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Genome-wide mapping reveals that deoxyuridine is enriched in the human centromeric DNA

Nature Chemical Biologyvolume 14pages680687 (2018) | Download Citation

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Abstract

Uracil in DNA can be generated by cytosine deamination or dUMP misincorporation; however, its distribution in the human genome is poorly understood. Here we present a selective labeling and pull-down technology for genome-wide uracil profiling and identify thousands of uracil peaks in three different human cell lines. Surprisingly, uracil is highly enriched at the centromere of the human genome. Using mass spectrometry, we demonstrate that human centromeric DNA contains a higher level of uracil. We also directly verify the presence of uracil within two centromeric uracil peaks on chromosomes 6 and 11. Moreover, centromeric uracil is preferentially localized within the binding regions of the centromere-specific histone CENP-A and can be excised by human uracil-DNA glycosylase UNG. Collectively, our approaches allow comprehensive analysis of uracil in the human genome and provide robust tools for mapping and future functional studies of uracil in DNA.

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Acknowledgements

The authors would like to thank G. Liu and H. Li for measurements with LC–MS/MS; B. Xia, X. Li and X. Xiong for technical advice and discussions. This work was supported by the National Natural Science Foundation of China (nos. 21522201 and 21472009 to C.Y.), the National Basic Research Foundation of China (nos. 2016YFC0900301 and 2014CB964900 to C.Y.) and the Fok Ying Tung Education Foundation (no. 161018 to C.Y.).

Author information

Author notes

  1. These authors contributed equally: Xiaoting Shu, Menghao Liu, Zhike Lu.

Affiliations

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

    • Xiaoting Shu
    • , Menghao Liu
    • , Zhike Lu
    • , Chenxu Zhu
    • , Haowei Meng
    • , Sihao Huang
    •  & Chengqi Yi
  2. Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China

    • Xiaoting Shu
    • , Menghao Liu
    •  & Xiaoxue Zhang
  3. Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China

    • Chengqi Yi

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Contributions

X.S. and C.Y. conceived the project; X.S., M.L. and C.Y. designed the experiments and wrote the manuscript with the help of Z.L.; X.S., M.L., C.Z., S.H. and X.Z. performed the experiments; Z.L. and H.M. performed bioinformatics analysis. All authors commented on and approved the paper.

Competing interests

The authors declare no competing interests.

Corresponding author

Correspondence to Chengqi Yi.

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https://doi.org/10.1038/s41589-018-0065-9