Theory and modeling of active nucleosome repositioning

Nucleosome positioning controls the accessible regions of chromatin and plays essential roles in DNA-templated processes. Its establishment in vivo is significantly influenced by ATP driven remodeling enzymes and transcription, which involves remodeler recruitment. On one hand, the non-equilibrium nature of remodelers has hindered the development of a unified theoretical framework for nucleosome positioning. On the other hand, explicit models are lacking in explaining the impact of transcription levels on nucleosome positioning since the complicated transcription process. For remodeling enzymes, we use a perturbation theory to show that the effect of these enzymes can be well approximated by effective equilibrium models with rescaled temperatures and interactions. Our theory provides an intuitive understanding for the impact of remodelers. By combining remodelers and RNAP II, we developed a transcription model, which illustrates opposite trends of nucleosome positioning patterns changing with transcription levels in yeasts and higher animals. This explanation qualitatively reproduces the experimental nucleosome positioning patterns.