identity of chromosome

Nucleosomes are the fundamental repeating units of eukaryotic chromatin, ^[1] with the exception of mature sperm. ^[2] They package DNA into chromosomes inside the cell nucleus and control gene expression. They are made up of DNA and four pairs of proteins called histones, and resemble "beads on a string of DNA" when observed with an electron microscope. The nucleosome hypothesis proposed by Don and Ada Olins^[3] and Roger Kornberg^[4][5] in 1974, was a paradigm shift for understanding eukaryotic gene expression. The proteins that make up the nucleosome are called histones. Histones H2A, H2B, H3 and H4 are part of the nucleosome while histone H1 is the linker DNA between the two nucleosomes.

Structure of the core particle

The crystal structure of the nucleosome has currently been determined with a resolution better than 2.0 Å,^[6] but most of the important features were known by 1997 with the publication of its structure at a resolution of 2.8 Å.^[7]

The nucleosome repeats, with some variations and exceptions, roughly every 200 base pairs (bp) throughout eukaryotic chromatin. The nucleosome core particle shown in the figure consists of about 146 bp of dsDNA wrapped in 1.65 left-handed superhelical turns around four identical pairs of proteins individually known as histones and collectively known as the histone octamer. The remaining 50 bp of the repeating unit consists of "linker DNA", dsDNA which separates the core particles.

Each of the four histones (H2A, H2B, H3, and H4) shares a very similar structural motif consisting of three alpha helices separated by loops. In solution, histones form pairs with identical copies of themselves and are referred to as dimers or histone-fold pairs. In the case of the H3 and H4 histones, they assemble further into tetramers, an association of two H3-H4 dimers, whereby buried charged groups of the same alpha helix on both of the H3 histones hydrogen bond to each other. The assembly of a nucleosome core particle occurs first by the attachment of the H3-H4 tetramer onto the dsDNA with the later association of two separate H2A-H2B dimers, a process that is likely to occur in a cooperative manner (i.e. both H2A-H2B dimers assemble onto the tetramer at once).

According to the crystal structure, the histone octamer likely interacts with the dsDNA around it roughly every 10 bp. Each of the four histone dimers contain three regions of interaction with the dsDNA. The central interaction site for each dimer is formed by an alpha helix from each histone in the pair pointing at a single phosphate group on the dsDNA to which they hydrogen bond. At positions 10 bp away on either side, a loop from both histones in the pair converge to hydrogen bond to other single phosphate groups. See the figure on the right for a visual representation. Two other interactions (for a total of 14) occur through the interaction of histone tails from each of the H3 histones. These interactions occur at the entry and exit points of the dsDNA wrapping around the nucleosome and help to clamp these regions onto the core particle.

Analysis of the structure of dsDNA wrapped around the histone octamer suggests that it is predominantly B-form, although more tightly constrained than free DNA due to its interaction with the octamer. Curvature into the superhelix comes primarily when either the minor or the major groove faces the octamer and therefore occurs in spurts of roughly 5 bp. Major groove bending around the octamer occurs smoothly. Minor groove bending is facilitated by arginine side chains inserted into the groove and occurs smoothly around the H3-H4 tetramer, but is kinked around the H2A/H2B dimer regions. The DNA is most tightly constrained in regions where it interacts with the double loop structures of the histone dimers mentioned above, which implies that there is more variability in how the DNA interacts with the double alpha helix structures of the histone dimers in order to accommodate the binding of different sequences.^[8]

Many proteins bind only to specific DNA sequences. Although nucleosomes tend to prefer some DNA sequences over others, they are capable of forming on just about any sequence. It has been shown that water molecules roughly double the number of histone-DNA interactions by acting as intermediates between atoms which would otherwise be too far apart to Hydrogen bond.^[9] It is the flexibility in the formation of these water-mediated interactions which allows for the histone octamer to wrap a very wide variety of DNA sequences.

Legend:

Nucleosome: Subunit of chromatin composed of a short length of DNA wrapped around a core of histone proteins.

The human genome contains about 3 billion nucleotide pairs organized as 23 chromosomes pairs. If uncoiled, the DNA contained by each of those chromosomes would measure between 1.7 and 8.5 cm (0.67 to 3.35 inches) long. This is too long to fit into a cell. Moreover, if chromosomes were composed of extended DNA, it is difficult to imagine how the DNA could be replicated and segregated into two daughter cells without breaking down.

In fact chromosomal DNA is packaged into a compact structure with the help of specialized proteins called histones. The complex DNA plus histones in eucaryotic cells is called chromatin.

The fundamental packing unit is known as a nucleosome. Each nucleosome is about 11nm in diameter. The DNA double helix wraps around a central core of eight histone protein molecules (an octamer) to form a single nucleosome. A second histone (H1 in the illustration) fastens the DNA to the nucleosome core. The total mass of this complex is about 100,000 daltons.

Nucleosomes are usually packed together, with the aid of a histone (H1,) to form a 30nm large fiber. As a 30nm fiber, the typical human chromosome would be about 0.1cm in length and would span the nucleus 100 times. This suggests higher orders of packaging, to give a chromosome the compact structure seen in a typical karyotype (metaphase) cell.