Biophysical Society Thematic Meeting | Hamburg 2022

Biophysics at the Dawn of Exascale Computers

Poster Abstracts

13-POS Board 13 LIQUID-LIQUID PHASE SEPARATION IN GENE TRANSCRIPTION Arya Changiarath Sivadasan 1,2,3 ; Lukas Stelzl 1,2,3 ; 1 Johannes Gutenberg University of Mainz, Institute of Physics, Mainz, Germany 2 Institute of Molecular Biology, Mainz, Germany 3 Johannes Gutenberg University of Mainz, Faculty of Biology, Mainz, Germany

Liquid-Liquid phase separation plays an important role in the formation of localized nuclear hubs of RNAP II during the transcription process. Recent experimental studies revealed that the Carboxy terminal domain (CTD), the largest subunit of RNAP II, is a low complexity domain, and has a very strong tendency to phase separate. Our research is focused on understanding the molecular basis of phase separation of CTD using multiscale molecular dynamics simulation methods. CTD is conserved in eukaryotes with the repeats of the heptapeptide sequence. However, there are small differences in CTD sequences of different species. We investigated how the CTD phase separation is affected by such differences in CTD sequences using coarse- grained molecular dynamics simulations. Our investigations indicate that deviation from the ideal heptapeptide sequence has less tendency to phase separate, which suggests that these deviations from the ideal heptapeptide repeats are important for responsive regulation of transcription. Also, the effects of temperature on CTD phase behavior and the influence of polymer length on critical temperature are as expected from Flory-Huggins theory. Moreover, we are looking at how phosphorylation of CTD and the presence of other biomolecules that can influence CTD phase behavior and regulate gene transcription. Hyper-phosphorylation prevents phase separation as the negatively charged phosphate groups repel each other. However CTD is hyper-phosphorylated in transcription elongation. We show how hyper-phosphorylated CTD might co-phase separate in elongation with HRD of Cylin T1 in accordance with experiment. To explore more on this, we studied the phase behavior of CTD and phosphorylated CTD in the presence of HRD and the results show that they co phase separate into a large cluster, but do not mix, which may help to physically distinguish between the initiation and elongation stages of transcription. A precise understanding of the molecular basis of interactions that leads to phase separation could be possible by employing atomistic simulations and this will, in turn, lead to improved coarse-grained simulation models.

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