BPCPPDYSOE21 – wissenschaftliches Programm
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BP: Fachverband Biologische Physik
BP 11: Poster A: Single Molecule, Multicellular, Bioimaging, Focus Sessions, etc.
BP 11.35: Poster
Montag, 22. März 2021, 16:30–19:00, BPp
Modeling RNA Polymerase II clusters by lattice kinetic Monte Carlo simulations — •Tim Klingberg1,2, Lennart Hilbert3, and Vasily Zaburdaev1,2 — 1Friedrich-Alexander-Universität Erlangen-Nürnberg — 2Max-Planck-Zentrum für Physik und Medizin — 3Karlsruher Institut für Technologie
Eukaryotic genes are mainly transcribed by RNA polymerase II (Pol II). Before active transcription starts, Pol II is recruited to the promoter region of a specific gene and then released from a paused state into transcript elongation. Clusters of paused Pol II of various sizes and morphologies can be observed in zebrafish embryos (Pancholi et al.). Here, we aim to understand the physical mechanisms that are essential for the cluster formation and determine their emerging properties. To this end, we apply two-dimensional lattice kinetic Monte Carlo simulations with single Pol II particles interacting with DNA polymers, whose dynamics are determined by the Verdier-Stockmayer algorithm. The model suggests that formation of Pol II clusters can be rationalized as phase separating phenomenon where polymerases form a liquid phase that wets the chromatin at the promoter region. Cluster properties such as size and morphology can be linked to the size of the promoter region and the respective gene. Despite the simplicity of the model, it is sufficient to qualitatively describe the experimentally observed cluster properties in normal conditions and under drug treatments interfering with the transcription process.