Célia
BAROUX
PD Dr., Group Leader
Department of Plant and Microbial Biology, University of Zurich
ORCID link : 0000-0001-6307-2229
Website links : Research
IRP : Characterisation of peripheral light-induced transcription clusters

Chromatin Dynamics and Quantitative Microscopy for Plant Sciences, University of Zürich, Switzerland
Chromatin dynamics, 3D genome organization & quantitative microscopy in plants
My research group investigates the three-dimensional organisation and dynamic behaviour of chromatin in plant nuclei, aiming to understand how chromatin structure influences cellular transitions during development and in response to environmental cues. Plants exhibit remarkable nuclear plasticity — the genome’s spatial arrangement changes throughout the plant’s life, yet the causal relationships between chromatin organisation and gene regulation remain poorly defined. To address this, we combine quantitative microscopy imaging , cell biology and molecular genetics to explore chromatin architecture and dynamics at high resolution. Our work also integrates efforts to develop community resources and tools for high-resolution imaging and data analysis, fostering collaboration among laboratories focused on plant nuclear organisation and microscopy.
We are currently
I
Investigating the roles of linker histone H1 proteins in chromatin organisation and gene regulation during developmental processes and in response to the environment.
II
Investigating the spatial dynamics of transcription induced by light, in collaboration with the Barneche lab (Sorbonne University, France)
III
Developing and optimising 3D super-resolution imaging and image segmentation workflows to quantify chromatin domain organisation and distribution in intact nuclei.
IV
Deploying analytical tools (e.g., DataViz, ChromNano, OvuleViz, see Github repo) for interactive visualization and quantitative analysis of segmented image data from plant nuclei and tissues.
Five Main Publications
Pre-meiotic H1.1 degradation is essential for Arabidopsis gametogenesis
Li, Y., Fei, D., Schubert, J. et al. .. Baroux C. (2026) EMBO J . doi: 10.1038/s44318-025-00671-2
Linker histones enhance robustness in diurnal transcription dynamics
Rutowicz K, Perseus L, Schmid MW, et al. (2025). Quantitative Plant Biology. 2025;6:e44. doi:10.1017/qpb.2025.10033
Multiscale chromatin dynamics and high entropy in plant iPSC ancestors
Rutowicz K., Lüthi J., de Groot R., Holtackers R., Yakimovich Y., Pazmiño D. M., Gandrillon O., Pelkmans L., Baroux C. (2024) Journal of Cell Science. doi: 10.1101/2023.09.28.559735
Methods for Plant Nucleus and Chromatin Studies.
Kracik-Dyer, E., Baroux, C. (2025). 3D STED Imaging of Isolated Arabidopsis thaliana Nuclei. In: Baroux, C., Tatout, C. (eds) Methods in Molecular Biology, vol 2873. Humana, New York, NY. doi: 10.1007/978-1-0716-4228-3_15
Image analysis workflows to reveal the spatial organisation of cell nuclei and chromosomes
Randall R. S., Jourdain C., Nowicka A., et al. .. Baroux C. (2022) Nucleus. doi: 10.1080/19491034.2022.2144013

