Molecular mechanisms and regulation of DNA repair
Our Focus
My group focusses on deciphering the molecular details of cellular processes that maintain genome integrity. This is critical to understand cancer development and could contribute to novel strategies for cancer treatment. We use a powerful biochemical system to recapitulate DNA replication and repair under physiological conditions in vitro, enabling molecular dissection of these processes.
A major topic is the repair of DNA interstrand crosslinks (ICLs), toxic DNA lesions that form endogenously but are also induced in cancer chemotherapy. The classical pathway of ICL repair is the FA pathway affected in the cancer predisposition disorder Fanconi anaemia. However, we and others have recently identified additional ICL repair pathways. Our current research focusses on: 1) Novel factors and the molecular mechanism of the FA pathway. 2) Characterization of new pathways that repair ICLs induced by reactive aldehydes. 3) Development of high throughput sequencing techniques to examine chromatin dynamics and mutation induction. Another main research line focusses on the resolution of mutagenic secondary DNA structures (such as G4 and other structures). We developed methods to study the resolution of these structures during DNA replication but also independent of DNA replication, and define the mechanisms involved.
About Puck Knipscheer
Puck Knipscheer
My Research
Puck Knipscheer has been interested in understanding the molecular details of biological processes since her PhD (2007) at the Netherlands Cancer Institute with Prof. Titia Sixma. Here she used X-ray crystallography and biochemistry to investigate posttranslational modification by the ubiquitin-like modifier SUMO. During her postdoc in the laboratory of Johannes Walter at Harvard Medical School she started to study genome maintenance.
She contributed to the development of a unique Xenopus egg extract based system that allows the repair of highly toxic DNA interstrand crosslinks (ICLs) under physiological conditions in vitro. Subsequently, she used this system to elucidate the role of the Fanconi anemia protein FANCD2 and showed for the first time how the activated Fanconi anemia pathway acts in a specific step in ICL repair.
In 2011 she started her own laboratory at the Hubrecht Institute in Utrecht where she continued her investigations into this poorly understood DNA repair pathway. She identified the long sought endonuclease that unhooks an ICL during repair. In addition, she developed a system to study G4 structure unwinding under physiologically relevant conditions and found a direct role for the helicase FANCJ. She currently continues to use this system to investigate the mechanisms by which stable secondary DNA structures are resolved during DNA replication.
Awards
2021: ERC consolidator grant
2016: KWF project grant
2011: NWO-Vidi grant
2010: Heineken Young Scientist Award for Biochemistry and Biophysics, Royal Netherlands Academy of Arts and Sciences (KNAW)
2007: KWF (Dutch Cancer Society) preclinical- and fundamental research fellowship
Key Publications
- 2025 | DNA polymerase kappa is the primary translesion synthesis polymerase for aldehyde ICLs | Roxanne V. van der Sluijs et al. | Nucleic Acids Research | View publication
- 2025 | RNA transcripts regulate G-quadruplex landscapes through G-loop formation | Koichi Sato et al. | Science | View publication
- 2021 | Multistep mechanism of G-quadruplex resolution during DNA replication | Koichi Sato et al. | Science Advances | View publication
- 2020 | Alcohol-derived DNA crosslinks are repaired by two distinct mechanisms | Michael R. Hodskinson et al. | Nature | View publication
- 2020 | HSF2BP negatively regulates homologous recombination in DNA interstrand crosslink repair | Koichi Sato et al. | Nucleic Acids Research | View publication
- 2019 | The role of SLX4 and its associated nucleases in DNA interstrand crosslink repair | Wouter S. Hoogenboom et al. | Nucleic Acids Research | View publication
- 2017 | Recruitment and positioning determine the specific role of the XPF-ERCC1 endonuclease in interstrand crosslink repair | Daisy Klein Douwel et al. | The EMBO Journal | View publication
- 2014 | FANCJ promotes DNA synthesis through G-quadruplex structures | Pau Castillo Bosch et al. | The EMBO Journal | View publication
- 2014 | XPF-ERCC1 acts in unhooking DNA interstrand crosslinks in cooperation with FANCD2 and FANCP/SLX4 | Daisy Klein Douwel et al. | Molecular Cell | View publication
- 2009 | The Fanconi anemia pathway promotes replication-dependent DNA interstrand cross-link repair | Puck Knipscheer et al. | Science | View publication
Members
| Puck Knipscheer Group leader | Collin Bos Technician | Eri Berkum Scientist |
| Hanneke Elemans PhD Student | Koichi Sato Postdoc fellow | Meira Neut Technician |
| Merlijn Witte Technician | Roxanne van der Sluijs PhD student | Themis Liolios Phd student |