TY - JOUR
T1 - qDSB-Seq is a general method for genome-wide quantification of DNA double-strand breaks using sequencing
AU - Zhu, Yingjie
AU - Biernacka, Anna
AU - Pardo, Benjamin
AU - Dojer, Norbert
AU - Forey, Romain
AU - Skrzypczak, Magdalena
AU - Fongang, Bernard
AU - Nde, Jules
AU - Yousefi, Razie
AU - Pasero, Philippe
AU - Ginalski, Krzysztof
AU - Rowicka, Maga
N1 - Funding Information:
This research was supported by the NIH grant R01GM112131 to M.R. (Y.Z., N.D., B.F., J. N., R.Y., and M.R.), Polish National Science Centre grant 2015/17/D/NZ2/03711 to M.S., and Foundation for Polish Science grant TEAM/2016–2 to K.G. This work was also supported by Ligue contre le Cancer (Equipe labelisee), Agence Nationale pour la Recherche (ANR), and Institut National du Cancer (INCa) grants to P.P. (B.P., R.F., and P.P.), National Science Center grant 2016/21/B/ST6/01471 to N.D., and a training fellowship from the Gulf Coast Consortia on the Computational Cancer Biology Training Program (CPRIT Grant Number RP170593) to Y.Z. We are grateful to Gaëlle Legube for kindly providing DIvA cells and for helpful discussions, to Andrzej Kudlicki for helpful discussions, and to Heather Lander of the Sealy Center for Structural Biology and Molecular Biophysics at UTMB, for editorial services for the manuscript.
Publisher Copyright:
© 2019, The Author(s).
PY - 2019/12/1
Y1 - 2019/12/1
N2 - 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.
AB - 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.
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U2 - 10.1038/s41467-019-10332-8
DO - 10.1038/s41467-019-10332-8
M3 - Article
C2 - 31127121
AN - SCOPUS:85066944344
SN - 2041-1723
VL - 10
JO - Nature Communications
JF - Nature Communications
IS - 1
M1 - 2313
ER -