When the histone octamer is mixed with purified dsDNA under appropriate ionic conditions, the same x-ray diffraction pattern is formed as that observed in freshly isolated chroma tin. Biochemical and electron microscopic studies confirm the existence of reconstituted nucleosomes in such in vitro generated preparations. Furthermore, the reconstitution of nucleosomes from DNA and histones H2A, H2B, H3, and H4 is independent of the organismal or cellular origin of the various components. A result argues that nucleosome formation is an ancient and evolutionarily conserved, fundamental cellular process. Moreover, neither the histone H1, nor the nonhistone proteins are necessary for the reconstitution of the nucleosome core.

In the nucleosome, the DNA is supercoiled in a left-handed helix over the surface of the disk-shaped histone octamer (see Figure 1). The majority of core histone proteins interact with the DNA on the inside of the supercoil without protruding, although the amino terminal tails of all the histones are thought to extend outside of this structure and are available for regulatory PTMs (see Table 1).

Fig1. Model for the structure of the nucleosome. DNA is wrapped around the surface of a protein cylinder consisting of two each of histones H2A, H2B, H3, and H4 that form the histone octamer. The ~145 bp of DNA, consisting of 1.75 superhelical turns, are in contact with the histone octamer. The position of histone H1, when it is present, is indicated by the dashed outline at the bottom of the figure. Note that histone H1 interacts with DNA as it enters and exits the nucleosome.

Table1. Possible Roles of Posttranslationally Modified Histones

The (H3–H4)₂ tetramer itself can confer nucleosome-like properties on DNA and thus has a central role in the formation of the nucleosome. The addition of two H2A–H2B dimers stabilizes the primary particle and firmly binds two additional half-turns of DNA previously bound only loosely to the (H3–H4)₂ . Thus, 1.75 superhelical turns of DNA are wrapped around the surface of the histone octamer, protecting 145 to 150 bp of DNA and forming the nucleosome core particle (see Figure 1). In chromatin, core particles are separated by a roughly 30-bp region of DNA termed “linker.” Most of the DNA is in a repeating series of these structures, giving chromatin a repeating “beads-on-a-string” appearance when examined by electron microscopy (see Figure 2).

Fig2. Electron micrograph of chromatin showing individual nucleosomes (white, ball-shaped) attached to strands of DNA (thin, gray line); see also Figure 2. (Reproduced with permission from Shao Z. Probing Nanometer Structures with Atomic Force Microscopy. News Physiol Sci. 1999;14:142-149.)

In vivo the assembly of nucleosomes is mediated by one of several nuclear chromatin assembly factors whose functions are facilitated by histone chaperones, a group of proteins that exhibit high affinity for binding histones. As the nucleosome is assembled, histones are released from the histone chaperones. Nucleosomes appear to exhibit preference for certain regions on specific DNA molecules, but the basis for this nonrandom distribution, termed phasing, is not yet completely understood. Phasing is likely related both to the relative physical flexibility of particular nucleotide sequences to accommodate the regions of kinking within the nucleosomal supercoil, as well as the presence of other DNA-bound factors that limit the sites of nucleosome deposition.

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