The Structure of Chromosomes:- Nucleosomes Are the Fundamental Organizational Units of Chromatin
The eukaryotic chromosome represents the compaction of a DNA molecule about 105 μm long into a cell nucleus that is typically 5 to 10 m in diameter. This compaction involves several levels of highly organized folding. Subjection of chromo somes to treatments that partially unfold them reveals a structure in which the DNA is bound tightly to beads of protein, often regularly spaced . The beads in this “beads-on-a-string” arrangement are complexes of histones and DNA. The bead plus the connecting DNA that leads to the next bead form the nucleosome, the fundamental unit of organization upon which the higher-order packing of chromatin is built. The bead of each nucleosome contains eight histone molecules: two copies each of H2A, H2B, H3, and H4. The spacing of the nucleosome beads provides a repeating unit typically of about 200 bp, of which 146 bp are bound tightly around the eight-part histone core and the remainder serve as linker DNA between nucleosome beads. Histone H1 binds to the linker DNA. Brief treat ment of chromatin with enzymes that digest DNA causes preferential degradation of the linker DNA, releasing his tone particles containing 146 bp of bound DNA that have been protected from digestion. Researchers have crystallized nucleosome cores obtained in this way, and x-ray diffraction analysis reveals a particle made up of the eight histone molecules with the DNA wrapped around it in the form of a left-handed solenoidal super coil (Fig. 1).
A close inspection of this structure reveals why eukaryotic DNA is underwound even though eukaryotic cells lack enzymes that underwind DNA. Recall that the solenoidal wrapping of DNA in nucleosomes is but one form of supercoiling that can be taken up by under wound (negatively supercoiled) DNA. The tight wrap ping of DNA around the histone core requires the removal of about one helical turn in the DNA. When the protein core of a nucleosome binds in vitro to a relaxed, closed-circular DNA, the binding introduces a negative supercoil. Because this binding process does not break the DNA or change the linking number, the formation of a negative solenoidal supercoil must be accompanied by a compensatory positive supercoil in the unbound region of the DNA (Fig. 2). As mentioned earlier, eukaryotic topoisomerases can relax positive supercoils. Relaxing the unbound positive supercoil leaves the negative supercoil fixed (through its binding to the nucleosome histone core) and results in an overall decrease in linking number. Indeed, topoisomerases have proved necessary for assembling chromatin from purified his tones and closed-circular DNA in vitro. Another factor that affects the binding of DNA to histones in nucleosome cores is the sequence of the bound DNA. Histone cores do not bind randomly to DNA; rather, they tend to position themselves at certain locations. This positioning is not fully understood but, in some cases, appears to depend on a local abundance of A=T base pairs in the DNA helix where it is in contact with the histones (Fig. 3). The tight wrapping of the DNA around the nucleosome’s histone core requires compression of the minor groove of the helix at these points, and a cluster of two or three A=T base pairs makes this compression more likely. Other proteins are required for the positioning of some nucleosome cores on DNA. In several organisms, certain proteins bind to a specific DNA sequence and then facilitate the formation of a nucleosome core nearby. Precise positioning of nucleosome cores can play a role in the expression of some eukaryotic genes.
FIGURE 1 DNA wrapped around a nucleosome core. (a) Space filling representation of the nucleosome protein core, with different colors for the different histones (PDB ID 1AOI). (b) Top and (c) side views of the crystal structure of a nucleosome with 146 bp of bound DNA. The protein is depicted as a gray surface contour, with the bound DNA in blue. The DNA binds in a left-handed solenoidal supercoil that circumnavigates the histone complex 1.8 times. A schematic drawing is included in (c) for comparison with other figures depicting nucleosomes.
FIGURE 2 Chromatin assembly. (a) Relaxed, closed-circular DNA. (b) Binding of a histone core to form a nucleosome induces one negative supercoil. In the absence of any strand breaks, a positive supercoil must form elsewhere in the DNA (ΔLk=0). (c) Relaxation of this positive supercoil by a topoisomerase leaves one net negative supercoil (ΔLk=1).
FIGURE 3 Positioning of a nucleosome to make optimal use of A=T base pairs where the histone core is in contact with the minor groove of the DNA helix.
