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Bisulfite-free, base-resolution analysis of 5-formylcytosine at the genome scale

Nature Methods volume 12, pages 10471050 (2015) | Download Citation

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Abstract

Active DNA demethylation in mammals involves oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). However, genome-wide detection of 5fC at single-base resolution remains challenging. Here we present fC-CET, a bisulfite-free method for whole-genome analysis of 5fC based on selective chemical labeling of 5fC and subsequent C-to-T transition during PCR. Base-resolution 5fC maps showed limited overlap with 5hmC, with 5fC-marked regions more active than 5hmC-marked ones.

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  • 21 September 2015

    In the version of this article initially published online, Chuan He is incorrectly affiliated with Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China, and is missing an affiliation with the Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, China. This error has been corrected for the print, PDF and HTML versions of this article.

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Acknowledgements

The authors thank R. Meng, S.T. Huang, J.Y. Liu, J.Y. Li, X.T. Shu, X.Y. Li and C.X. Zhu for technical assistance; X.X. Zhang and H.S. Guo (Peking University, Beijing, China) for providing genomic DNA at the beginning of the project; C.F. Xia for synthetic suggestions; and O. Stovicek for editing the manuscript. This work was supported by the National Basic Research Foundation of China (grant 2014CB964900 to C.Y.), the National Natural Science Foundation of China (grants 31270838 and 21472009 to C.Y.), and the US National Institutes of Health (grant R01 HG006827 to C.H.). C.H. is supported by the Howard Hughes Medical Institute.

Author information

Author notes

    • Bo Xia
    • , Dali Han
    •  & Xingyu Lu

    These authors contributed equally to this work.

Affiliations

  1. State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.

    • Bo Xia
    • , Zhaozhu Sun
    • , Ankun Zhou
    • , Hu Zeng
    • , Menghao Liu
    • , Xiang Jiang
    •  & Chengqi Yi
  2. Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.

    • Bo Xia
    • , Zhaozhu Sun
    • , Ankun Zhou
    • , Hu Zeng
    • , Menghao Liu
    • , Xiang Jiang
    •  & Chengqi Yi
  3. Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois, USA.

    • Dali Han
    • , Xingyu Lu
    •  & Chuan He
  4. Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois, USA.

    • Dali Han
    • , Xingyu Lu
    •  & Chuan He
  5. Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.

    • Qiangzong Yin
    •  & Wei Xie
  6. Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.

    • Chuan He
    •  & Chengqi Yi
  7. Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.

    • Chuan He
    •  & Chengqi Yi

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Contributions

B.X. and C.Y. conceived the original idea and designed the experiments with the help of X.L. and C.H.; B.X. performed the experiments with the help of X.L., H.Z., M.L. and X.J.; D.H. performed bioinformatics analysis; Z.S. and A.Z. synthesized the chemicals; Q.Y. and W.X. helped with the library preparation; C.H. and C.Y. supervised the project; and B.X. and C.Y. wrote the manuscript with contributions from D.H., X.L. and C.H.

Competing interests

B.X., A.Z. and C.Y. are co-inventors on a filed patent (WO2015043493) for the labeling strategies and sequencing methods reported herein.

Corresponding authors

Correspondence to Chuan He or Chengqi Yi.

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    Supplementary Figures 1–15, Supplementary Tables 1–3 and Supplementary Notes 1–3

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DOI

https://doi.org/10.1038/nmeth.3569

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