Berlin 2012 – wissenschaftliches Programm
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BP: Fachverband Biologische Physik
BP 13: DNA/RNA and Related Enzymes
BP 13.7: Vortrag
Mittwoch, 28. März 2012, 11:30–11:45, H 1058
Computer simulation of chromatin: Effects of nucleosome positioning on chromatin structure — •Oliver Müller1, Robert Schöpflin1, Nick Kepper2, Ramona Ettig2, Karsten Rippe2, and Gero Wedemann1 — 1CC Bioinformatics, University of Applied Sciences Stralsund, Zur Schwedenschanze 15, 18435 Stralsund, Germany — 2Deutsches Krebsforschungszentrum & BioQuant, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
The three-dimensional structure of chromatin is a key factor for DNA accessibility, replication and repair. Most theoretical models of chromatin imply a static, periodical positioning and uniform occupancy of nucleosomes. However, recent studies suggest a dynamic nucleosome positioning, which is both actively regulated by chromatin-remodeling complexes and passively influenced by thermal fluctuations. In turn, nucleosomes deviating from regular positions can introduce changes into chromatin fiber structure. To investigate the effects of nucleosome repositioning, we carried out Monte Carlo simulations with a coarse-grained chromatin model incorporating elastic fiber properties as well as electrostatic and internucleosomal interactions. We created fiber models based on experimental results and modified these by repositioning nucleosomes by a range of base pairs. After simulation, the chromatin energy landscape and fiber shape were analyzed. We observed a significant energy barrier against nucleosome repositioning which is larger than thermal fluctuations but within the range of ATP-dependent biological processes. Moreover, the region proximate to a repositioned nucleosome revealed an increased kinking susceptibility.