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    • Utrecht
  • Full time
  • Recruitment


  • Biochemistry


  • Phd

Apply by: 2022-09-28

PhD position on the Structural Dynamics of Pioneer Factors and Genomic Nucleosomes (1.0 FTE)

Published 2022-09-05

Help revealing the true nature of chromatin and how silenced genes can be activated by pioneer factors using integrative structural biology!

Chromatin is the essential guardian and gatekeeper of the genome, controlling expression of genes and repair of DNA damage. We are looking for a highly motivated PhD student who will join our research efforts to understand the interaction between proteins and nucleosomes and how this controls chromatin function.

Perhaps the most fascinating class of proteins that bind nucleosomes are pioneer transcription factors that bind specific DNA sequences within closed chromatin, promote chromatin opening and activate silenced genes. Pioneer factors can drive changes in cellular identity and are used in cellular reprogramming. Yet how these factors function on a molecular level and can promote nucleosome opening is not understood. In this project you will study the structural dynamics of genomic nucleosomes and their interaction with pioneer factors Sox2.

In this PhD position you will reconstitute nucleosomes containing genomic DNA sequences that are targeted by Sox2 in cells. You will study the structural dynamics of these nucleosomes and the interaction with Sox2 using an integrative, NMR-driven approach to derive molecular mechanism of Sox2 pioneer factor function. Due to the intrinsic dynamics in both genomic nucleosome and Sox2, NMR is ideal to study their structural dynamics and to understand how Sox2 binds and impacts native target nucleosomes at atomic resolution. A better understanding of Sox2 function will help to combat its role in cancer and to develop improved reprogramming factors for regenerative therapies.

The project involves biochemistry, biophysical assays, and structural and dynamical characterization, using NMR and other techniques, allowing you to become an all-round structural biologist, chromatin and NMR expert. The project is a collaboration with the groups of Abdenour Soufi (University of Edinburgh, cell biology of pioneer factors), John van Noort (Leiden University, single molecule dynamics) and Vlad Cojocaru (Utrecht University, molecular dynamics simulations).

We are looking for someone who recently finished or soon will finish a Master’s degree and that recognizes one or multiple the following skills: You are a social team player, you are curious and inventive, and you are creative in finding solutions. You will bring:
  • a Master's degree (or equivalent) in Biochemistry, Biophysics, Molecular Life Sciences or a similar program. If you are within a few months of completing your MSc degree, we also welcome you to apply! Please indicate in your application letter when you are likely to graduate;
  • a fascination for the relation between protein structure, dynamics and function;
  • a strong background in recombinant protein work (bacterial expression, chromatography-based purification) and PCR;
  • experience in NMR is not required, but is an advantage.
  • A position for 4 years;
  • A full-time gross salary starting at €2,541 and increasing to €3,247 (scale P Collective Labour Agreement Dutch Universities).
  • 8% holiday bonus and 8.3% end-of-year bonus;
  • A pension scheme, partially paid parental leave, and flexible employment conditions based on the Collective Labour Agreement Dutch Universities.
In addition to the employment conditions laid down in the CAO for Dutch Universities, Utrecht University has a number of its own arrangements. For example, there are agreements on professional development, leave arrangements and sports. We also give you the opportunity to expand your terms of employment via the Employment Conditions Selection Model. This is how we like to encourage you to continue to grow.

For more information, please visit working at Utrecht University.

Utrecht University is a friendly and ambitious university at the heart of an ancient city. We love to welcome new scientists to our city – a thriving cultural hub that is consistently rated as one of the world’s happiest cities. We are renowned for our innovative interdisciplinary research and our emphasis on inspirational research and excellent education. We are equally well-known for our informal atmosphere and the can-do mentality of our people. This lively and inspiring academic environment attracts professors, researchers and PhD candidates from all over the globe, making both the University and the Faculty of Science a vibrant international and wonderfully diverse community.

At the Faculty of Science, there are 6 departments to make a fundamental connection with: Biology, Chemistry, Information and Computing Sciences, Mathematics, Pharmaceutical Sciences, and Physics. Each of these is made up of distinct institutes that work together to focus on answering some of humanity’s most pressing problems. More fundamental still are the individual research groups – the building blocks of our ambitious scientific projects.

You will work in the group of dr. Hugo van Ingen in the Utrecht NMR Group, sharing office and lab space with the groups of prof. Marc Baldus (in-cell & solid-state NMR), dr. Markus Weingarth, (antibiotics & solid-state NMR) and the computational structural biology group of prof. dr. Alexandre Bonvin. In addition, the group regularly meets with other chromatin groups on campus. You will be part of an interdisciplinary and dynamic team of researchers that share many common interests and approaches. You will be able to make use of the excellent NMR infrastructure of 9 NMR machines, including the 1.2 GHz machine, which will greatly benefit this project.

If you have any questions that you’d like us to answer, please contact Hugo van Ingen via h.vaningen@uu.nl.

Do you have a question about the application procedure? Please send an email to science.recruitment@uu.nl.

For more information, please visit working at the Faculty of Science