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

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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Fig. 1: dU-seq is a selective labeling and pull-down technology for genome-wide uracil profiling.
Fig. 2: dU-seq reveals the genome-wide profile of uracil in K562, WPMY-1 and HEK293T cells, respectively.
Fig. 3: Uracil is enriched in the human centromeric DNA.
Fig. 4: Uracil peaks colocalize with the CENP-A binding regions at the centromere.
Fig. 5: Uracil at the centromere can be excised by UNG.

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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.).

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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.

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Correspondence to Chengqi Yi.

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Shu, X., Liu, M., Lu, Z. et al. Genome-wide mapping reveals that deoxyuridine is enriched in the human centromeric DNA. Nat Chem Biol 14, 680–687 (2018). https://doi.org/10.1038/s41589-018-0065-9

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