The proteins that bind to the DNA to form eukaryotic chromosomes are traditionally divided into two classes: the histones and the non-histone chromosomal proteins, each contributing about the same mass to a chromosome as the DNA. The complex of both classes of protein with the nuclear DNA of eukaryotic cells is known as chromatin (Figure 4–20).
Histones are responsible for the first and most basic level of chromosome packing, the nucleosome, a protein–DNA complex discovered in 1974. When interphase nuclei are broken open very gently and their contents examined under the electron microscope, most of the chromatin appears to be in the form of a fiber with a diameter of about 30 nm (Figure 4–21A). If this chromatin is subjected to treatments that cause it to unfold partially, it can be seen under the electron microscope as a series of “beads on a string” (Figure 4–21B). The string is DNA, and each bead is a “nucleosome core particle” that consists of DNA wound around a histone core (Movie 4.2).
The structural organization of nucleosomes was determined after first isolating them from unfolded chromatin by digestion with particular enzymes (called nucleases) that break down DNA by cutting between the nucleosomes. After digestion for a short period, the exposed DNA between the nucleosome core particles, the linker DNA, is degraded. Each individual nucleosome core particle consists of a complex of eight histone proteins—two molecules each of histones H2A,
Figure 4–20 Chromatin. As illustrated, chromatin consists of DNA bound to both histone and non-histone proteins. The mass of histone protein present is about equal to the total mass of non-histone protein, but—as schematically indicated here—the latter class is composed of an enormous number of different species. In total, a chromosome is about one-third DNA and two-thirds protein by mass.
H2B, H3, and H4—and double-stranded DNA that is 147 nucleotide pairs long. The histone octamer forms a protein core around which the double-stranded DNA is wound (Figure 4–22).
The region of linker DNA that separates each nucleosome core particle from the next can vary in length from a few nucleotide pairs up to about 80. (The term nucleosome technically refers to a nucleosome core particle plus one of its adjacent DNA linkers, but it is often used synonymously with nucleosome core particle.) On average, therefore, nucleosomes repeat at intervals of about 200 nucleotide pairs. For example, a diploid human cell with 6.4 × 109 nucleotide pairs contains approximately 30 million nucleosomes. The formation of nucleosomes converts a DNA molecule into a chromatin thread about one-third of its initial length.
The Structure of the Nucleosome Core Particle Reveals How DNA Is Packaged
The high-resolution structure of a nucleosome core particle, solved in 1997, revealed a disc-shaped histone core around which the DNA was tightly wrapped in a left-handed coil of 1.7 turns (Figure 4–23). All four of the histones that make up the core of the nucleosome are relatively small proteins (102–135 amino acids), and they share a structural motif, known as the histone fold, formed from three α helices connected by two loops (Figure 4–24). In assembling a nucleosome, the histone folds first bind to each other to form H3–H4 and H2A–H2B dimers, and the H3–H4 dimers combine to form tetramers. An H3–H4 tetramer then further combines with two H2A–H2B dimers to form the compact octamer core, around which the DNA is wound.