Dresden 2011 – scientific programme
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BP: Fachverband Biologische Physik
BP 9: Posters: DNA \& DNA Enzymes
BP 9.7: Poster
Monday, March 14, 2011, 17:15–20:00, P3
Computer simulation of chromatin: Modeling the influence of nucleosome repositioning — •Oliver Müller1, René Stehr1, Robert Schöpflin1, Ramona Ettig2, Nick Kepper2, Karsten Rippe2, and Gero Wedemann1 — 1University of Applied Sciences Stralsund, 18435 Stralsund, Germany — 2German Cancer Research Center & BioQuant, 69120 Heidelberg, Germany
The three-dimensional structure of chromatin is a key factor for controlling the DNA accessibility for protein factors, DNA replication and repair. However, it is still subject to extensive research since the interpretation of the experimental data is fraught with difficulties. Several structural models exist, many of which assume a strictly regular fiber. This regularity implies a highly periodical positioning as well as equal occupancy of the fiber nucleosomes, which is unlikely for in vivo chromatin. Recent studies indicate that only a small subset of nucleosomes seems to be strongly positioned whereas the majority of nucleosomes adhere to a statistical positioning mechanism. Other important factors, such as chromatin remodelers and transcription factors are also implicated in nucleosome repositioning and occupancy. Here, we carry out Monte Carlo simulations with a coarse-grained chromatin model incorporating elastic fiber properties as well as a detailed description of the electrostatic and internucleosomal interactions to investigate the effects of nucleosome repositioning. Depending on the extent of the displacements the fiber geometry changes significantly. This serves as a tentative explanation for the effects of different remodeling complexes on processes such as DNA transcription.