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BP: Fachverband Biologische Physik
BP 8: Focus Session: Phase Separation in Biochemical Systems
BP 8.2: Talk
Tuesday, September 6, 2022, 10:00–10:15, H15
RNA polymerase II clusters form in line with surface condensation on regulatory chromatin — •Tim Klingberg1,2, Agnieszka Pancholi3, Weichun Zhang3, Roshan Prizak3, Irina Mamontova3, Marcel Sobucki3, Andrei Yu Kobitski3, Gerd Ulrich Nienhaus3, Vasily Zaburdaev1,2, and Lennart Hilbert3 — 1Friedrich-Alexander-Universität Erlangen-Nürnberg — 2Max-Planck-Zentrum für Physik und Medizin — 3Karlsruhe Institute of Technology
Transcription of eukaryotic genes by the RNA polymerase II (Pol II) has two major control points: recruitment to the regulatory region of a specific gene, and subsequent release into the elongation of RNA transcripts. We find that recruited Pol II forms macromolecular clusters with a large variety of shapes in the embryos of zebrafish, which we investigated by live and super-resolution microscopy. To delineate the essential physical mechanisms underlying Pol II cluster formation, we use coarse-grained lattice kinetic Monte Carlo simulations containing monomeric particles (recruited Pol II) that can interact with polymer chains (regulatory regions). We propose that the regulatory chromatin regions act as surfaces for the condensation of recruited Pol II into a liquid-phase. The numerical simulations of our model qualitatively reproduce the different forms of RNA Pol II clusters that we detected with microscopy. Taken together, our results suggest that recruited Pol II contributes to the surface-associated condensates, whereas elongating Pol II is excluded from these condensates and thereby drives unfolding of the condensates.