Letter

A ubiquitin-dependent signalling axis specific for ALKBH-mediated DNA dealkylation repair

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Published online:

Abstract

DNA repair is essential to prevent the cytotoxic or mutagenic effects of various types of DNA lesions, which are sensed by distinct pathways to recruit repair factors specific to the damage type. Although biochemical mechanisms for repairing several forms of genomic insults are well understood, the upstream signalling pathways that trigger repair are established for only certain types of damage, such as double-stranded breaks and interstrand crosslinks1,2,3. Understanding the upstream signalling events that mediate recognition and repair of DNA alkylation damage is particularly important, since alkylation chemotherapy is one of the most widely used systemic modalities for cancer treatment and because environmental chemicals may trigger DNA alkylation4,5,6. Here we demonstrate that human cells have a previously unrecognized signalling mechanism for sensing damage induced by alkylation. We find that the alkylation repair complex ASCC (activating signal cointegrator complex)7 relocalizes to distinct nuclear foci specifically upon exposure of cells to alkylating agents. These foci associate with alkylated nucleotides, and coincide spatially with elongating RNA polymerase II and splicing components. Proper recruitment of the repair complex requires recognition of K63-linked polyubiquitin by the CUE (coupling of ubiquitin conjugation to ER degradation) domain of the subunit ASCC2. Loss of this subunit impedes alkylation adduct repair kinetics and increases sensitivity to alkylating agents, but not other forms of DNA damage. We identify RING finger protein 113A (RNF113A) as the E3 ligase responsible for upstream ubiquitin signalling in the ASCC pathway. Cells from patients with X-linked trichothiodystrophy, which harbour a mutation in RNF113A, are defective in ASCC foci formation and are hypersensitive to alkylating agents. Together, our work reveals a previously unrecognized ubiquitin-dependent pathway induced specifically to repair alkylation damage, shedding light on the molecular mechanism of X-linked trichothiodystrophy.

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Acknowledgements

We thank B. Sleckman, G. Oltz, T. Stappenbeck, S. Virgin, and K. Murphy for their advice on this manuscript. J.R.B. and A.K.B. are supported by a Cell and Molecular Biology Training Grant (5T32GM007067-40), and J.R.B. is also supported by a Shawn Hu and Angela Zeng Student Scholarship. J.M.S. is supported by a Monsanto Graduate Program Fellowship. P.M.L. is supported by a fellowship from the American Cancer Society (PF-14-182-01-DMC). We thank the patients and their families, whose help and participation made this work possible. We acknowledge the Alvin J. Siteman Cancer Center at Washington University and Barnes-Jewish Hospital for the use of the GEiC Core. The Siteman Cancer Center is supported by a National Cancer Institute Cancer Center Support Grant (P30 CA091842; Eberlein, PI). This work was supported by the National Institutes of Health (R01 GM108648 to A.V., R01 GM109102 to C.W., and R01 CA193318 to N.M.), the Alvin Siteman Cancer Research Fund, the Siteman Investment Program (both to N.M.), and the Children’s Discovery Institute of St. Louis Children’s Hospital (MC-II-2015-453 to N.M.).

Author information

Author notes

    • Jennifer M. Soll
    •  & Patrick M. Lombardi

    These authors contributed equally to this work.

Affiliations

  1. Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, USA

    • Joshua R. Brickner
    • , Jennifer M. Soll
    • , Miranda C. Mudge
    • , Clement Oyeniran
    • , Meagan E. Sullender
    • , Andrea K. Byrum
    • , Yu Zhao
    •  & Nima Mosammaparast
  2. Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA

    • Patrick M. Lombardi
    • , Elyse Blazosky
    •  & Cynthia Wolberger
  3. Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, NO-7491 Trondheim, Norway

    • Cathrine B. Vågbø
    • , Renana Rabe
    •  & Geir Slupphaug
  4. PROMEC Core Facility for Proteomics and Metabolomics, NTNU and the Central Norway Regional Health Authority, NO-7491 Trondheim, Norway

    • Cathrine B. Vågbø
    •  & Geir Slupphaug
  5. Edward A. Doisy Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, Missouri 63104, USA

    • Jessica Jackson
    •  & Alessandro Vindigni
  6. Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, South Australia 5000, Australia

    • Mark A. Corbett
    •  & Jozef Gécz
  7. Healthy Mothers and Babies, South Australian Medical Research Institute, Adelaide, South Australia 5000, Australia

    • Jozef Gécz
  8. Genetics of Learning Disability Service, Hunter Genetics, Waratah, New South Wales 2298, Australia

    • Michael Field

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Contributions

J.R.B., J.M.S., C.O., M.E.S. and N.M. performed cellular and biochemical experiments. P.M.L. performed isothermal titration calorimetry experiments. C.B.V. and R.R. performed alkylated lesion quantification. M.C.M., A.K.B. and Y.Z. assisted with providing reagents and technical help. P.M.L. and E.B. performed the structural analysis. M.A.C., J.G. and M.F. provided X-TTD patient cells. J.J. performed DNA fibre analysis and was supervised by A.V. C.W. supervised P.M.L. and E.B. G.S. supervised C.B.V. and R.R. N.M. supervised the project and wrote the manuscript with J.R.B., with input from all other authors.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Nima Mosammaparast.

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Supplementary information

PDF files

  1. 1.

    Life Sciences Reporting Summary

  2. 2.

    Supplementary Figure 1

    This file contains uncropped western blots and gels used in this study. Black rectangles denote how the blots and gels were cropped for final figures.

  3. 3.

    Supplementary Table 4

    All antibodies used in this study with concentrations noted. The antibodies were produced in either rabbit or mouse. Applications include Western blot (WB), immunofluorescence microscopy (IF), flow cytometry (FC) and proximity ligation assay (PLA).

Excel files

  1. 1.

    Supplementary Table 1

    Mass spectrometry data for TAP-ASCC2 purified from HeLa-S cells with or without prior exposure to MMS.

  2. 2.

    Supplementary Table 2

    A comprehensive list of each shRNA, including TRC numbers, used in the focused shRNA screen to identify the relevant E3 ligase.

  3. 3.

    Supplementary Table 3

    Mass spectrometry data for TAP-ASCC2 WT or the TAP-ASCC2 L506A CUE mutant purified from HeLa-S cells after MMS treatment.