PhD position (RNA Biology): DNA:RNA hybrids in epigenetic regulation (m/f/d)PhD – Individual Supervisor

Description

Thinking of doing your PhD in the Life Sciences? The International PhD Programme (IPP) Mainz is offering talented, young scientists the chance to work on cutting edge research projects. As an IPP PhD student, you will join a community of exceptional scientists working on diverse topics ranging from how organisms age or how our DNA is repaired, to how epigenetics regulates cellular identity or neural memory.

Activities and responsibilities

In the fields of “Epigenetics & Nuclear Dynamics” and “RNA Biology”, the research group of Christof Niehrs offers the following PhD project:

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.
The student will also be part of the Research Training Group (RTG) 4R: R-loop Regulation in Robustness and Resilience. 4R aims to gain mechanistic insights regarding how RNA-based processes contribute to robustness and resilience, especially through R-loops.  www.cha-mainz.de/joint-programmes/4r

If you are interested in this project, please select Niehrs (Rloop) as your group preference in the IPP application platform.

Qualification profile

Are you an ambitious, young scientist looking to push the boundaries of research while interacting with colleagues from multiple disciplines and cultures? Then joining the IPP is your opportunity to give your scientific career a flying start!
All you need is:

• Master or equivalent
• Interactive personality & good command of English
• 2 letters of reference

We offer

• Exciting, interdisciplinary projects in a lively international environment, with English as our working language
• Advanced training in scientific techniques and professional skills
• Access to our state-of-the-art Core Facilities and their technical expertise
• Fully funded positions with financing until the completion of your thesis
• A lively community of more than 190 PhD students from 44 different countries

For more details on the projects offered please visit  www.imb.de/phd  .

The deadline for applications is 8 November 2023. Interviews will take place at IMB in Mainz on 22-24 January 2024.
Starting date: 1 March 2024 – 1 August 2024