Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects
Oxidative modification of 5-methylcytosine (5mC) by TET DNA dioxygenases generates 5-hydroxymethylcytosine (5hmC), the most abundant form of oxidized 5mC. Existing single-cell bisulfite sequencing methods cannot resolve 5mC and 5hmC, leaving the cell-type-specific regulatory mechanisms of TET and 5hmC largely unknown. Here we present Joint single-nucleus (hydroxy)methylcytosine sequencing (Joint-snhmC-seq), a scalable and quantitative approach that simultaneously profiles 5hmC and true 5mC in single cells by harnessing differential deaminase activity of APOBEC3A towards 5mC and chemically protected 5hmC. Joint-snhmC-seq profiling of single nuclei from the mouse brains reveals an unprecedented level of epigenetic heterogeneity of both 5hmC and true 5mC at single-cell resolution. We show that cell-type-specific profiles of 5hmC or true 5mC improve multi-modal single-cell data integration, enable accurate identification of neuronal subtypes, and uncover context-specific regulatory effects of cell-type-specific genes by TET enzymes.
- Codes for plotting figures can be found here.
- Raw and processed data can be found at GEO.
Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects
Emily B. Fabyanic*, Peng Hu*, Qi Qiu*, Kiara N. Berríos, Daniel R. Connolly, Tong Wang, Jennifer Flournoy, Zhaolan Zhou, Rahul M. Kohli, Hao Wu $
*: These authors contributed equally: E.F., P.H. and Q.Q.
$: Correspondence should be addressed to H.W. (haowu2@pennmedicine.upenn.edu)
Nat Biotechnol. 2023 Aug 28. Online PDF. doi: 10.1038/s41587-023-01909-2. PMID: 37640946.
doi: https://doi.org/10.1101/2021.03.23.434325
- Hao Wu (haowu2@pennmedicine.upenn.edu) & Peng Hu (penghu41@gmail.com)
- Wu lab, Department of Genetics, University of Pennsylvania