1 PhD project offered in the IPP winter call Molecular Mechanisms in Genome Stability & Gene Regulation

Scientific Background

R-loops are secondary DNA structures consisting of an RNA-DNA hybrid and a single stranded DNA that can form behind the elongating RNA polymerase II during transcription. R-loops play regulatory roles during transcription initiation and termination. However, the accumulation of R-loops in the genome results in replication stress, DNA double-strand breaks and genomic instability. A number of proteins including ribonucleases, helicases and translocases have been shown to regulate R-loop levels in cells. In recent years, R-loops have been recognized as a major cell-intrinsic source of genomic instability, and dysregulation of R-loop processing is associated with cancer and neurodegenerative diseases. We have developed an unbiased mass spectrometry-based proteomics approach to identify proteins that regulate R-loops in human cells and discovered a role for the tumor suppressor DDX41 in R-loop resolution. 

PhD Project: Mechanisms opposing R-loop-associated DNA double strand breaks

The specific aims of this PhD project are to decipher how proteins are selected and recruited for degradation to the nuclear, proteolytic centers under proteotoxic stress conditions. To this end the PhD candidate will use quantitative proteomics approaches in combination with confocal microscopy and biochemistry. You will work closely together with a co-funded second PhD student situated in the Luck group at IMB and a co-funded postdoctoral researcher in the Kukharenko and Kremer labs at the MPI for Polymer Research in Mainz. The project is part of a large collaborative research centre (CRC 1551) that involves about 30 other research groups in and around Mainz with regular meetings of all members. For more information please visit https://crc1551.com/. We seek for a PhD candidate with basic expertise in programming and data analysis as well as cell and molecular biology techniques. The candidate should have a strong interest in the biological processes that are subject to this study and bring a high collaborative spirit.

The PhD project will be part of the DFG-funded 4R Research Training Group “R-loop Regulation in Robustness and Resilience”. The PhD student will profit from collaboration and networking with other research groups, all focusing on understanding the role of R-loops in cellular stress responses and disease. The Beli group has expertise in quantitative proteomics approaches in analyzing protein interactions and regulation on chromatin. The project will focus on understanding the regulation of Ribonuclease H1, which digests the RNA moiety in the R-loops and plays a central role in R-loop resolution. We will analyze how the activity of this enzyme is directed to pathological compared to regulatory R-loops to maintain genome stability. In this regard, we will focus on phosphorylation and ubiquitylation as well as the compartmentalization of pathological R-loops in biological condensates. Furthermore, we will analyze systems-wide responses to R-loop-associated genomic instability, also exploring the interplay between R-loop accumulation and inflammatory response. We will take advantage of unique tools that were previously developed in our lab to map R-loops and associated proteins with proximity-based proteomics and high-content microscopy.

If you are interested in this project, please select Beli as your group preference in the IPP application platform.

Publications relevant to this project

Mosler T, Conte F, Longo GMC, Mikicic I, Kreim N, Möckel MM, Petrosino G, Flach J, Barau J, Luke B, Roukos V, Beli P (2021) R-loop proximity proteomics identifies a role of DDX41 in transcription-associated genomic instability. Nat Commun. Dec 16;12(1):7314. Link

Longo GMC, Sayols S, Kotini AG, Heinen S, Möckel MM, Beli P, Roukos V. (2024) Linking CRISPR-Cas9 double-strand break profiles to gene editing precision with BreakTag. Nat Biotechnol. 13. Link