Base-Pair Resolution Mapping of Nucleosomes In Vitro

The position of a nucleosome describes the arrangement of its core 147 base pairs of DNA relative to the core histone octamer (1 ). The DNA superhelix spiraling around the histone octamer has an outer, solvent exposed face and an inner, histone-associated face (2 ). Fixing of a particular exposed helical face is known as a rotational phasing of the double helix and controls the accessibility for particular sequences, such as for transcription factor binding sites (3 ). In general, because DNA on the nucleosome has an approximately 10-bp pitch, bases 10 bp apart have similar accessibility at a first approximation. The rotational phase is easily determined by any nucleolytic digestion pattern of the nucleosomal (e.g., DNaseI, free solution hydroxyl radicals, [4 ]), although the distinction in solvent exposure of DNA shows variability at the edges of the core 147 bp directly associated with the histone proteins. The more rigorous fixing of the exact region of DNA in contact with the histone octamer is known as translational positioning. This not only implies a rotational phase, but also locates the detailed features of nucleosomal DNA relative to the histone octamer structure for a particular sequence (2 ). For example, the intermediate resolution crystal structure of the nucleosome core particle revealed that the path of the DNA around the histone octamer is not uniform but undergoes a series of sharper bends at specific locations (5 ). Likewise, biochemical studies have shown that the basic tails of individual histones associate with particular regions of the DNA superhelix (6 ).