14 S.D. Levene
information in a cell nucleus that is of order 5–10μm in diameter. In the case
of the human genome, there is about 2 m of DNA per nucleus if the single
molecules that comprise each of the 46 chromosomes in a diploid human cell
are stretched to their length and placed end to end. Storing a molecule that
is 2 m in length and 2 nm in width in a nucleus that is 10μm in diameter is
comparable to storing a string about 60 km long and of cross section 50μm
in an object the size of a basketball. This enormous level of compaction,
which is achieved in such a way as to preserve accessibility of the genome for
transcription, replication, recombination, and repair, is one of the supremely
remarkable feats of biology.
The basic structural unit of organization in eukaryotic chromosomes is the
nucleosomal core particle. This is a complex consisting of 147 base pairs of
DNA wrapped 1.7 times around a protein core that contains two copies each
of the core histone proteins H2A, H2B, H3, and H4 [24, 25]. Nucleosomes
are strung together along the DNA, like beads on a string, separated by in-
tervals of 10–80 base pairs of unwrapped DNA. In a chromosome, thousands
of these nucleosomes are arranged in a continuous helical array to generate
a fiber that is 30 nm in cross section; this 30-nm fiber is in turn folded to
generate the higher-level structures that comprise the so-calledchromonema
fiber. Interactions that mediate the association of 30-nm fibers are thought
to involve solvent-exposed domains of the core nucleosomes as well as other
histone proteins that are associated with nucleosomal arrays, such as H1 and
H5 [26, 27].
One critical, but often overlooked, factor that facilitates this compaction is
the role played by negative DNA supercoiling. Interwound superhelices, which
exemplify the form of superhelical winding that takes place free in solution, are
in equilibrium with toroidally wound superhelices generated during wrapping
of DNA on the surface of histone proteins in the case of eukaryotic chromatin
(Fig. 2.8). In prokaryotic cells, histone-like architectural proteins play similar
roles in genome organization [28]. The particular biological advantage achieved
by such high levels of organization must have been accompanied by the parallel
evolution of mechanisms needed to reorganize local regions of chromatin as
required by the cell.
The mechanisms involved in chromatin reorganization have begun to re-
veal themselves at the molecular level, although many details remain to be
worked out. Known as chromatin remodeling, the repositioning of histone oc-
tamers on DNA involves interactions with complexes of specific proteins that
facilitate the transfer of histones to other available binding sites along the
same DNA molecule (in cis) [29]. All known chromatin-remodeling activities
appear to require ATP as a source of free energy. These protein complexes
often work in concert with enzymes that carry out covalent modifications of
histone proteins such as histone transacetylase. This suggests that at least
these two activities, and possibly others, are coordinated to make naked DNA
available to other cellular factors. There is evidence that acetylation of his-
tones destabilizes histone–histone interactions among individual 30-nm fibers;