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Cell Stem Cell. 2017 May 4;20(5):720-731.e5. doi: 10.1016/j.stem.2017.02.013. Epub 2017 Mar 23.

Single-Cell 5-Formylcytosine Landscapes of Mammalian Early Embryos and ESCs at Single-Base Resolution.

Author information

1
State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, PRC.
2
Biodynamic Optical Imaging Center and Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing 100871, PRC.
3
Biodynamic Optical Imaging Center and Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing 100871, PRC; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, PRC.
4
Center for Stem Cell Biology and Regenerative Medicine, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.
5
Biodynamic Optical Imaging Center and Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing 100871, PRC; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, PRC; Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Peking University, Beijing 100871, PRC. Electronic address: tangfuchou@pku.edu.cn.
6
State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, PRC; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, PRC; Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, PRC. Electronic address: chengqi.yi@pku.edu.cn.

Abstract

Active DNA demethylation in mammals involves ten-eleven translocation (TET) family protein-mediated oxidation of 5-methylcytosine (5mC). However, base-resolution landscapes of 5-formylcytosine (5fC) (an oxidized derivative of 5mC) at the single-cell level remain unexplored. Here, we present "CLEVER-seq" (chemical-labeling-enabled C-to-T conversion sequencing), which is a single-cell, single-base resolution 5fC-sequencing technology, based on biocompatible, selective chemical labeling of 5fC and subsequent C-to-T conversion during amplification and sequencing. CLEVER-seq shows intrinsic 5fC heterogeneity in mouse early embryos, Epi stem cells (EpiSCs), and embryonic stem cells (ESCs). CLEVER-seq of mouse early embryos also reveals the highly patterned genomic distribution and parental-specific dynamics of 5fC during mouse early pre-implantation development. Integrated analysis demonstrates that promoter 5fC production precedes the expression upregulation of a clear set of developmentally and metabolically critical genes. Collectively, our work reveals the dynamics of active DNA demethylation during mouse pre-implantation development and provides an important resource for further functional studies of epigenetic reprogramming in single cells.

KEYWORDS:

5-formylcytosine; CLEVER-seq; ESC; active DNA demethylation; biocompatible labeling; early embryo; gene expression regulation; heterogeneity; single-cell sequencing

PMID:
28343982
DOI:
10.1016/j.stem.2017.02.013
[Indexed for MEDLINE]
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