Heterogeneity in Nucleosome Spacing Governs Chromatin Elasticity

Abstract

Within a living cell, the myriad of proteins that bind DNA introduce heterogeneously spaced kinks into an otherwise semiflexible DNA double helix. To investigate the effects of heterogeneous nucleosome binding on chromatin organization, we extend the wormlike chain (WLC) model to include statistically spaced, rigid kinks. On time scales where nucleosome positions are fixed, we find that the probability of chromatin loop formation can differ by up to six orders of magnitude between two sets of nucleosome positions drawn from the same distribution. On longer time scales, we show that continuous re-randomization due to nucleosome turnover results in chromatin tracing out an effective WLC with a dramatically smaller Kuhn length than bare DNA. Together, these observations demonstrate that heterogeneity in nucleosome spacing acts as the dominant source of chromatin elasticity and governs both local and global chromatin organization.