Genome instability is one of the main drivers of cancer. Integrity of the genome is protected by a temporal arrest of the cell cycle in the presence of DNA damage and by efficient DNA repair. Tumor suppressor p53 and its downstream target p21 are efficient inducers of the cell cycle checkpoint. Inversely, protein phosphatase PPM1D is a negative regulator of p53/p21 pathway and allows renewal of the proliferation after DNA repair. Defects in p53 pathway or overexpression of PPM1D promote tumorigenesis by silencing the cell cycle checkpoint. This project aims to elucidate new molecular mechanisms of PPM1D function besides its established role in checkpoint recovery. We have recently identified that a fraction of PPM1D localizes at human telomeres and controls phosphorylation of the shelterin complex.
We will investigate how PPM1D activity affects DNA replication and DNA repair at telomeres. To this end we will use CRISPR/Cas9 technique to induce damage of the telomeric DNA and recruitment of DNA repair factors will be followed by quantitative microscopy. Molecular biology and biochemistry will be used to map the regions involved in PPM1D function at telomeres and for control of its protein stability. Overall, the project will contribute to understanding of PPM1D function in control of genome integrity.
The laboratory of Cancer Cell Biology seeks for a motivated a curious PhD student with deep interest in basic mechanisms of cell function. The candidate should hold degree in cell/molecular biology or biochemistry. The candidate should be able to efficiently work in the team and communicate in English. Previous hands-on experience with cell biology, telomere biology or DNA repair techniques is considered advantage but is not required.
DNA replication is an essential and one of the most complex processes in the cell. Not only exogenous DNA damage but also intrinsic DNA structures including G-quadruplexes (G4) and R-loops, their stabilization or unscheduled formation represent serious obstacles for replication progression, and have possible detrimental effects on genome integrity. Not surprisingly, those processes are pharmacologically targeted in anticancer therapy, despite the fact that only little is known about the underlying molecular mechanisms. It becomes apparent that maintenance of processive DNA replication requires sophisticated protein networks beyond the core replisome. Whether there is a direct crosstalk between G4 and R-loops, what proteins are involved in their homeostasis and what are the factors diversifying between their beneficial and pathological roles is not well understood.
The goals of our research are to identify proteins associated with G4 and R-loop structures and understand their roles in G4/R-loop formation and resolution as well as relationship to replication fork progression and associated repair. We are currently working on mass spectrometry-based proteomics approaches, including APEX-based proximity labeling and chromatin affinity precipitation methods, coupled with functional siRNA screens to identify new factors involved in metabolism of R-loops and G4s in conjunction with ongoing replication. The PhD student will use the well-established methods in the laboratory to validate hits and for selected protein to explore its role in replication stress and genomic instability.
Applicants should be graduates in Molecular Biology/Cellular Biology/Biochemistry with a strong interest in basic research and experimental work. Good English and independent thinking is required. The projects offer training in a broad range of molecular, cell biological and biochemical techniques. The student can also undergo short-term trainings at the Institute of Molecular Cancer Research of the University of Zurich and/or at Masaryk university/CEITEC in Brno, where he/she will be exposed to front-line research in the field of DNA repair and cancer.