Interactions and Stacking in Ordered Mononucleosomes and Folded Chromatin: Effects of Histone Tail Modifications

Abstract

Folding of genomic DNA into compact but dynamic eukaryotic chromatin is driven by attractive interactions between nucleosome core particles (NCPs) and is inherently related to regulation of DNA replication, transcription and repair.However, little is known about the molecular details of the NCP-NCP contacts as well as of the nature and scale of forces involved. Chromatin folding is sensitive to both the ionic environment and to the sequence and modifications of the positively charged N-terminal histone tails.Combining experimental and computer modelling approaches, we study nucleosome-nucleosome interaction in ordered phases of stacked mono-nucleosomes as well as in folded nucleosome arrays (chromatin). Folding of chromatin fibres and intermolecular association of NCPs have been investigated as a function of ionic conditions and in the presence of posttranslational modifications in the histone tails, prepared by semi-synthetic ligation chemistry methods. Using sedimentation velocity analytical ultracentrifugation (AUC), X-ray diffraction (SAXS) and single molecule force spectroscopy methods, the dependence of NCP stacking and the stability of the folded fibres were investigated.Furthermore, using an advanced coarse-grained (CG) NCP model, computational modelling was used to investigate cation-induced NCP-NCP interactions. The CG model takes into account the detailed shape and charge distribution on the NCP, thus adequately describing the electrostatic interactions. The experimental behaviour is mostly dominated by unspecific electrostatic interactions. However, the close NCP-NCP stacking contacts show great sensitivity to the presence of the H4 histone tail and to modifications within this tail.