Modulating gene expression through perturbations of 3D chromosome organization in E. coli

• Applicant: Dr. Janina Müller
• Subject Area: Metabolism, Biochemistry and Genetics of Microorganisms ; Biophysics
• Term: since 2026
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 574221429

Bacteria, like all living organisms, must carefully control which genes are turned on or off to survive and adapt. Traditionally, scientists have studied this regulation by looking at factors like promoter sequences and transcription factors. However, recently it has become clear that the three-dimensional (3D) structure of the chromosome—how the DNA is physically arranged and folded inside the cell—may also play a key role in shaping gene expression. In this project, I will explore how the spatial organization of the bacterial chromosome affects gene expression. My project focuses on Escherichia coli, a widely used model organism, and specifically on a region near the chromosome’s origin of replication, the origin macrodomain. This region is structured by a system called MaoP/maoS, which consists of a single DNA-binding protein (MaoP) and its target sequence (maoS). The simplicity of this system makes it ideal for studying how chromosome structure influences local gene expression. Preliminary data suggest that when the MaoP/maoS system is deleted, gene expression in this region changes. However, it is still unclear how the chromosome’s structure leads to these changes. To answer this question, I will combine genetic tools with single-cell techniques that allow me to watch gene expression unfold in individual bacteria over time. These include the mother machine, a microfluidic device that enables time-lapse imaging of single cells, and flow cytometry, which together provide high-throughput, single-cell data. In the first phase of the project, I will build a library of genetically engineered strains that contain both chromosome structure mutations and fluorescent reporters of gene expression. In the second phase, I will measure how these structural changes affect expression patterns, focusing especially on when and how genes are turned on or off in individual cells. Finally, I will use a method called Hi-C to directly map the 3D chromosome structure in different gene expression states, linking physical organization t gene expression outcomes. By combining targeted genetic modifications with single-cell expression profiling, this project seeks to uncover a fundamental mechanism of gene regulation in bacteria. The findings may also open up new directions in synthetic biology by showing how chromosome structure can be used to fine-tune gene activity.

• DFG Programme: Fellowship
• International Connection: USA
• Host: Professor Philippe Cluzel, Ph.D.