Single-Cell 5-Formylcytosine Landscapes of Mammalian Early Embryos and ESCs at Single-Base Resolution.
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.
State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, PRC.
Chenxu
C
Zhu
Biodynamic Optical Imaging Center and Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing 100871, PRC.
Yun
Y
Gao
Biodynamic Optical Imaging Center and Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing 100871, PRC.
Hongshan
H
Guo
State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, PRC.
Bo
B
Xia
State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, PRC.
Jinghui
J
Song
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.
Xinglong
X
Wu
State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, PRC.
Hu
H
Zeng
Center for Stem Cell Biology and Regenerative Medicine, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.
Kehkooi
K
Kee
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.
Fuchou
F
Tang
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.
Chengqi
C
Yi
D000818:Animals; D003596:Cytosine / Q000031:analogs & derivatives* / Q000378:metabolism; D019175:DNA Methylation / Q000235:genetics; D004622:Embryo, Mammalian / Q000378:metabolism*; D053595:Embryonic Stem Cells / Q000378:metabolism*; D005786:Gene Expression Regulation; D051379:Mice; D011401:Promoter Regions, Genetic / Q000235:genetics
C560973:5-formylcytosine; D003596:Cytosine
5-formylcytosine; CLEVER-seq; ESC; active DNA demethylation; biocompatible labeling; early embryo; gene expression regulation; heterogeneity; single-cell sequencing