Assembly and structural properties of subsaturated chromatin arrays

Nucleosomes have been reconstituted onto dodecameric repeats of a 208-base pair nucleosome positioning sequence at various subsaturating molar ratios of histone octamer to DNA repeat (r). These reconstitutes have been characterized with respect to lattice site occupancy distributions, nucleosome positioning, chromatin folding, and histone octamer dissociation. Reconstitution at 0.3 < or = r < or = 0.9 produces subsaturated chromatin templates with distinct compositional limits, n +/- 2 nucleosomes, where n is the average number of nucleosomes present on the template at that r value. Nucleosomes on subsaturated arrays occupy the same set of specific positions within the repeat unit as they do on saturated templates, with only very slight differences in the relative frequency of occupation of the various positions. The nucleosomes on very subsaturated templates, i.e. r < or = 0.5, are generally spread out. However, some nucleosome clustering is observed on these very subsaturated templates. These results indicate that assembly of nucleosomes onto this DNA lattice is not a strongly cooperative process. In 200 mM NaCl, subsaturated reconstitutes exhibit reduced levels of folding and histone octamer dissociation compared with saturated arrays. These results provide a framework for understanding the structural features of regions of chromatin partially depleted of nucleosomes.