Marieke Oudelaar becomes new Director at MPI-IE in Freiburg
The Dutch scientist researches how the three-dimensional organization of the genome controls gene activity
Marieke Oudelaar is the new Director at the Max Planck Institute of Immunobiology and Epigenetics (MPI-IE) in Freiburg and will head the newly established Department of Genome Biology. With the appointment, the institute expands its profile in gene regulation research by adding a spatial dimension. The department aims to understand how the three-dimensional folding of DNA in the cell nucleus controls the activity of our genes during cell differentiation and development – and what consequences disruptions of this three-dimensional architecture have for diseases such as cancer.
Marieke Oudelaar is a leading scientist specialising in 3D genome organisation. She and her team have made significant contributions to our understanding of how regulatory DNA segments, which can be located far apart in the linear genome, communicate with each other in the three-dimensional space of the nucleus. These regulatory DNA segments include enhancers and promoters — short DNA sequences that determine when, where and how strongly individual genes are expressed. While promoters sit directly at the start of a gene, enhancers can lie hundreds of thousands of DNA building blocks away, yet still must reliably control their target gene. For this regulation to succeed, the approximately two-meter-long DNA of a cell must be folded in the tiny nucleus so that the right segments come into spatial proximity. Oudelaar and her team aim to understand the principles by which these folded three-dimensional structures emerge and how they contribute to the precise control of gene activity.
Decoding the Genome’s Folding Plan
To decode DNA folding, the lab uses state-of-the-art Chromosome Conformation Capture (3C) techniques. In this approach, DNA segments that are spatially adjacent within the nucleus are chemically linked together and identified by DNA sequencing. Using computational methods, the original 3D structures are reconstructed. “It’s like molecular origami. Once reconstructed, these data allow us to understand which regulatory DNA segments communicate with each other and which genes they control,” says Marieke Oudelaar, who is moving to Freiburg from the Max Planck Institute for Multidisciplinary Sciences in Göttingen. Since 2020, she has led a research group in Göttingen funded by the Lise Meitner Excellence Program of the Max Planck Society, which supports exceptionally qualified female scientists.
From Basic Research to Medicine
“A fundamental question in biology is how one genome (one DNA sequence) can give rise to the remarkable diversity of cell types that make up multicellular organisms,” says Oudelaar. This is precisely the question she wants to explore further in Freiburg, with a particular focus on the spatial interplay of regulatory segments in the genome. Her laboratory combines high-resolution methods based on genomics and microscopy with biochemical experiments and computational modelling.
Beyond its relevance for basic biology, this research is increasingly important for medicine and diagnostics. Many disease-associated genetic variants lie in non-coding regulatory regions of the genome. However, it is often unclear which genes are regulated by which regulatory regions, since they are not necessarily located next to each other. Only by knowing the three-dimensional folding of DNA in the nucleus can these relationships be deciphered. In the long term, this knowledge could open up new avenues for diagnostics and therapy.
About Marieke Oudelaar
Marieke Oudelaar studied Biomedical Sciences, completing her BSc at Utrecht University in the Netherlands and her MSc at the Karolinska Institute in Stockholm, Sweden. She then moved to the United Kingdom for her doctoral studies at the Weatherall Institute of Molecular Medicine, University of Oxford, where she obtained her PhD in 2018. She remained in Oxford for two more years as a Junior Research Fellow. In 2020, she moved to Germany to establish the independent research group “Genome Organization and Regulation” at the Max Planck Institute for Multidisciplinary Sciences, with support from the Lise Meitner Excellence Program. In 2026, she was appointed Director at the Max Planck Institute of Immunobiology and Epigenetics in Freiburg, where she now leads the Department of Genome Biology.
Her scientific achievements have been recognised by several honours, including the Radcliffe Department of Medicine Graduate Prize from the University of Oxford in 2018, the Bayer Early Excellence in Science Award in Biology in 2022, selection as an EMBO Young Investigator in 2023, and an ERC Starting Grant from the European Research Council in 2023.
