PhD Student (m/w/d) - Understanding the Influence of eRNA Association Modes on Transcriptional Condensates

About us IMB (www.imb.de) is a research institute on the campus of Johannes Gutenberg University in Mainz, Germany. It is generously funded by the Boehringer Ingelheim Foundation and the state of Rhineland-Palatinate. Our research focuses on the biology of the cell nucleus and ranges from the molecular level to systems and computational approaches. Researchers at IMB are supported by strong core facilities that offer state-of-the-art equipment and training in protein production, microscopy, proteomics, cytometry, genomics and bioinformatics. The position Multicellular organisms rely on differential gene expression to create cellular diversity. Precise gene regulation is crucial, as failures can lead to reduced fitness, developmental defects, and disease. Enhancers, DNA elements with binding sites for transcription factors, play a key role in this process. Recently, it has become clear that enhancer activity requires the formation of sub-micrometer-sized transcriptional condensates. Enhancers also produce enhancer RNAs (eRNAs). While proteins have been extensively studied in transcriptional condensate formation, the role of RNAs has received less attention. However, previous studies suggest that short RNAs like eRNAs can trigger phase separation of proteins in transcriptional condensates, and transcription factors can interact directly with RNAs. The presence of eRNAs at enhancer sites, often forming R-loop structures, may be more important than the specific eRNA molecule itself. This leads to the hypothesis that eRNAs play a crucial role in the formation and function of transcriptional condensates, with their impact on transcriptional condensate formation remaining largely unexplored. Join our dynamic research group at IMB and contribute to the exciting field of gene regulation. We are seeking a motivated PhD student to contribute to our investigations of how transcriptional condensates form and regulate gene expression. In this project, you will focus on the role of eRNAs in condensate formation by exploring different RNA association modes. By combining classic phase separation assays and single molecule reconstitution, you will address the following questions:

• How does the eRNA association mode impact transcription factor condensation in solution?
• How does the eRNA association mode affect the formation of condensates on single molecules of DNA?
• How does the eRNA association mode influence DNA:DNA interaction?

See also https://www.imb.de/wittmann For a more detailed description of the project including relevant literature, see here. This PhD position is part of 4R Research Training Group (GRK2859) “R-loop Regulation in Robustness and Resilience (4R)”, funded by the German Research Foundation (DFG). 4R investigates how R-loops regulate biological processes across scales, from molecules to organisms. At the same time the mechanistic regulation of R-loops themselves is studied. As one of a cohort of 12 4R PhD positions, you will be part of a vibrant interdisciplinary research and training environment with specialized seminar series and tech talks and training courses that develop both scientific and complementary skills. As a 4R-RTG PhD student, you will be integrated into the International PhD Programme (IPP; https://www.imb.de/phd), which is organized by IMB (www.imb.de). The IPP offers an exciting, interdisciplinary and lively international community of more than 200 PhD students from over 40 different countries. You will receive a broad range of support including supervision, training and career development opportunities. Requirements

• Masters degree or equivalent in a relevant area
• Good experience in molecular biology
• Good communication skills and good team spirit
• Ability to solve problems independently
• Fluent in English (spoken and written)

Why join us? We offer a stimulating, diverse and international research environment, with a pleasant working atmosphere, and informal culture. The institute is modern, well-equipped and centrally located with good public transport links and parking. Are you an ambitious scientist looking to push the boundaries of research while interacting with colleagues from multiple disciplines and cultures? Then joining the 4R-RTG and the IPP is your opportunity to give your scientific career a flying start! Our offer

• Competitive salary and favourable pension scheme
• Advanced training opportunities
• Flexible working hours
• Employee events
• Job Ticket

What else you need to know

• Starting Date: as soon as possible
• Duration: the position is initially funded until 30 June 2028; with a possibility of extension
• Deadline: 31 August 2025
• International applicants: we will assist you through the visa process, and also with your application for a residence/work permit after your arrival in Mainz.

Have we sparked your interest? To apply, please upload your application containing your cover letter stating research and career interests, CV, scans of your degrees (including copies of Abitur- and Master degree if existing), 2 reference letters to our application form on imb.de/jobs/scientific-positions. Should you have any questions regarding the application process, please contact us by email hr@imb-mainz.de, quoting Ref. No. #SWIPhD01. Informal enquires should be addressed to Dr Sina Wittmann. IMB is an equal opportunity employer.