qDSB-Seq is a general method for genome-wide quantification of DNA double-strand breaks using sequencing

Yingjie Zhu, Anna Biernacka, Benjamin Pardo, Norbert Dojer, Romain Forey, Magdalena Skrzypczak, Bernard Fongang, Jules Nde, Razie Yousefi, Philippe Pasero, Krzysztof Ginalski, Malgorzata Rowicka-Kudlicka

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

DNA double-strand breaks (DSBs) are among the most lethal types of DNA damage and frequently cause genome instability. Sequencing-based methods for mapping DSBs have been developed but they allow measurement only of relative frequencies of DSBs between loci, which limits our understanding of the physiological relevance of detected DSBs. Here we propose quantitative DSB sequencing (qDSB-Seq), a method providing both DSB frequencies per cell and their precise genomic coordinates. We induce spike-in DSBs by a site-specific endonuclease and use them to quantify detected DSBs (labeled, e.g., using i-BLESS). Utilizing qDSB-Seq, we determine numbers of DSBs induced by a radiomimetic drug and replication stress, and reveal two orders of magnitude differences in DSB frequencies. We also measure absolute frequencies of Top1-dependent DSBs at natural 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.

Original languageEnglish (US)
Article number2313
JournalNature communications
Volume10
Issue number1
DOIs
StatePublished - Dec 1 2019

Fingerprint

sequencing
Double-Stranded DNA Breaks
genome
strands
deoxyribonucleic acid
Genes
Genome
Endonucleases
DNA
Genomic Instability
DNA Damage
Pharmaceutical Preparations
1,2-di-(4-sulfamidophenyl)-4-butylpyrazolidine-3,5-dione
forks
loci
organisms
spikes
drugs

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

Cite this

qDSB-Seq is a general method for genome-wide quantification of DNA double-strand breaks using sequencing. / Zhu, Yingjie; Biernacka, Anna; Pardo, Benjamin; Dojer, Norbert; Forey, Romain; Skrzypczak, Magdalena; Fongang, Bernard; Nde, Jules; Yousefi, Razie; Pasero, Philippe; Ginalski, Krzysztof; Rowicka-Kudlicka, Malgorzata.

In: Nature communications, Vol. 10, No. 1, 2313, 01.12.2019.

Research output: Contribution to journalArticle

Zhu, Y, Biernacka, A, Pardo, B, Dojer, N, Forey, R, Skrzypczak, M, Fongang, B, Nde, J, Yousefi, R, Pasero, P, Ginalski, K & Rowicka-Kudlicka, M 2019, 'qDSB-Seq is a general method for genome-wide quantification of DNA double-strand breaks using sequencing', Nature communications, vol. 10, no. 1, 2313. https://doi.org/10.1038/s41467-019-10332-8
Zhu, Yingjie ; Biernacka, Anna ; Pardo, Benjamin ; Dojer, Norbert ; Forey, Romain ; Skrzypczak, Magdalena ; Fongang, Bernard ; Nde, Jules ; Yousefi, Razie ; Pasero, Philippe ; Ginalski, Krzysztof ; Rowicka-Kudlicka, Malgorzata. / qDSB-Seq is a general method for genome-wide quantification of DNA double-strand breaks using sequencing. In: Nature communications. 2019 ; Vol. 10, No. 1.
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