A Markov model for the dynamics of the nucleosome

Abstract

We study the dynamics of the nucleosome, the most abundant DNA protein complex in eukaryotic cells. The dynamics consist of two mechanisms, site exposure and sliding, which are crucial for making DNA accessible to DNA-binding proteins. The intertwining of both effects leads to a rich stochastic process that has not been studied before. Within the assumptions of our model, nucleosomes perform a symmetric random walk along the DNA strand. We investigate how the diffusion constant depends on the relative rates of site exposure and sliding.