DNA:RNA hybrids in epigenetic regulation

1 PhD project offered in the IPP winter call 2023/2024

Scientific Background

R-loops are genomic DNA:RNA hybrids that are assembled either co-transcriptionally or by local unwinding of DNA and hybridization of homologous RNAs. R-loops were originally identified as toxic by-products of transcription. Consistently, many factors including helicases, nucleases and RNA-binding

A subclass, regulatory R-loops, is involved in epigenetic gene regulation and that contain long non-coding RNAs (lncRNAs). We previously described the stress response protein Gadd45a as the first epigenetic reader of such regulatory R-loops, which recruits the TET demethylation machinery to modulate target gene activity.  A key method in R-loop characterization is their genome-wide mapping.

PhD Project: DNA:RNA hybrids in epigenetic regulation

A standard method for R-loop mapping is DRIP-seq, which employs the hybrid-binding antibody S9.6 to pull down hybrids in fragmented genomic DNA. However, DRIP-seq is a laborious and unreliable technique. Therefore, you will optimize an improved R-loop mapping protocol that we have implemented and to use it for the characterization of R-loops in embryonic stem cells (ESC) under diverse settings. In this modified method (C&T S9.6), we combined the time-saving CUT & Tag technology with S9.6 antibody for hybrid recognition and by Next-Generation-Sequencing we found confirmed that it yields genome-wide profiles expected. You will develop the protocol further and use it to map R-loops in ESCs that are genetically modified and will learn to apply bioinformatics methods to analyze them. The ultimate aim is to reveal the role of R-loops in gene regulation during pluripotency and differentiation.

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 Niehrs (Rloop) as your group preference in the IPP application platform.

Publications relevant to this project

Arab K*, Karaulanov E, Musheev M, Trnka P, Schäfer A., Grummt I*, and Niehrs C.* (2019). GADD45A binds R-loops and recruits TET1 to CpG island promoters. Nat. Genet. 51, 217-223  *corresponding authors. Link

Niehrs C and Luke B. (2020). Regulatory R-loops as facilitators of gene expression and genome stability. Nat Rev Mol Cell Biol.  21, 167–178. Link


Contact Details

Prof. Christof Niehrs