Nucleosomal arrays self-assemble into supramolecular globular structures lacking 30-nm fibers
Kazuhiro Maeshima, Ryan Rogge, Sachiko Tamura, Yasumasa Joti, Takaaki Hikima, Heather Szerlong, Christine Krause, Jake Herman, Erik Seidel, Jennifer DeLuca, Tetsuya Ishikawa, and Jeffrey C. Hansen
The EMBO Journal Published online 12.04.2016 DOI:10.15252/embj.201592660
The existence of a 30-nm fiber as a basic folding unit for DNA packaging has remained a topic of active discussion. Here we characterize the supramolecular structures formed by reversible Mg2+-dependent self-association of linear 12-mer nucleosomal arrays using microscopy and physicochemical approaches. These structures, which we call ’oligomers’, were globular throughout all stages of the cooperative assembly process, and ranged in size from ~50 nm to a maximum diameter of ~1000 nm. The nucleosomal arrays were packaged within the oligomers as interdigitated 10-nm fibers, rather than folded 30-nm structures. Linker DNA was freely accessible to micrococcal nuclease, although the oligomers remained partially intact after linker DNA digestion. The organization of chromosomal fibers in human nuclei in situ was stabilized by 1 mM MgCl2 but became disrupted in the absence of MgCl2, conditions that also dissociated the oligomers in vitro. These results indicate that a 10-nm array of nucleosomes has the intrinsic ability to self-assemble into large chromatin globules stabilized by nucleosome-nucleosome interactions, and suggest that the oligomers are good in vitro model for investigating the structure and organization of interphase chromosomes.
The 12-mer nucleosomal array is a well-defined model chromatin system. Without Mg2+, the nucleosomal array is extended by repulsion (Left). In 1-2 mM Mg2+, the nucleosomal array folds into a regular 30-nm chromatin fiber structure (Center). With further increases in Mg2+, the nucleosome arrays assemble into supramolecular structures (Right). The large structures are not assemblies of the 30-nm chromatin fibers, but interdigitated and melted structures of 10-nm nucleosomal arrays, reflecting on the native chromatin structure in the cell.