Projects Offered

1 PhD project offered in the IPP summer 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. DNA damage and 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, TAR DNA binding protein of 43 kDa (TDP-43) and Fused in Sarcoma (FUS). 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, TDP-43 and FUS are largely absent from the nucleus and accumulate in cytosolic aggregates of neurons and glial cells, resulting in a loss of nuclear TDP-43 or FUS function. TDP-43 or FUS depletion by RNA interference causes DNA damage and R-loop accumulation and DNA damage markers are elevated in brains of ALS/FTD patients. The molecular mechanisms by which TDP-43 and FUS contribute to DNA repair and suppress R-loops are largely unknown.

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

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

1) Does TDP-43 help to resolve R-loops by directly binding to RNA-DNA hybrids?

2) How is TDP-43 recruited to R-loops and DNA damage sites? Is the phase separation/condensation behavior of TDP-43 required for this? 

3) What post-translational modifications occur on TDP-43 in response to DNA damage, and how do they regulate TDP-43’s function in R-loop suppression and the DNA damage response?

4) Where in the genome do R-loops appear upon TDP-43 loss-of-function?

The project involves a wide methods spectrum, ranging from protein biochemistry and biophysics (in vitro assays with recombinant proteins) to molecular cell biology (advance fluorescence microscopy, live imaging) and the possibility to learn and apply genome-wide R-loop mapping techniques.

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