UBE2D3 facilitates NHEJ by orchestrating ATM signalling through multi-level control of RNF168

Nature Communications, vol. 15, pp. 5032

Abstract

Maintenance of genome integrity requires tight control of DNA damage response (DDR) signalling and repair, with phosphorylation and ubiquitination representing key elements. How these events are coordinated to achieve productive DNA repair remains elusive. Here we identify the ubiquitin-conjugating enzyme UBE2D3 as a regulator of ATM kinase-induced DDR that promotes non-homologous end-joining (NHEJ) at telomeres. UBE2D3 contributes to DDR-induced chromatin ubiquitination and recruitment of the NHEJ-promoting factor 53BP1, both mediated by RNF168 upon ATM activation. Additionally, UBE2D3 promotes NHEJ by limiting RNF168 accumulation and facilitating ATM-mediated phosphorylation of KAP1-S824. Mechanistically, defective KAP1-S824 phosphorylation and telomeric NHEJ upon UBE2D3-deficiency are linked to RNF168 hyperaccumulation and aberrant PP2A phosphatase activity. Together, our results identify UBE2D3 as a multi-level regulator of NHEJ that orchestrates ATM and RNF168 activities. Moreover, they reveal a negative regulatory circuit in the DDR that is constrained by UBE2D3 and consists of RNF168- and phosphatase-mediated restriction of KAP1 phosphorylation.

Authors 16

1. Zeliha Yalçin

   The Netherlands Cancer Institute

   Affiliation as printed

   Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands

2. Shiu Yeung Lam

   The Netherlands Cancer Institute

   Affiliation as printed

   Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands

3. Marieke H. Peuscher

   The Netherlands Cancer Institute

   Affiliation as printed

   Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands

4. Jaco van der Torre

   The Netherlands Cancer Institute

   Affiliation as printed

   Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands

5. Sha Zhu

   The Netherlands Cancer Institute

   Affiliation as printed

   Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands

6. Prasanna Vasudevan Iyengar

   The Netherlands Cancer Institute

   Affiliation as printed

   Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands

7. Daniel Salas‐Lloret Aachen Department of Cell and Chemical Biology

   Leiden University Medical Center

   Affiliation as printed

   Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, the Netherlands

8. Inge de Krijger

   The Netherlands Cancer Institute

   Affiliation as printed

   Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands

9. Nathalie Moatti

   The Netherlands Cancer Institute

   Affiliation as printed

   Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands

10. Ruben van der Lugt

    The Netherlands Cancer Institute

    Affiliation as printed

    Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands

11. Mattia Falcone

    The Netherlands Cancer Institute

    Affiliation as printed

    Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands

12. Aurora Cerutti

    The Netherlands Cancer Institute

    Affiliation as printed

    Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands

13. Onno B. Bleijerveld

    The Netherlands Cancer Institute

    Affiliation as printed

    Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands

14. Liesbeth Hoekman

    The Netherlands Cancer Institute

    Affiliation as printed

    Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands

15. Román González‐Prieto Aachen Department of Cell and Chemical Biology

    Consejo Superior de Investigaciones Científicas · Leiden University Medical Center · Centro Andaluz de Biología Molecular y Medicina Regenerativa · Universidad de Sevilla · Universidad Pablo de Olavide

    Affiliation as printed

    Andalusian Center for Molecular Biology and regenerative Medicine (CABIMER), Universidad de Sevilla-CSIC-Universidad-Pablo de Olavide, Sevilla, Spain

    Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain

    Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, the Netherlands

16. Jacqueline J.L. Jacobs corresponding

    The Netherlands Cancer Institute

    Affiliation as printed

    Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands. j.jacobs@nki.nl

    Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands