The Influence of Nucleosome Energetics on Chromatin Structure Across Multiple Length-Scales

The physics governing nucleosome interactions influence structural features of chromatin across a range of length-scales. Here, we assess the extent of these interactions through Brownian dynamics simulations using a recently-developed coarse-grained model of chromatin. Simulations are used to interpret the hierarchy of interactions in chromatin fibers by quantifying the energetics of small-fibers including di- and trinucleosomes and isolating the factors which facilitate condensed configurations. Among these factors, we consider the influences of DNA sequence, nucleosome repeat length, and inclusion of the H1 linker histone. These small-fiber results are then used to assess the structure of larger chromatin fibers, revealing that nucleosomes in larger fibers favor configurations related to those exhibited in the small-scale systems. Lastly, we show that the linker histone significantly shifts the energetic minima of smaller systems, which corresponds to similar configuration changes of the larger chromatin fiber structure.