Chromatin configuration affects the dynamics and distribution of a transiently interacting protein

The interaction of proteins with chromatin regulates many cellular functions. Most DNA-binding proteins interact both non-specifically and transiently [1] with many chromatin sites as well as specifically and more stably with cognate binding sites. These interactions and chromatin structure are important in governing protein dynamics [2, 3]. However, the effect of these transient interactions on protein motion and distribution has yet been shown from a first principle.\n\nSome aspects of protein interactions with DNA have been studied in the context of the search of a gene promoter site by a transcription factor (TF) [4]. It was first noted [5] that the search for a promoter site by a TF would be faster if it involves 3d excursions, as well as sliding of the protein along DNA [6], as was shown in prokaryotes [7]. These different types of motion were observed ex ...