Identification of RNF114 as ADPr-Ub reader through non-hydrolysable ubiquitinated ADP-ribose
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Abstract
Abstract Crosstalk between the post-translational modification processes ubiquitination and ADP-ribosylation occurs in DNA-damage and immune-responses, in addition the physical linkage of ADP-ribose and ubiquitin is found during bacterial infection. Here, we study the ubiquitination of ADP-ribose mediated by human Deltex E3 ligases and the subsequent fate of the formed hybrid post-translational modification. We prepare a non-hydrolysable ADPr-Ub probe that we employ in a chemoproteomics approach and identify RNF114 as an interacting protein. Using biophysical and biochemical experiments, we validate that RNF114 preferentially interacts with ubiquitinated ADP-ribose over non-modified ubiquitin. Subsequently, RNF114 can elongate the ubiquitinated ADP-ribose with a K11-linked ubiquitin chain. Using domain deletion analysis, we pinpoint the tandem zinc fingers and ubiquitin interacting motif (ZnF2+ZnF3+UIM) domains of RNF114 to be crucial for recognising ubiquitinated ADP-ribose. Moreover, these domains are essential for the recruitment of RNF114 to the sites of laser-induced DNA damage.
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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works
Accurate structure prediction of biomolecular interactions with AlphaFold 3
Abramson, J., Adler, J., Dunger, J., Evans, R., Green, T., Pritzel, A., Ronneberger, O., Willmore, L., Ballard, A. J., Bambrick, J., et al. (2024) · Nature · doi:10.1038/s41586-024-07487-w · Cited by 15,861 · see citing works
ColabFold - Making protein folding accessible to all
Mirdita, M., Schütze, K., Moriwaki, Y., Heo, L., Ovchinnikov, S., & Steinegger, M. (2021) · doi:10.1101/2021.08.15.456425 · Cited by 9,391 · see citing works
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- Authors
- Kloet, M. S., Chatrin, C., Mukhopadhyay, R., van Tol, B. D. M., Smith, R., Rotman, S. A., Tjokrodirijo, R. T. N., Zhu, K., Gorelik, A., Maginn, L., Elliott, P. R., van Veelen, P. A., Ahel, D., Ahel, I., & van der Heden van Noort, G. J.
- Affiliations
- Leiden University Medical Center (NL)
- University of Oxford (GB)
- Corresponding author
- Chatrin, Chatrin
- Ahel, Ivan
- ORCID
- Venue
- Nature Communications
- Published
- 2025-07-09
- Volume
- 16
- Issue
- 1
- Pages
- 6319-6319
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC12241653
- OpenAlex
- W4412177821
- Cited by
- 30
- References
- 3
- Citations by year
- 2026: 17 · 2025: 13
- FWCI
- 9.02
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nature Communications (publishedVersion, cc-by-nc-nd)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Leiden Repository (Leiden University) (submittedVersion, cc-by-nc-nd)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Wellcome Trust (USCF 456, 223107, 302632, BB/R007195/1, BB/W016613/1, 224095, C35050/A22284, 224095/Z/21/Z, 813369)
- Ovarian Cancer Research Alliance (223107, USCF 456, 813369, BB/W016613/1, BB/R007195/1, C35050/A22284)
- UK Research and Innovation (BB/W016613/1, BB/R007195/1)
- Cancer Research UK (BB/R007195/1, USCF 456, A22284, C35050 / A22284, DRCPFA-Jun24/100003, 223107, 813369, BB/W016613/1)
- University of Oxford (USCF 456)
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (VI.Vidi.192.011)
- Leids Universitair Medisch Centrum
- Directorate for Biological Sciences
- Medical Research Council (MR/Z506217/1)
- Biotechnology and Biological Sciences Research Council (USCF 456, C35050/A22284, 223107, BB/W016613/1, 813369, BB/Y008936/1, BB/R007195/1)
- HORIZON EUROPE European Research Council (101087582)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- RNF114, ADP-ribosylation, ubiquitination, ubiquitin-interacting motif, DNA damage response, laser-induced DNA damage, protein-protein interaction
- MeSH terms
- Protein Domains, ADP-Ribosylation, Adenosine Diphosphate Ribose, DNA Damage, Humans, Protein Binding, Protein Processing, Post-Translational, Ubiquitin, Ubiquitin-Protein Ligases, Ubiquitination, HEK293 Cells
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