Hilbert/Zaburdaev

Active Microemulsification as a Principle of Chromatin Organization and its Role in Cell Fate Induction

The cell nucleus displays a striking, widely conserved spatial compartmentalization. Inactive regions of the genome are sequestered to and compacted within a distinct comparment; active regions of the genome are unfolded and occupy another compartment. Recent work has demonstrated that this architecture is established by physical process. In particular, actively transcribed regions of the genome are unfolded similar to the physical process of microemulsification. In this project, we aim to investigate (i) how microemulsification might contribute to the rapid induction of genes in zebrafish mesendoderm formation, and (ii) how non-equilibrium processes shape bring about unique properties otherwise not seen in conventional microemulsions.


Current State of Research

In our previous work, we have developed the fundamental experimental protocols as well as theoretical framework for the investigation of genome microemulsification in zebrafish cells. In the current, initial phase of the project, we are applying and expanding the existent experimental protocols to the in vitro induction of the zebrafish Nodal pathway. Also, we are expanding the theoretical framework to account for regulatory aspects. Each of these branches of the project is carried out by a doctoral trainee. Both trainees and overall research groups are working in close coordination to align experimental and theoretical work.


About us

The Hilbert lab explores three-dimensional (3D) organization as the foundation of effective information processing in dense DNA suspensions. In particular, we study the cell nucleus as a highly evolved, DNA-based information processing system. In our work, we visualize the inner workings of the nucleus with live and super-resolution microscopy. We translate our observations into physical principles and information processing strategies by means of physical models and computer simulations. Ultimately, we hope to contribute to cell-embedded DNA computing, and the predictive design of DNA-based hardware.

In particular wokring on the project:
Irina Mamontova (PhD Student)

http://hilbertlab.org/publications/

Contact:
Lennart Hilbert
Karlsruhe Institute of Technology
Phone: Campus North +49 721 608 22887 (office)/ -28584 (lab)
Email


The Zaburdaev group is using and developing methods of statistical physics to address exciting problems in biology and medicine. We are a part of the newly established, interdisciplinary “Max-Planck-Zentrum für Physik und Medizin” in Erlangen.

In particular working on the project:
Tim Klingberg (PhD Student)

https://www.mathlife.nat.fau.de/publications/

Contact:
Vasily Zaburdaev
Friedrich-Alexander-Universität Erlangen-Nürnberg

Department Biologie – AbteiluLehrstuhl für Mathematik in den Lebenswissenschaften
Cauerstr. 11
91058 Erlangen
Phone: Telefonnummer: +49 9131 85-67123
Email

 

Publications

Noa A, Kuan HS, Aschmann V, Zaburdaev V, Hilbert L (2021) The hierarchical packing of euchromatin domains can be described as multiplicative cascades. PLOS Computational Biology 17(5): e1008974. https://doi.org/10.1371/journal.pcbi.1008974
 
Lennart Hilbert, Yuko Sato, Hiroshi Kimura, Frank Jülicher, Alf Honigmann, Vasily Zaburdaev, Nadine L. Vastenhouw. Transcription organizes euchromatin similar to an active microemulsion.
 
Agnieszka Pancholi, Tim Klingberg, Weichun Zhang, Roshan Prizak, Irina Mamontova, Amra Noa, Andrei Yu Kobitski, Gerd Ulrich Nienhaus, Vasily Zaburdaev, Lennart Hilbert. RNA polymerase II clusters form in line with liquid phase wetting of chromatin.
 
Amra Noa, Hui-Shun Kuan, Vera Aschmann, Vasily Zaburdaev, Lennart Hilbert. The domain-within-domain packing of euchromatin can be described as multiplicative cascades.