Biophysical Society Thematic Meeting| Santa Cruz 2018

Genome Biophysics: Integrating Genomics and Biophysics to Understand Structural and Functional Aspects of Genomes Board 18 Modeling Effects of Nucleosome Positioning in Chromatin Gero Wedemann . University of Applied Sciences Stralsund, Stralsund, Germany. 18-POS

Poster Abstracts

In higher organisms, DNA is complexed with proteins into a structure named chromatin. The basic packaging unit of chromatin is the nucleosome in which DNA is wrapped around a histone octamer. For the structure of chromatin many models were proposed. Experiments indicate that chromatin exhibits different kinds of packaging in distinct activation states. Packaging and activation states are closely linked to positions of nucleosomes on the DNA which are actively regulated. Determination of the positions of nucleosomes from experimental data is not straight forward, because of experimental uncertainty and data averages over a heterogeneous cell population. We developed a method based on Monte Carlo combined with a simulated annealing scheme to determine occupancy maps. Applying parallelization techniques, this method can determine occupancy maps genome wide. This method exhibits several advantages over existing tools for synthetic nucleosome maps and real data. To improve the understanding of the interplay between nucleosome positions and chromatin structure we applied computer simulations of a coarse-grained chromatin model including fundamental physical properties such as elasticity, electrostatics and nucleosome interactions. We simulated chromatin models based on experimentally derived nucleosome positions from cells at different stages of cell differentiation and after stimulation with a cytokine for different loci. Simulation results revealed a significant influence of nucleosome positions on the three dimensional structure of chromatin.

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