Projects Offered

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

Scientific background

R-loops occur naturally during transcription and can have important regulatory functions, however, persistence of R-loops can have deleterious effects and result in the accumulation of DNA double-strand breaks and genome instability. Thus, aberrant R-loops have been linked to human diseases, including neurodegenerative disorders. For instance, several genes that are mutated in the neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) have been implicated in DNA damage repair and the regulation of R-loops, suggesting that DNA damage and genome instability may contribute to neurodegeneration in these disorders. Two of these ALS/FTD-associated genes encode for the major aggregating proteins in ALS and FTD patients, Fused in Sarcoma (FUS) and TAR DNA binding protein of 43 kDa (TDP-43). They are ubiquitously expressed DNA/RNA-binding proteins that are normally predominantly localized in the nucleus. However, in the degenerating brain regions of ALS and FTD patients, FUS and TDP-43 are largely absent from the nucleus and accumulate in cytosolic aggregates of neurons and glial cells, resulting in a loss of nuclear FUS or TDP-43 function. FUS or TDP-43 depletion by RNA interference renders cells more sensitive to transcription-arresting agents and results in R-loop accumulation. The molecular mechanisms by which FUS and TDP-43 suppress R-loops and how the two proteins are recruited to sites of DNA damage in active genes are largely unknown.

PhD project: Role of FUS and TDP-43 in R-loop regulation and genome stability

This project will focus on the molecular mechanisms involved in FUS and TDP-43-mediated R-loop suppression and recruitment of TDP-43 and FUS to DNA damage sites, using a combination of in vitro and cellular systems. Specifically, we aim to address the following questions:

1) Do FUS and TDP-43 resolve R-loops by directly binding to RNA-DNA hybrids?
2) Which domains of FUS and TDP-43 are required for the R-loop suppressing activity and for their recruitment to DNA damage sites? 
3) Is the phase separation/condensation behavior of FUS or TDP-43 required for these activities? 
4) Are DNA-damage-induced post-translational modifications (PTMs), e.g. ADP-ribosylation or phosphorylation of FUS, essential for R-loop suppression and recruitment to sites of DNA damage?

Methods involve protein biochemistry (in vitro assays with recombinant proteins) and molecular cell biology (incl. genome-wide R-loop mapping and advance fluorescence microscopy).

This project will be part of the RTG on R-loop Regulation in Robustness and Resilience (4R). More information can be found at: Project 6. R-loop regulation by neurodegeneration-linked DNA/RNA-binding proteins FUS and TDP-43. - 4R-RTG

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

Publications relevant to the project

Gruijs da Silva LA, Simonetti F, Hutten S, Riemenschneider H, Sternburg EL, Pietrek LM, Gebel J, Dötsch V, Edbauer D, Hummer G, Stelzl LS and Dormann D (2022) Disease-linked TDP-43 hyperphosphorylation suppresses TDP-43 condensation and aggregation. EMBO J, 41:e108443 Link

Sternburg EL, Gruijs da Silva LA, Dormann D (2022) Post-translational modifications on RNA-binding proteins: accelerators, brakes, or passengers in neurodegeneration?Trends Biochem Sci. 47(1):6-22 Link

Alberti S, Dormann D. (2019) Liquid-Liquid Phase Separation in Disease. Annu Rev Genet. Dec 3;53:171-194. Link

Hofweber M*, Hutten S*, Bourgeois B, Spreitzer E, Niedner-Boblenz A, Schifferer M, Ruepp MD, Simons M, Niessing D, Madl T and Dormann D (2018) Phase separation of FUS is suppressed by its nuclear import receptor and arginine methylation. Cell, 173:706–719.e13 Link