Research Area: Proteomics and ADP-ribosylation Signaling
ADP-ribosylation (ADPr) is a key player in many physiological and disease conditions, including cancer, ageing and premature ageing syndromes.
Using advanced proteomics to make sense of a mysterious ADPr attachment chemistry, we uncovered serine ADPr as a new type of histone mark (Nature Chemical Biology 2016) and described the underlying molecular mechanisms by identifying its ‘readers’ (Mol Cell 2017) and ‘eraser’ (eLife 2017). Crucially, we and others have shown that Ser-ADPr is the primary form of ADPr in the DNA damage response (eLife 2018). Overall, these findings are reversing 50 years of consensus understanding and have opened up a large and novel research area aiming to elucidate how ADPr regulates the DNA damage response and chromatin dynamics. Thus, an increasing number of laboratories are shifting their focus towards Ser-ADPr to determine the functional consequences of site-specific ADPr by PARP-1. In this context, we and others have revealed an interplay between Ser-ADPr and canonical histone marks (Cell Reports 2018). Currently, we are capitalizing on our lead and combining a newly established chemical biology-based technology with state-of-the-art proteomics, biochemistry, molecular biology and microscopy technique to study elusive, but biologically and clinically important, forms of ADPr.
2. Research questions addresses by the group:
System-wide analysis of ADP-ribosylation sites
We will establish a “next generation” proteomics platform for in-depth ADPr site mapping. This will be achieved by combining four key elements: our partial FASP approach (Nat Chem Bio 2016); unbiased data analysis; high-resolution ETD, and newly developed antibodies for enrichment of ADPr peptides. This approach will not only reveal the full scope of Ser-ADPr and the extent of its dependency on HPF1, but also elucidate the relative extent of the two PARP-1/-2 conjugation specificities (Mol Cell 2017). Furthermore, it will enable a variety of systemwide studies of Ser-ADPr and other types of ADPr in DNA repair signalling and beyond.
ADP-ribosylation sites in ageing
Taking advantage of the knowledge and approaches obtained from our ongoing projects, we will focus on investigating the role of ADPr in the persistent DNA damage response during the ageing process. High-profile studies have established that in both normal ageing and genetic disorders characterized by premature ageing, activation of PARP-1 increases the global level of protein poly-ADPr. This in turn leads to NAD+ depletion and concomitant mitochondrial dysfunction, a well-known aspect of ageing. However, due to the lack of experimental tools, the still incomplete understanding of ADPr dynamics leaves even basic questions unanswered. How does this chronic accumulation of DNA damage compare with the “acute” DNA damage response? How does mono-ADP-ribosylation change in ageing? Do other ADP-ribosylating enzymes play a role in ageing? How does Ser-ADPr change during the ageing process compared with other types of ADPr? What is the role of HPF1, the Ser-ADPr-inducing factor important for genome stability?
3. Possible projects:
- ADP-ribosylation in ageing (see above)
- Identification and characterization of the “readers” of Ser-ADPr by quantitative proteomics
- ADP-ribosylation and stem cells
- Next-generation global site-specific ADPr proteomics
4. Applied Methods and model organisms:
- Methods: advanced mass spectrometry, computational proteomics, chemical biology, biochemical purification, cell culture, western blotting
- Model organisms (in collaboration with different groups at MPI-AGE and CECAD): Model organisms (in collaboration with different groups at MPI-AGE and CECAD): worm, fish, mouse and fruitfly, mammalian cell culture
5. Desirable skills and qualifications:
Excellent, ambitious and easy going.
Ability to join an interdisciplinary, collaborative and highly productive research environment and flexibility to operate in a fast-paced research filed. The candidate will receive extensive training (under the direct supervision of both the group leader and a senior postdoc) in the much sought-after proteomics technology, which will boost his/her career within and beyond academia. As our lab has been selected to the EMBO Young Investigator Programme, additional opportunities will be available to PhD students that join the lab: lab member visiting fellowship to carry out experiments/learn a technique in another lab (e.g. Ahel lab at Oxford University); access to EMBL core facilities; grants for attending conferences or courses; nomination of students to attend the Annual Nobel Laurate meeting. Furthermore, the candidate will have the opportunity of publishing regularly in high profile journals as illustrated by our publication rate over the last 4 years:
- An HPF1/PARP1-based chemical biology strategy for exploring ADP-ribosylation, Juan José Bonfiglio, Orsolya Leidecker, Helen Dauben, Edoardo José Longarini, Thomas Colby, Pablo San Segundo‐Acosta, Kathryn A. Perez, and Matic, I. (2020), Cell, in press
- Interplay of Histone Marks with Serine ADP-Ribosylation
Bartlett, E. * Bonfiglio, J. J. * Prokhorova, E. Colby, T. Zobel, F. Ahel, I.**Matic, I.**
(2018) Cell Reports, 24(13):3488-3502.e5
- Serine is the major residue for ADP-ribosylation upon DNA damage
Palazzo, L.*Leidecker, O.*Prokhorova, E.*Dauben, H. Matic, I.**Ahel, I.**
(2018) Elife, 7
- Serine ADP-ribosylation reversal by the hydrolase ARH3
Fontana, P.*Bonfiglio, J. J.*Palazzo, L.*Bartlett, E. Matic, I.**Ahel, I.**
(2017) Elife, 6
- Serine ADP-Ribosylation Depends on HPF1
Bonfiglio, J. J. Fontana, P.Zhang, Q. Colby, T. Gibbs-Seymour, I. Atanassov, I.Bartlett, E.Zaja, R. Ahel, I.**Matic, I.**
(2017) Mol Cell, 65, 5, 932-940 e6
- Serine is a new target residue for endogenous ADP-ribosylation on histones
Leidecker, O.*Bonfiglio, J. J.*Colby, T.Zhang, Q.Atanassov, I.Zaja, R.Palazzo, L.Stockum, A.Ahel, I.Matic, I. (2016) Nat Chem Biol, 12, 12, 998-1000
- Phosphoribosylation of Ubiquitin Promotes Serine Ubiquitination and Impairs Conventional Ubiquitination
Bhogaraju, S.Kalayil, S.Liu, Y.Bonn, F.Colby, T.Matic, I.Dikic, I.
(2016) Cell, 167, 6, 1636-1649 e13
* Co-first authors
** Co-corresponding authors