IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v10y2019i1d10.1038_s41467-019-10332-8.html
   My bibliography  Save this article

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

Author

Listed:
  • Yingjie Zhu

    (University of Texas Medical Branch at Galveston)

  • Anna Biernacka

    (University of Warsaw)

  • Benjamin Pardo

    (Université de Montpellier)

  • Norbert Dojer

    (University of Texas Medical Branch at Galveston
    University of Warsaw)

  • Romain Forey

    (Université de Montpellier)

  • Magdalena Skrzypczak

    (University of Warsaw)

  • Bernard Fongang

    (University of Texas Medical Branch at Galveston)

  • Jules Nde

    (University of Texas Medical Branch at Galveston)

  • Razie Yousefi

    (University of Texas Medical Branch at Galveston)

  • Philippe Pasero

    (Université de Montpellier)

  • Krzysztof Ginalski

    (University of Warsaw)

  • Maga Rowicka

    (University of Texas Medical Branch at Galveston
    University of Texas Medical Branch at Galveston
    University of Texas Medical Branch at Galveston
    University of Texas Medical Branch at Galveston)

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.

Suggested Citation

  • Yingjie Zhu & Anna Biernacka & Benjamin Pardo & Norbert Dojer & Romain Forey & Magdalena Skrzypczak & Bernard Fongang & Jules Nde & Razie Yousefi & Philippe Pasero & Krzysztof Ginalski & Maga Rowicka, 2019. "qDSB-Seq is a general method for genome-wide quantification of DNA double-strand breaks using sequencing," Nature Communications, Nature, vol. 10(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-10332-8
    DOI: 10.1038/s41467-019-10332-8
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-019-10332-8
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-019-10332-8?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Lorenzo Corazzi & Vivien S. Ionasz & Sergej Andrejev & Li-Chin Wang & Athanasios Vouzas & Marco Giaisi & Giulia Di Muzio & Boyu Ding & Anna J. M. Marx & Jonas Henkenjohann & Michael M. Allers & David , 2024. "Linear interaction between replication and transcription shapes DNA break dynamics at recurrent DNA break Clusters," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    2. Razie Yousefi & Maga Rowicka, 2019. "Stochasticity of replication forks’ speeds plays a key role in the dynamics of DNA replication," PLOS Computational Biology, Public Library of Science, vol. 15(12), pages 1-19, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-10332-8. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.