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Sequencing abasic sites in DNA at single-nucleotide resolution

Nature Chemistry volume 11, pages 629–637 (2019)Cite this article

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Abstract

In DNA, the loss of a nucleobase by hydrolysis generates an abasic site. Formed as a result of DNA damage, as well as a key intermediate during the base excision repair pathway, abasic sites are frequent DNA lesions that can lead to mutations and strand breaks. Here we present snAP-seq, a chemical approach that selectively exploits the reactive aldehyde moiety at abasic sites to reveal their location within DNA at single-nucleotide resolution. Importantly, the approach resolves abasic sites from other aldehyde functionalities known to exist in genomic DNA. snAP-seq was validated on synthetic DNA and then applied to two separate genomes. We studied the distribution of thymine modifications in the Leishmania major genome by enzymatically converting these modifications into abasic sites followed by abasic site mapping. We also applied snAP-seq directly to HeLa DNA to provide a map of endogenous abasic sites in the human genome.

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Fig. 1: Chemical tagging of DNA AP sites.
Fig. 2: Outline of snAP-seq and analysis of synthetic DNA spike-ins.
Fig. 3: Representative genome browser view of sites called by SMUG1–snAP-seq in the L. major genome.
Fig. 4: SMUG1–snAP-seq sites in the L. major genome.
Fig. 5: Analysis of SMUG1–snAP-seq sites in the L. major genome.
Fig. 6: Mapping of AP sites in human (HeLa) DNA.

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Data availability

Sequencing data are available in the ArrayExpress database under accession number E-MTAB-7152.

Code availability

We have released all the computational code in the manuscript’s accompanying GitHub page (https://github.com/sblab-bioinformatics/snAP-seq).

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Acknowledgements

S.B. is a senior investigator of the Wellcome Trust (grant no. 209441/Z/17/Z). The Balasubramanian laboratory is also supported by core funding from Cancer Research UK (C14303/A17197). Z.J.L. is supported by Pembroke College, Cambridge, and the Herchel Smith Fund. P.V.D. was funded by a Marie Curie Fellow of the European Union (grant no. FP7-PEOPLE-2013-IEF/624885).

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Authors and Affiliations

  1. Department of Chemistry, University of Cambridge, Cambridge, UK

    Zheng J. Liu, Sergio Martínez Cuesta, Pieter van Delft & Shankar Balasubramanian

  2. Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK

    Sergio Martínez Cuesta & Shankar Balasubramanian

  3. School of Clinical Medicine, University of Cambridge, Cambridge, UK

    Shankar Balasubramanian

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  1. Zheng J. Liu
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Contributions

Z.J.L., P.V.D. and S.B. designed the study. Z.J.L. performed the experiments. S.M.C. performed the computational analysis. All the authors analysed and interpreted the data. Z.J.L. and S.B. wrote the manuscript, with contributions from all authors.

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Correspondence to Shankar Balasubramanian.

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S.B. is a founder, adviser and shareholder of Cambridge Epigenetix Ltd. The methodology described in this manuscript is subject to a patent application.

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Liu, Z.J., Martínez Cuesta, S., van Delft, P. et al. Sequencing abasic sites in DNA at single-nucleotide resolution. Nat. Chem. 11, 629–637 (2019). https://doi.org/10.1038/s41557-019-0279-9

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