PhD position: Regulation of genomic parasites by small non-coding RNAs (m/f/d)

The research group of René Ketting offers the following PhD project:

The genomes of basically all living organisms on our planet are invaded by genetic elements called transposable elements (TEs). These TEs can be considered as parasites in our genome, although they also contribute to proper gene regulation and other aspects of normal cellular homeostasis. TEs tend to be most active in the germ cells, as their activity in these cells will be remembered in new generations. Hence, the control of these elements is particularly important in these cells. One of the major defense mechanisms that helps to keep TEs in check is known as the piRNA pathway. This mechanism is driven by small non-coding RNAs (piRNAs) that help to guide the effector proteins to their targets in a sequence specific manner. Hence, deciding which RNAs will be turned into piRNAs is a crucial step. How piRNA precursor transcripts are selected and processed is poorly understood in vertebrates. This project will help address that lack of insight.

PhD Project: Biogenesis of small RNA precursors

The basics of the piRNA system in zebrafish have been described by us in past work. However, studies on piRNA precursors have been hampered by a number of technical aspects. In the past years, we have developed a reporter system, based on GFP silencing, that helps us study piRNA activity in this animal. At the same time, it provides insights into piRNA precursor biology. In this DFG-funded project you will study the generation and nuclear export of piRNA precursor transcripts in zebrafish. To do so you will use a combination of genetics, genomics and proteomics. This will reveal fundamental aspects of nuclear RNA export in general, and piRNA specific aspects in particular. This project will also make use of long read RNA/DNA sequencing, as the loci you will study are very repetitive and hard to study using standard NGS methods. In addition, this may reveal the potential involvement of RNA modifications in piRNA precursor biogenesis and processing. Finally, in a sideline to this project, you will work to develop the piRNA reporter system into a genetic tool for studying maternally provided transcripts, that help the development of the early embryo.

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

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

• 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 200 PhD students from 44 different countries

For more details on the projects offered and how to apply via our online form, please visit www.imb.de/phd.
The deadline for applications is 3 April 2025. Interviews will take place at IMB in Mainz on 23 & 24 June 2025.
Starting date: 1 August 2025 - 1 January 2026