The zinc-finger domains of PARP1 cooperate to recognize DNA strand breaks

A Corrigendum to this article was published on 05 August 2015

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Abstract

Poly(ADP-ribose) polymerase 1 (PARP1) is a primary DNA damage sensor whose (ADP-ribose) polymerase activity is acutely regulated by interaction with DNA breaks. Upon activation at sites of DNA damage, PARP1 modifies itself and other proteins by covalent addition of long, branched polymers of ADP-ribose, which in turn recruit downstream DNA repair and chromatin remodeling factors. PARP1 recognizes DNA damage through its N-terminal DNA-binding domain (DBD), which consists of a tandem repeat of an unusual zinc-finger (ZnF) domain. We have determined the crystal structure of the human PARP1-DBD bound to a DNA break. Along with functional analysis of PARP1 recruitment to sites of DNA damage in vivo, the structure reveals a dimeric assembly whereby ZnF1 and ZnF2 domains from separate PARP1 molecules form a strand-break recognition module that helps activate PARP1 by facilitating its dimerization and consequent trans-automodification.

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Figure 1: PARP1-DNA interactions.
Figure 2: DNA-end binding by the ZnF1-ZnF2 complex.
Figure 3: DNA break detection by PARP1 ZnF2.
Figure 4: DNA damage focus formation by PARP1 and its mobility.
Figure 5: Intermolecular dimerization of PARP1 Znf1 and ZnF2 domain.
Figure 6: A mechanism for DNA damage–dependent trans-automodification by PARP1.

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  • 10 July 2015

    In the version of this article initially published, the image in the bottom row of Figure 4a (full-length PARP1-EGFP mutant R138E) was mistakenly replaced with a duplicate of the bottom-row image in Figure 4c (full-length PARP1-EGFP mutant M43D F44D) during preparation of the accepted version of the manuscript, after peer review and editorial evaluation had taken place. The error has been corrected in the HTML and PDF versions of the article.

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Acknowledgements

We thank M. Roe for assistance with X-ray data collection and K. Caldecott for useful discussion. We are grateful to the Diamond Light Source Ltd., Didcot, UK, for access to synchrotron radiation. We thank the Advanced Light Microscopy Facility (ALMF) at the European Molecular Biology Laboratory (EMBL) and Olympus Europe for supporting EMBL's ALMF. This work was supported by EMBL, the Human Frontiers Science Program and the EU FP6 Marie Curie Research and Training Network “Chromatin Plasticity” to A.G.L. and a Cancer Research UK Programme Grant (C302/A8265) to L.H.P. L.H.P. is supported by a Wellcome Trust Senior Investigator Award.

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A.A.E.A. purified the protein, crystallized the complex and collected the X-ray diffraction data; G.T. designed and constructed the PARP1-EGFP constructs and performed the laser DNA-damage experiments; M.K. performed the FRAP experiments; P.O.H. engineered the knockdown PARP1 cell line and the wild-type imaging reporter constructs and performed the in vitro complementation assays; M.H. and R.A.-B. engineered and purified the mutant PARP1 constructs; A.G.L. designed the study and analyzed the data; L.H.P. designed the study, analyzed the data and wrote the paper; A.W.O. designed the study, made the baculovirus constructs, performed the EMSA experiments, designed the purification protocol and solved and refined the crystal structure. All authors discussed the results and commented on the manuscript.

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Correspondence to Andreas G Ladurner or Laurence H Pearl or Antony W Oliver.

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Ali, A., Timinszky, G., Arribas-Bosacoma, R. et al. The zinc-finger domains of PARP1 cooperate to recognize DNA strand breaks. Nat Struct Mol Biol 19, 685–692 (2012). https://doi.org/10.1038/nsmb.2335

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