Projects Offered

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

Scientific Background

An R-loop is an RNA-DNA hybrid that displaces the second DNA strand. R-loops occur frequently in genomes and have significant physiological importance, regulating gene expression and telomere stability. On the other hand, R-loops are a source of genomic instability e. g. in diseases associated with repetitive sequences including amyotrophic lateral sclerosis, Fragile X syndrome, Friedreich’s ataxia and trinucleotide repeat sequences. 

Several pathways regulate the stability of R-loops. RNase H1 and RNase H2 are the central endonucleases that process RNA specifically in RNA-DNA hybrids. Loss of either enzyme results in an accumulation of R-loops and genome instability. Conversely overexpression of RNase H1 is frequently used to counteract the toxic effects of R-loop associated DNA damage. What regulates the role and activity of the RNase H1 and RNase H2 enzymes at “regulatory” and “toxic” R-loops is largely unknown. This is a central question in the field and mechanistical studies are complicated by the pleiotropic effects of the deletion mutants. 

Interestingly C. elegans has four RNase H1 enzymesand a single RNase H2 enzyme. In this project we want to characterize these enzymes to understand:

1. 1. Is there a natural separation of function for the RNase H1 enzymes?
   2. How are the RNase H enzymes regulated during development, stress, and aging?
   3. What is the binding specificity of the four different RNase H1 enzymes?

Initial data suggests that while 3 RNase H enzymes are ubiquitously expressed, two enzymes are differentially expressed in undifferentiated embryonic and germline cells compared to differentiated tissues. Interestingly, we see a strong upregulation of a subset of the RNase H enzymes in conditions known to trigger toxic R-loops, such as the aberrant expression of repetitive elements, or heat stress. 

PhD project: Regulation and specificity of RNase H1/2 enzymes upon stress and aging

In this project you will use CRISPR to complete our existing collection of AID degron tagged strains. Using genomics and quantitative microscopy you will map R-loops, the RNase H enzymes, possible DNA damage and the effects on transcription, both upon degradation of specific enzymes and under stress conditions. Using C. elegans as a model we can correlate these molecular changes with stress resistance and aging of the organism.

We are looking for a highly motivated team player, interested in utilizing this unique opportunity to combine genome wide epigenetic profiling techniques with a CRISPR based screening approach and quantitative microscopy.

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 Padeken as your group preference in the IPP application platform.

Publications relevant to this project

Padeken J, Zeller P, Towbin B, Katic I, Kalck V, Methot SP, Gasse SM (2019) Synergistic lethality between BRCA1 and H3K9me2 loss reflects satellite derepression. Genes Dev 33:436-451. Link

Lockhart A, Borges Pires V, Bento F, Kellner V, Luke-Glaser S, Yakoub G, Ulrich H, Luke B (2019) RNase H1 and H2 Are Differentially Regulated to Process RNA-DNA Hybrids. Cell Rep 29:2890-2900. Link

Zeller P, Padeken J, van Schendel R, Kalck V, Tijstman M, Gasser SM (2016) Histone H3K9 methylation is dispensable for Caenorhabditis elegans development but suppresses RNA:DNA hybrid-associated repeat instability.Nature Genetics 48:1385-1395. Link