The repeating packing unit of chromatin is the nucleosome (Kornberg and Lorch 1999), which consists of ∼147 bp of double-stranded DNA wrapped around a disk formed by the globular domains of eight histone proteins (two copies of histones H2A, H2B, H3, and H4) (Luger et al. 1997). This core structure is highly conserved throughout Eukaryota. Longer double-stranded DNA molecules are assembled into an array of nucleosomes, forming a structure often referred to as the “beads on a string.” At this scale, the structure of interest is the location of nucleosomes along the genome: Which ∼150-bp regions are wrapped around histones, and which DNA sequences form the relatively accessible “linker” DNA between nucleosomes? Much of what we know of nucleosome structure is based on differences in susceptibility of DNA to various fractionation processes, with nucleosomal DNA being protected from many enzymes and from chemical attack, and linker DNA being relatively accessible. We can divide genomic assays of nucleosome packing into two classes.
