Cryo-EM structures of NHEJ assemblies with nucleosomes
DNA double-strand breaks (DSBs) are highly deleterious lesions that can trigger cell death or carcinogenesis if unrepaired or misrepaired. In mammals, most DSBs are repaired by non-homologous end joining (NHEJ), which begins when Ku70/80 binds DNA ends and recruits DNA-PKcs to form the DNA-PK holoenzyme. Although recent cryo-EM studies have resolved several NHEJ assemblies, how these factors access DSBs within nucleosomes remains unclear. Here, we present cryo-EM structures of human Ku70/80 and DNA-PK bound to nucleosomes. Ku70/80 binds the DNA end and bends it away from the nucleosome core, while the Ku70 C-terminal SAP domain makes an additional, specific DNA contact. Our DNA-PK-nucleosome structure further reveals the opening of the Ku80 vWA domain, and we show that non-hydrolysable ATP promotes synapsis by stabilising the Ku80-mediated DNA-PK dimer. These structures reveal a model for DSB recognition on nucleosomal DNA and provide insights relevant to targeting NHEJ in cancer therapy.
Authors
- Ammarah Tariq
- J. Charbonnier
- Matthew K. Bilyard
- Katheryn Meek (ORCID: https://orcid.org/0000-0002-0454-4414)
- Chris Hall
- Virginie Ropars (ORCID: https://orcid.org/0000-0002-3372-6030)
- Dimitri Y. Chirgadze (ORCID: https://orcid.org/0000-0001-9942-0993)
- Thomas Schalch
- Himani Amin (ORCID: https://orcid.org/0000-0002-5467-6642)
- Steven W. Hardwick (ORCID: https://orcid.org/0000-0001-9246-1864)
- Sayma Zahid (ORCID: https://orcid.org/0000-0002-1354-9209)
- Philippe Frit (ORCID: https://orcid.org/0000-0002-6571-8860)
- MAURO MODESTI
- Antonia Kefala-Stavridi
- Amandine Pelletier
- Taiana Maia De Oliviera
- A. J. Chaplin
- Patrick Calsou
- Sébastien Britton
- Tom L. Blundell
- Shankar Balasubramanian
Institutions
- AstraZeneca (United Kingdom) (GB)
- Roche (Switzerland) (CH)
- Centre National de la Recherche Scientifique (FR)
- Université Toulouse III - Paul Sabatier (FR)
- University of Leicester (GB)
- Inserm (FR)
- Université Fédérale de Toulouse Midi-Pyrénées (FR)
- University of Cambridge (GB)
- Commissariat à l'Énergie Atomique et aux Énergies Alternatives (FR)
- Université Paris-Saclay (FR)
- Institut de Pharmacologie et de Biologie Structurale (FR)
- Lung Institute (US)
- Institut de Biologie Intégrative de la Cellule (FR)
- CEA Paris-Saclay (FR)
- Michigan State University (US)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-12-24
- DOI
- https://doi.org/10.1038/s41467-025-67376-2
- Primary Topic
- DNA Repair Mechanisms
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- Lister Institute of Preventive Medicine
- Agence Nationale de la Recherche
- Institut National de la Santé et de la Recherche Médicale
- Medical Research Council