University (CN)
- University of Oxford (GB)
- Ludwig Cancer Research (GB)
- Ningbo University Affiliated Hospital (CN)
- Ningbo First Hospital (CN)
- University of Birmingham (GB)
Publication Details
- Journal
- Genome biology
- Published
- 2025-08-18
- DOI
- https://doi.org/10.1186/s13059-025-03708-1
- Citations
- 1
- Primary Topic
- Epigenetics and DNA Methylation
- Type
- article
- Field-Weighted Citation Impact
- 0.81
Funders
- National Science Foundation
- 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