Insights into the role of nucleosomal DNA folding on chromatin fiber properties

DNA in eukaryotic cell nuclei is packaged in a highly compact, yet dynamic chromatin structure that provides a regulatory mechanism for many biological processes, such as gene expression. The basic packaging unit of chromatin is the nucleosome, which consists of ~1.7 turns of DNA wrapped around an octamer core of histone proteins (H3, H4, H2A, H2B). Chains of nucleosome-decorated DNA, which resemble beads on a string, fold into a higher-order arrangement, often referred to as the 30-nm fiber. However, the structure of this fiber remains poorly understood, despite decades of research. Many proposed models for the 3D organization of the nucleosomes and intervening DNA in chromatin vary quite significantly, and the very existence and relevance of a 30-nm structure in vivo has been questioned. An analysis of the available high-resolution nucleosome structures shows subtle, yet significant differences in DNA wrapping around the histone core. Monte Carlo simulations of regular nucleosome arrays generated using a meso-scale representation of DNA suggest that these local differences can lead to large changes in global nucleosome arrangements, comparable to the effect of changes in nucleosome spacing by ~2–3 base pairs. Our results suggest that a regular nucleosome array with a 177-base-pair (bp) repeat can display a loose three-stack or a more compact two-stack arrangement, on average, depending on the DNA wrapping profile of the nucleosome. These findings imply a very dynamic chromatin fiber with a multitude of mechanisms to control its folding. Using this meso-scale model, we have studied the role of chromatin fiber architecture and histone tails on chromatin compaction and long-range communication in constructs containing 177-bp repeats. Our predictions for chromatin fibers with a loose three-stack nucleosome arrangement can qualitatively account for experimental data from in vitro assays of enhancer-promoter communication (EPC) under physiologically-relevant conditions. On the other hand, fibers that display a two-stack arrangement are in better agreement with sedimentation velocity experiments performed under a different set of ionic conditions. Removal of histone tails diminishes EPC efficiency, and our simulations predict that H3/H4 tail removal has the biggest impact, in agreement with in vitro experiments.Ph.D.Includes bibliographical referencesby Stefjord Todoll