Regensburg 2022 – scientific programme

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BP: Fachverband Biologische Physik

BP 7: Poster 1

BP 7.17: Poster

Monday, September 5, 2022, 18:00–20:00, P1

Effects of CTCF and Cohesin complexes and nucleosome positions on chromatin loops. — •Aymen Attou, TIlo Zülske, and Gero Wedemann — University of Applied Sciences Stralsund, Institute for Applied Computer Science, 18435 Stralsund, Germany

The spatial organization of the eukaryotic genome plays an important role in regulating transcriptional activity. In the nucleus, chromatin forms loops that assemble into fundamental units called topologically associating domains, which facilitate or inhibit long range contacts. These loops are formed and held together by a ring-shaped protein complex involving cohesin and CTCF. To analyse the effects of cohesin and CTCF, an established coarse-grained computer model of chromatin with a resolution of single nucleosomes was extended by integrating potentials describing CTCF and cohesin. We performed Monte Carlo simulations combined with replica exchange procedure with regular spaced nucleosomes and experimentally determined nucleosome positions in presence of cohesin-CTCF as well as depleted systems as control. The simulations generated a statistical representative ensemble of configurations in thermal equilibrium. We studied differences in the spatial structure and of contacts probabilities of different domains. That allowed us to understand the impact of cohesin and CTCF on the 3D structure of chromatin and how nucleosome positions can impact the conformations of the chromatin loops during the residence time of the loop anchor, with presumed consequences for transcriptional activity.