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

Scientific Background

RNA-DNA hybrids have important implications in the cell and play critical roles in processes like DNA replication, telomere elongation and transcription termination, not to mention CRISPR/Cas gene editing. RNA-DNA hybrids are primarily removed by the RNase H family of endonucleases. RNA-DNA hybrid misregulation has recently been strongly implicated in senescence, ageing as well as neurodegenerative diseases and cancer. When RNA-DNA hybrids (and R-loops) are not properly removed, they lead to severe genomic instability, increased rates of mutagenesis and inflammation. RNA-DNA hybrids can be formed as a by-product of transcription, however they are also formed during DNA replication, when the polymerases use RNA bases instead of DNA bases (NTPs instead of dNTPs). Very little is understood regarding how the RNase H enzymes are regulated and especially how RNA-DNA hybrids are regulated in aged and senescent cells and how this may influence the rate of aging and the prevalence of disease in aged, compared to young, organisms.

PhD Project: R-loop and rNMP regulation in ageing and senescence

It has recently been shown that the speed of transcription increases with age, and it was suggested that this may be responsible for some aspects of aging. Interestingly, transcription is responsible for the formation of R-loops (co-transcriptional three stranded structures with an RNA-DNA hybrid) as well as the mutagenesis of ribonucleotides inserted into the genome. This project will be performed in yeast and worms, as model systems, and will be comparing young and old cells. We will determine if R-loops and genomic ribonucleotides are age regulated and if so where in the genome this is occurring and why is the regulation different as we age. We will be employing RNA polymerase mutants that have increased and decreased rates of elongation and assay their effects on lifespan, ribonucleotide-associated mutagenesis and R-loop and ribonucleotide levels. Similarly, we will be trying to answer the same questions in senescent cells that are experiencing telomere shortening, as my lab has previously shown that short telomeres accumulate very stable R-loops. Finally, we be using interventions that are known to either extend or decrease lifespan to determine their effects on the RNA-DNA hybrid regulation during aging and senescence. Within this project students will use a host of molecular, biochemical, genetic and genomic approaches to tackle these questions. The answers to these questions will have important implications regarding aging and age-related disease.

This project will be part of the RTG on R-loop Regulation in Robustness and Resilience (4R).

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

Publications relevant to this project

Pires V, Lohner N, Wagner T, Wagner C, Wilkens M, Hajikazemi M, Paeschke K, Butter F and Luke B (2023) RNA-DNA hybrids prevent resection at dysfunctional telomeres. Cell Rep, 42(2), 112077 Link

Schindler N^*, Tonn M^*, Kellner V, Fung JJ, Lockhart A, Vydzhak O, Juretschke T, Möckel S, Beli P, Khmelinskii A and Luke B(2023)Genetic requirements for repair of lesions caused by single genomic ribonucleotides in S phase. Nat Commun 14:1227 Link

Misino S, Busch A, Wagner C, Bento F and Luke B (2022) TERRA increases at short telomeres in yeast survivors and regulates survivor associated senescence (SAS). Nucleic Acids Res, 50, 12829 – 12843 Link

Lockhart A, Pires VB, Bento F, Kellner V, Luke-Glaser S, Luke B (2019). RNase H1 and RNase H2 are differentially regulated to process RNA-DNA hybrids. Cell Reports, 10.1016/j.celrep.2019.10.108. Link

Graf M, Bonetti D, Lockhart A, Serhal K, Kellner V, Maicher A, Jolivet P, Teixeira MT, Luke B (2017). Telomere length determines TERRA and R-loop regulation through the cell cycle. Cell, 170, 72-85 Link