New insights into nucleosome and chromatin structure: an ordered state or a disordered affair?

Abstract

Nucleosomes exist in an assortment of structural states that differ from the various crystal structures. The equilibrium between the nucleosomal states is affected by post-translational modifications (PTMs) of histones, histone variants and DNA sequence. A common interface formed by residues from H2A and H2B is used by several nucleosome-interacting proteins. This 'acidic patch' varies between different histone variants. Several types of chromatin 'secondary structure' may coexist depending on the functional context. An important aspect of chromatin higher-order three-dimensional organization (or 'tertiary structure') is that specific nucleosomes may be distant with respect to their primary structure but may be within interacting distance in the context of tertiary structures, in analogy with protein folding. Small changes in chromatin primary structure yield dramatic effects in its large-scale organization. Numerous and often subtle changes by PTMs, histone variants and DNA sequence can significantly affect nucleosome shape, stability and its protein surface.