DNA sites buried in nucleosome become accessible at room temperature: A Discrete-Event-Simulation based modeling approach

Abstract

Conformation of a canonical nucleosome inhibits the direct access of the binding proteins to portions of nucleosomal DNA. Nucleosome dynamics establish certain pathways through which nucleosome gets remodeled (spontaneously, covalently or non-covalently) and the buried DNA sites become accessible. Currently for most pathways no single model is available to capture the temporal behavior of these pathways. Plus traditional diffusion-based models in most cases are not precise. In this work we have given a systematic overview of such pathways. Then, we manipulate the probability of a binding site on array of N nucleosomes and chromatin of length G base pairs. We further identify three of the widely accepted thermal-driven (passive) pathways and model those based on stochastic process and the Discrete-Event-Simulation. For the output of the models we have sought either the site access rate or the sliding rate of the nucleosome. We also show that results from these models match the experimental data where available. © Springer-Verlag Berlin Heidelberg 2007.