The nucleosome reference frame and standard geometries for octasomes.

Unlabelled: There are over 533 nucleosome structures in the Research Collaboratory for Structural Bioinformatics (RCSB). Collectively, numerous variants and species are present, as are sub-nucleosomal and super-nucleosomal assemblies within the nucleosome family. The organization of the histones and DNA is highly conserved in all standard octasomes containing 145, 146, or 147 base pairs. This observation is used to establish a nucleosome reference frame that enables us to describe and compare the gross structure and organization of all nucleosomes. We observe that cumulative sums of Rise, Twist, and DNA arc length are linear functions of the base pair index with values exceeding 0.999 for almost all octasome structures. These relationships enable us to readily compare the location and orientation of DNA director frames extracted from the crystal structures to ideal superhelix values. Such comparisons reveal that the DNA superhelix extracted from X-ray structures exhibits a sinusoidal variation with an amplitude of approximately 5Å  about a constant superhelix radius of Å, in agreement with early descriptions of nucleosome organization as tripartite. There is also a distinct straightening of the nucleosomal DNA over the outermost turn of DNA's double helix. The straightening of the DNA superhelix marks the transition to linker DNA and is easily recognized as a rapid increase in superhelix radius and is concomitant with a change in pitch. This provides a rigorous means of separating nucleosomal DNA from linker DNA. For all X-ray structures, we find that near the dyad, there exists a set of DNA director frames for which the spatial location and orientation are highly conserved. Away from the dyad, the DNA superhelix exhibits "singletrack" and "multipath" regions. In the singletrack region, all structures exhibit a single highly conserved pathway along which all base pairs must track, but at varying rates. In the multipath regions, the base pairs are allowed to map out a limited number of different pathways along the surface of the histone octamer. To demonstrate the utility of the proposed reference geometries, standard and distorted octasome structures, super-nucleosomal structures, nucleosomes with linker DNA, and nucleosomes in closed circular DNA are analyzed.

Supplementary Information: The online version contains supplementary material available at 10.1007/s12551-024-01206-5.