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

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

Department of Central Laboratory, The First Affiliated Hospital of Ningbo University, Ningbo, 315010, China.Department of Central Laboratory, The First Affiliated Hospital of Ningbo University, Ningbo, 315010, China. · pubmed

Paper

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.

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Research summary

The paper presents new methodologies for sequencing 5-methylcytosine and 5-hydroxymethylcytosine at single-cell resolution. The findings regarding the increase in 5hmC in aging mice suggest potential insights into epigenomic changes associated with aging, which could contribute to understanding the biological mechanisms of aging.

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