SKM 2023 – wissenschaftliches Programm
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BP: Fachverband Biologische Physik
BP 27: Computational Biophysics II
BP 27.6: Vortrag
Donnerstag, 30. März 2023, 16:30–16:45, BAR 0106
Effects of chromatin fibers characteristics on cohesin mediated loop architecture — •Aymen Attou, TIlo Zülske, and Gero Wedemann — University of Applied Sciences Stralsund, System Engineering and Information Management, 18435 Stralsund, Germany
The spatial organization of DNA in eucaryotes starts at nucleosome chains forming chromatin loops that can cluster together establishing fundamental units called topologically associating domains (TADs). TADs are an important factor for gene regulation by facilitation or repressing long range contacts in the genome. Those loops are formed and held together by a ring-shaped protein complex called cohesin together with the effect of CTCF. A loop has a residence time of several minutes. To clarify the spatial structure of a loop, we established a coarse-grained computer model of chromatin with a resolution of single nucleosomes integrating potentials describing CTCF and cohesin. We performed Metropolis 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 for different loop sizes. We studied differences in the spatial structure and of contacts probabilities of different domains, what allowed us to understand the role of cohesin and CTCF, and their impact on the 3D structure of chromatin. This study also allowed clarifying 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.