Theoretical estimates of exposure timescales of protein binding sites on DNA regulated by nucleosome kinetics.

ABSTRACT: It is being increasingly realized that nucleosome organization on DNA crucially regulates DNA-protein interactions and the resulting gene expression. While the spatial character of the nucleosome positioning on DNA has been experimentally and theoretically studied extensively, the temporal character is poorly understood. Accounting for ATPase activity and DNA-sequence effects on nucleosome kinetics, we develop a theoretical method to estimate the time of continuous exposure of binding sites of non-histone proteins (e.g. transcription factors and TATA binding proteins) along any genome. Applying the method to Saccharomyces cerevisiae, we show that the exposure timescales are determined by cooperative dynamics of multiple nucleosomes, and their behavior is often different from expectations b

SUBMITTER: Parmar JJ 

PROVIDER: S-EPMC4770213 | biostudies-literature | 2016 Feb

REPOSITORIES: biostudies-literature