1. Research Background:

A vital factor in comprehending ageing and age-related diseases involves deciphering the signaling pathways that dictate crucial fate decisions. Key among these pathways is regulation by ADP-ribosylation (ADPr), a biologically and clinically significant yet challenging post-translational modification known for its crucial role in maintaining genome stability. The overarching aim of our research group is to investigate the molecular mechanisms of DNA repair and ageing by elucidating the role of ADPr in these biological processes. Our group's seminal discoveries, including the identification of Serine ADPr by the HPF1/PARP1 writer complex as a novel type of histone mark (NatureChemBiol2016, MolCell2017, eLife2018, and CellReports 2018), have opened a broad and dynamic research area, with an increasing number of laboratories shifting their focus towards Ser-ADPr to understand DNA repair signaling, chromatin dynamics and develop new inhibitors. Our second major contribution is the transformation of these fundamental discoveries into a foundational technology, enabling the generation of essential and broadly applicable ADPr tools (Cell 2020, Mol Cell 2023, Trends Biochem Sci. 2023 and Nat Comms 2024). This has enabled us to uncover DNA damage-induced mono-ADPr as a second wave of PARP1 signaling that recruits, among others, RNF114 (Mol Cell 2023). Excitingly, this ubiquitin E3 ligase acts as a reader of ADP-ribosyl- ubiquitylation, an emerging composite PTM that we recently showed targets specific serine mono-ADPr marks on histones and PARP1 in response to DNA damage (Nature Chem Biol 2025).

2. Research questions addressed by the group:

Future breakthroughs in aging research, from basic biology to clinical applications, depend on understanding the precise molecular mechanisms that govern the many biological pathways involved in aging and age-related diseases. Yet, uncovering the biochemical basis of specific biological processes often presents significant challenges. Our ambition is to make transformative discoveries by uncovering the complex molecular mechanisms of aging through the development of cutting-edge proteomics, chemical biology and synthetic antibody tools and technologies.

Our most exciting direction is to elucidate the crosstalk between ADPr and ubiquitination that has emerged over the last few years. Although the fascinating discovery of phosphoribose-linked attachment of ubiquitin by Legionella, to which we contributed (Cell 2016), established a connection between these two PTMs, our research points to a more profound interplay. RNF114, which we identified as the reader of the mono-ADPr wave of PARP1 signaling (Mol Cell 2023), along with additional E3 ligases of the same family, recognizes both ubiquitin and ADPr. Excitingly, we have recently discovered that, during the DNA damage response, serine ADP-ribosylation—whose identification we pioneered at the start of our laboratory (Nature Chem Biol 2016, Mol Cell 2017)—is a cellular target of ADP- ribosyl-ubiquitylation on PARP1 and histones (Nature Chem Biol 2025). This composite modification has become a hot topic, as several groups have recently shown it to be involved in diverse signaling pathways.

3. Possible project(s):

Through pioneering proteomic approaches and the development of the first dedicated detection reagent (Nature Chem Biol 2025), our laboratory has established a leading position in the emerging field of ADP-ribosyl-ubiquitylation. Building on these technological advances and our seminal discovery that serine ADP-ribosylation is a target of this unconventional ubiquitylation (Nature Chem Biol 2025), we aim to decipher ADP-ribosyl-ubiquitylation signaling in the DNA damage response by addressing the following questions:

1. Is Serine ADP-ribosyl-ubiquitylation a widespread modification, targeting hundreds of proteins in the DNA damage response?
2. Do histone ADP-ribosyl-ubiquitylation marks play a role in DNA damage- induced chromatin relaxation triggered by PARP1?
3. Does Serine ADP-ribosyl-ubiquitylation recruit DNA repair factors and/or chromatin remodelers to the sites of the DNA damage?
4. Does Serine ADP-ribosyl-ubiquitylation change PARP1 interactome?
5. What is the role of the K11 chains formed by RNF114 on ADP-ribose?

To address these questions, we will expand the scope of our serine ADP-ribosylation technology (Cell 2020, Mol Cell 2023) to develop new tools, which we will integrate with our advanced proteomics approaches tailored to ADPr-based modifications.

4. Applied Methods and model organisms:

Methods: advanced proteomics, computational data analyses, chemical biology approaches, phage display for generating modular antibodies, SpyTag protein ligation technology, biochemical enrichment (immunoprecipitation/pull downs), cell culture, western blotting, live-cell imaging, immunofluorescence, cell culture. Model organisms: mammalian cell culture and the model organism African killifish.

5. Desirable skills and qualifications:

Ability to join an interdisciplinary, collaborative, and highly productive research environment, demonstrating flexibility to thrive in a rapidly advancing research field. The selected candidate will receive extensive training under the direct supervision of the group leader, made possible by the small size of the research group, gaining proficiency in a variety of highly sought-after advanced technologies. Such experience will significantly enhance their career prospects within academia and beyond.

6. References and key publications:

1. Kolvenbach, A., Palumbieri, M.D., Colby, T. Nadarajan, D., Bode, R., Matić, I. Serine ADPr on histones and PARP1 is a cellular target of ester- linked ubiquitylation. Nature Chemical Biology, 2025 Jul 9, doi.org 10.1038/s41589-025-01974-5.
2. Longarini, E. J. Matić, I. Preserving ester-linked modifications reveals glutamate and aspartate mono-ADP-ribosylation by PARP1 and its reversal by PARG. Nature Communications, 2024 May 18;15(1):4239
3. Longarini, E. J. Dauben, H. Locatelli, C. Wondisford, AR. Smith, R. Muench, R. Kolvenbach, A., Pope, A. Bonfiglio, J. J. Pinto Jurado, E. Fajka-Boja, R. Colby, T. Schuller, M. Ahel, I. Timinszhy, G. O’Sullivan, RJ., Huet, S. Matic, I. Modular antibodies reveal DNA damage-induced mono- ADP-ribosylation as a second wave of PARP1 signaling. Molecular Cell, 2023 May 18;83(10):1743-1760.e11
   ‘Tools of the trade’ highlight in Nature Reviews Molecular Cell Biology 25, page 3 (2024) ‘Deciphering ADP-ribosylation signalling’
   ‘Technology of the Month’ in Trends in Biochemical Sciences (2023) ‘A chemical biology/modular antibody platform for ADP-ribosylation signaling’ – Front cover featuring an artistic illustration of our technology
   Spotlight in Cell Reports Methods ‘Molecular tools unveil distinct waves of ADP-ribosylation during DNA repair’
   Selected for Molecular Cell’s ‘Best of 2023’ collection
4. Bonfiglio, J. J. Leidecker, O. Dauben, H. Longarini, E. J. Colby, T. San Segundo-Acosta, P. Perez, K. A. Matic, I*. (2020) An HPF1/PARP1-Based Chemical Biology Strategy for Exploring ADP-Ribosylation. Cell, 2020 Nov,183, 4, 1086-1102 e23
   Recommended by Polo S: Faculty Opinions (formerly F1000) of [Bonfiglio JJ et al., Cell 2020 183(4):1086-1102.e23]. In Faculty Opinions, 03 Dec 2020; 10.3410/f.739034237.793580334
   Granted EPO Patent EP3853241B1 (2039-09-17 anticipated expiration) “Site-specific serine adp-ribosylated proteins and peptides and method for producing the same” by Juan José Bonfiglio and Ivan Matic
5. Bonfiglio JJ, Fontana P, Zhang Q, Colby T, Gibbs-Seymour I, Atanassov I, Bartlett E, Zaja R, Ahel I, Matic I* (2017) Serine ADP-Ribosylation Depends on HPF1. Molecular Cell 65: 932-940 e6
   This study was selected by Molecular Cell as the best paper (“Featured Article”) of the March 2, 2017 issue
   MolecularCell’s interview: “Meet the author Juan José Bonfiglio”
   Front Cover in MolecularCell. It takes two to tango: PARP1 and HPF1
   Preview in Molecular Cell: 2 March 2017, Pages 777-778 “SERious Surprises for ADP-Ribosylation Specificity: HPF1 Switches PARP1 Specificity to Ser Residues”
   Preview in Cell Chemical Biology 2017 Apr 20;24(4):431-432 “ADP- Ribosylation Goes Normal: Serine as the Major Site of the Modification”
6. Leidecker O, Bonfiglio JJ, Colby T, Zhang Q, Atanassov I, Zaja R, Palazzo L, Stockum A, Ahel I, Matic I* (2016) Serine is a new target residue for endogenous ADP-ribosylation on histones. Nature Chemical Biology 12: 998-+
   Highlighted by the magazine Chemical & Engineering News (C&EN), the world's most comprehensive and authoritative source of news about chemistry and related fields: “Tracking a tricky chemical protein modification” (October 17, 2016 Volume 94, Issue 41)
   Interview by the New York-based GenomeWeb, the largest online newsroom focused on advanced molecular research tools: “Max Planck PTM Studies Suggest Benefits of Manual Inspection of Mass Spec Data” (Dec 16, 2016)