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Genome-wide mapping of long-range contacts unveils clustering of DNA double-strand breaks at damaged active genes

Nature Structural & Molecular Biology volume 24, pages 353361 (2017) | Download Citation

Abstract

The ability of DNA double-strand breaks (DSBs) to cluster in mammalian cells has been a subject of intense debate in recent years. Here we used a high-throughput chromosome conformation capture assay (capture Hi-C) to investigate clustering of DSBs induced at defined loci in the human genome. The results unambiguously demonstrated that DSBs cluster, but only when they are induced within transcriptionally active genes. Clustering of damaged genes occurs primarily during the G1 cell-cycle phase and coincides with delayed repair. Moreover, DSB clustering depends on the MRN complex as well as the Formin 2 (FMN2) nuclear actin organizer and the linker of nuclear and cytoplasmic skeleton (LINC) complex, thus suggesting that active mechanisms promote clustering. This work reveals that, when damaged, active genes, compared with the rest of the genome, exhibit a distinctive behavior, remaining largely unrepaired and clustered in G1, and being repaired via homologous recombination in postreplicative cells.

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Acknowledgements

We thank S. Andrews, K. Tabbada and S. Wingett (Babraham Institute) for probe design and quality control of Hi-C data. Funding was provided by the Polish National Science Centre (2011/02/A/NZ2/00014 to K.G. and 2015/17/D/NZ2/03711 to M.S.) and the Foundation for Polish Science (TEAM to K.G.). Funding to M.R. was provided by NIH (NIH 5 R01 GM 112131). M.A. and E.G. were supported by the Fondation pour la Recherche Médicale (FRM). Funding in G.L.'s laboratory was provided by grants from the European Research Council (ERC-2014-CoG 647344), Agence Nationale pour la Recherche (ANR-14-CE10-0002-01and ANR-13-BSV8-0013), the Institut National contre le Cancer (INCA PLBIO15-199) and the Ligue Nationale contre le Cancer (LNCC).

Author information

Author notes

    • François Aymard
    • , Marion Aguirrebengoa
    •  & Emmanuelle Guillou

    These authors contributed equally to this work.

Affiliations

  1. LBCMCP, Centre de Biologie Integrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France.

    • François Aymard
    • , Marion Aguirrebengoa
    • , Emmanuelle Guillou
    • , Beatrix Bugler
    • , Coline Arnould
    • , Vincent Rocher
    •  & Gaëlle Legube
  2. Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK.

    • Biola M Javierre
    •  & Peter Fraser
  3. Bioinformatic Plateau I2MC, INSERM and University of Toulouse, Toulouse, France.

    • Jason S Iacovoni
  4. Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw, Poland.

    • Anna Biernacka
    • , Magdalena Skrzypczak
    •  & Krzysztof Ginalski
  5. Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA.

    • Maga Rowicka

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Contributions

F.A., E.G., B.M.J., B.B. and C.A. performed experiments. M.A., V.R. and J.S.I. performed bioinformatic analyses of Hi-C and BLESS data sets. A.B., K.G., M.S., and M.R. performed BLESS experiments. P.F. contributed to capture Hi-C experimental design, experiments and analyses. G.L. conceived and analyzed experiments. F.A. and G.L. wrote the manuscript. All authors commented and edited the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Gaëlle Legube.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–8 and Supplementary Note

Excel files

  1. 1.

    Supplementary Table 1

    Genomic coordinates (hg19) of probes used for Capture Hi-C

  2. 2.

    Supplementary Table 2

    Domain names, associated AsiSI sites and size of the gaps between Captured domains

  3. 3.

    Supplementary Table 3

    Oligonucleotides for quantitative PCR used in this study

  4. 4.

    Supplementary Table 4

    siRNA sequences used in this study

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DOI

https://doi.org/10.1038/nsmb.3387

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