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

Yingjie Zhu (1) , Anna Biernacka (2) , Benjamin Pardo (3) , Norbert Dojer , Romain Forey (3) , Magdalena Skrzypczak (2) , Bernard Fongang , Jules Nde (4) , Razie Yousefi , Philippe Pasero (3) , Krzysztof Ginalski (2) , Maga Rowicka (1)

1 Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77555 USA.
2 Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 02-089 Warsaw, Poland
3 IGH - Institut de génétique humaine
4 University of Texas Medical Branch at Galveston

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.

Domaines: Génomique, Transcriptomique et Protéomique [q-bio.GN]; Biochimie, Biologie Moléculaire; Bio-Informatique, Biologie Systémique [q-bio.QM]

Yingjie Zhu, Anna Biernacka, Benjamin Pardo, Norbert Dojer, Romain Forey, et al.. qDSB-Seq is a general method for genome-wide quantification of DNA double-strand breaks using sequencing. Nature Communications, 2019, 10 (1), ⟨10.1038/s41467-019-10332-8⟩. ⟨hal-02358678⟩