Chapter 9: Monte Carlo Simulations of Nucleosome Chains to Identify Factors that Control DNA Compaction and Access

Despite extensive research over the last three decades, the spatial organization of the nucleosome chain in chromatin is still only partially understood, although the nucleosome structure as its basic building block is known at atomic resolution. Here, we discuss the application of Monte Carlo simulations to investigate the conformational flexibility of the nucleosome chain in a systematic manner. Its folding into compacted structures provides an additional layer for regulating access to the DNA sequence information. The contributions of nucleosome positioning, local nucleosome geometry, nucleosome-nucleosome and histone octamer-DNA interactions into MC models are considered. It is discussed how relatively minor local variations of the nucleosome structure can translate into large changes of the overall conformation of the nucleosome chain.