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Identification of the elementary structural units of the DNA damage response

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Official URL:https://doi.org/10.1038/ncomms15760
PubMed:View item in PubMed
Creators Name:Natale, F. and Rapp, A. and Yu, W. and Maiser, A. and Harz, H. and Scholl, A. and Grulich, S. and Anton, T. and Hoerl, D. and Chen, W. and Durante, M. and Taucher-Scholz, G. and Leonhardt, H. and Cardoso, M.C.
Journal Title:Nature Communications
Journal Abbreviation:Nat Commun
Volume:8
Page Range:15760
Date:12 June 2017
Keywords:DNA Damage and Repair, Histone Post-Translational Modifications, Super-Resolution Microscopy
Abstract:Histone H2AX phosphorylation is an early signalling event triggered by DNA double-strand breaks (DSBs). To elucidate the elementary units of phospho-H2AX-labelled chromatin, we integrate super-resolution microscopy of phospho-H2AX during DNA repair in human cells with genome-wide sequencing analyses. Here we identify phospho-H2AX chromatin domains in the nanometre range with median length of ∼75 kb. Correlation analysis with over 60 genomic features shows a time-dependent euchromatin-to-heterochromatin repair trend. After X-ray or CRISPR-Cas9-mediated DSBs, phospho-H2AX-labelled heterochromatin exhibits DNA decondensation while retaining heterochromatic histone marks, indicating that chromatin structural and molecular determinants are uncoupled during repair. The phospho-H2AX nano-domains arrange into higher-order clustered structures of discontinuously phosphorylated chromatin, flanked by CTCF. CTCF knockdown impairs spreading of the phosphorylation throughout the 3D-looped nano-domains. Co-staining of phospho-H2AX with phospho-Ku70 and TUNEL reveals that clusters rather than nano-foci represent single DSBs. Hence, each chromatin loop is a nano-focus, whose clusters correspond to previously known phospho-H2AX foci.
ISSN:2041-1723
Publisher:Nature Publishing Group (U.K.)
Item Type:Article

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