DSBCapture: in situ capture and sequencing of DNA breaks.

Double-strand DNA breaks (DSBs) continuously arise and cause mutations and chromosomal rearrangements. Here, we present DSBCapture, a sequencing-based method that captures DSBs in situ and directly maps these at single-nucleotide resolution, enabling the study of DSB origin. DSBCapture shows substantially increased sensitivity and data yield compared with other methods. Using DSBCapture, we uncovered a striking relationship between DSBs and elevated transcription within nucleosome-depleted chromatin.

Keywords

Cell Culture Techniques, Cell Nucleus, Chromatin, DNA, DNA Breaks, Double-Stranded, DNA End-Joining Repair, Epigenesis, Genetic, HeLa Cells, High-Throughput Nucleotide Sequencing, Humans, Keratinocytes, Sensitivity and Specificity, Sequence Analysis, DNA

Journal Title

Nat Methods

Journal ISSN

1548-7091
1548-7105

Volume Title

13

Publisher

Springer Nature

Publisher DOI

https://doi.org/10.1038/nmeth.3960

Rights and licensing

Except where otherwised noted, this item's license is described as http://www.rioxx.net/licenses/all-rights-reserved

Sponsorship

European Molecular Biology Organization (EMBO) (EMBO ALTF 330-2013)
Cancer Research UK (CB4330)
Cancer Research UK (C14303/A17197)
Cancer Research UK (19836)

We thank G. Legube, LBCMCP, Center for Integrative Biology (CBI), Université de Toulouse, Toulouse, France for providing U2OS AID-DIvA cells. We thank the genomic core facility at the Cancer Research UK Cambridge Institute. R.H.-H. acknowledges EMBO for support (EMBO Long-Term Fellowship to R.H.-H.). We acknowledge support from the University of Cambridge and the Cancer Research UK program. The Balasubramanian laboratory is supported by core funding from Cancer Research UK (C14303/A17197 to S.B.) and by an ERC Advanced Grant (S.B.). S.B. is a senior investigator of the Wellcome Trust.

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