Chromatin is a dense structure of DNA and histone proteins. DNA wraps in units of 147 bps around 8 histones forming the nucleosomes. Strings of nucleosomes stack into dense 30 nm fibers, but the...Show moreChromatin is a dense structure of DNA and histone proteins. DNA wraps in units of 147 bps around 8 histones forming the nucleosomes. Strings of nucleosomes stack into dense 30 nm fibers, but the structure of these fibers remains disputed. Force spectroscopy experiments show that the linker length affects the characteristic unfolding of nucleosome-arrays and suggests two alternative conformations. However, the precise influence of linker base pairs remains unclear. Here we use Monte Carlo simulations and show that DNA twist-energy largely determines whether nucleosomes stack in a 1-start or 2-start conformation. In addition, we show with Mutation Monte Carlo simulations that the sequence of the linker DNA may affect nucleosome stacking. Thus both the sequence and length of the linker DNA are important for the higher-order structure of 30 nm chromatin fibers. Furthermore, the simulations form a bridge between theory and experiment as predicted changes in chromatin folding can be verified experimentally.Show less
