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qDSB-Seq: quantitative DNA double-strand break sequencing

Yingjie Zhu, View ORCID ProfileAnna Biernacka, View ORCID ProfileBenjamin Pardo, Norbert Dojer, Romain Forey, Magdalena Skrzypczak, View ORCID ProfileBernard Fongang, View ORCID ProfileJules Nde, Raziyeh Yousefi, Philippe Pasero, Krzysztof Ginalski, View ORCID ProfileMaga Rowicka
doi: https://doi.org/10.1101/171405
Yingjie Zhu
1Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
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Anna Biernacka
2Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw, Poland
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Benjamin Pardo
3Institute of Human Genetics, Montpellier, France
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Norbert Dojer
1Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
4Institute of Informatics, University of Warsaw, Warsaw, Poland
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Romain Forey
3Institute of Human Genetics, Montpellier, France
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Magdalena Skrzypczak
3Institute of Human Genetics, Montpellier, France
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Bernard Fongang
1Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
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Jules Nde
1Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
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Raziyeh Yousefi
1Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
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Philippe Pasero
3Institute of Human Genetics, Montpellier, France
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Krzysztof Ginalski
2Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw, Poland
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Maga Rowicka
1Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
5Institute for Translational Sciences, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
6Sealy Center for Molecular Medicine, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
7Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
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  • ORCID record for Maga Rowicka
  • For correspondence: Maga.Rowicka@utmb.edu
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Abstract

Sequencing-based methods for mapping DNA double-strand breaks (DSBs) allow measurement only of relative frequencies of DSBs between loci, which limits our understanding of the physiological relevance of detected DSBs. We propose quantitative DSB sequencing (qDSB-Seq), a method providing both DSB frequencies per cell and their precise genomic coordinates. We induced spike-in DSBs by a site-specific endonuclease and used them to quantify labeled DSBs (e.g. using i-BLESS). Utilizing qDSB-Seq, we determined numbers of DSBs induced by a radiomimetic drug and various forms of replication stress, and revealed several orders of magnitude differences in DSB frequencies. We also measured for the first time Top1-dependent absolute DSB frequencies at replication fork barriers. qDSB-Seq is compatible with various DSB labeling methods in different organisms and allows accurate comparisons of absolute DSB frequencies across samples.

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Posted January 02, 2019.
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qDSB-Seq: quantitative DNA double-strand break sequencing
Yingjie Zhu, Anna Biernacka, Benjamin Pardo, Norbert Dojer, Romain Forey, Magdalena Skrzypczak, Bernard Fongang, Jules Nde, Raziyeh Yousefi, Philippe Pasero, Krzysztof Ginalski, Maga Rowicka
bioRxiv 171405; doi: https://doi.org/10.1101/171405
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qDSB-Seq: quantitative DNA double-strand break sequencing
Yingjie Zhu, Anna Biernacka, Benjamin Pardo, Norbert Dojer, Romain Forey, Magdalena Skrzypczak, Bernard Fongang, Jules Nde, Raziyeh Yousefi, Philippe Pasero, Krzysztof Ginalski, Maga Rowicka
bioRxiv 171405; doi: https://doi.org/10.1101/171405

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