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

Journal article

: 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: Chen, X; Cheng, J; Kong, L; Shu, X; Xu, H

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: BioMed Central
• Journal: Genome Biology
• Volume: 26
• Issue: 1
• Article number: 244
• Publication date: 2025-08-18
• Acceptance date: 2025-07-23
• DOI: 10.1186/s13059-025-03708-1
• EISSN: 1474760X
• ISSN: 1474-7596
• Language: English
• Keywords: scCAPS +; 5mC; 5hmC; Single-cell sequencing; Neuron; Aging; scTAPS