What is a chromosome?

In the nucleus of each cell, the DNA molecule is packaged into thread-like structures called chromosomes. Each chromosome is made up of DNA tightly coiled many times around proteins called histones that support its structure.

To achieve the overall packing ratio, DNA is not packaged directly into final structure of chromatin. Instead, it contains several hierarchies of organization. The first level of packing is achieved by the winding of DNA around a protein core to produce a "bead-like" structure called a nucleosome. This gives a packing ratio of about 6. This structure is invariant in both the euchromatin and heterochromatin of all chromosomes.

The second level of packing is the coiling of beads in a helical structure called the 30 nm fiber that is found in both interphase chromatin and mitotic chromosomes. This structure increases the packing ratio to about 40. The final packaging occurs when the fiber is organized in loops, scaffolds and domains that give a final packing ratio of about 1000 in interphase chromosomes and about 10,000 in mitotic chromosomes.

Eukaryotic chromosomes consist of a DNA-protein complex that is organized in a compact manner which permits the large amount of DNA to be stored in the nucleus of the cell. The subunit designation of the chromosome is chromatin. The fundamental unit of chromatin is the nucleosome.

Chromatin is the unit of analysis of the chromosome; chromatin reflects the general structure of the chromosome but is not unique to any particular chromosome

Nucleosome is simplest packaging structure of DNA that is found in all eukaryotic chromosomes; DNA is wrapped around an octamer of small basic proteins called histones; 146 bp is wrapped around the core and the remaining bases link to the next nucleosome; this structure causes negative supercoiling.

The nucleosome consists of about 200 bp wrapped around a histone octamer that contains two copies of histone proteins H2A, H2B, H3 and H4. These are known as the core histones. Histones are basic proteins that have an affinity for DNA and are the most abundant proteins associated with DNA. The amino acid sequence of these four histones is conserved suggesting a similar function for all.

The length of DNA that is associated with the nucleosome unit varies between species. But regardless of the size, two DNA components are involved. Core DNA is the DNA that is actually associated with the histone octamer. This value is invariant and is 146 base pairs. The core DNA forms two loops around the octamer, and this permits two regions that are 80 bp apart to be brought into close proximity.

Thus, two sequences that are far apart can interact with the same regulatory protein to control gene expression. The DNA that is between each histone octamer is called the linker DNA and can vary in length from 8 to 114 base pairs. This variation is species specific, but variation in linker DNA length has also been associated with the developmental stage of the organism or specific regions of the genome.

The next level of organization of the chromatin is the 30 nm fiber. This appears to be a solenoid structure with about 6 nucleosomes per turn. This gives a packing ratio of 40, which means that every 1 µm along the axis contains 40 µm of DNA. The stability of this structure requires the presence of the last member of the histone gene family, histone H1. Because experiments that strip H1 from chromatin maintain the nucleosome, but not the 30 nm structure, it was concluded that H1 is important for the stabilization of the 30 nm structure.

The final level of packaging is characterized by the 700 nm structure seen in the metaphase chromosome. The condensed piece of chromatin has a characteristic scaffolding structure that can be detected in metaphase chromosomes. This appears to be the result of extensive looping of the DNA in the chromosome.

The last definitions that need to be presented are euchromatin and heterochromatin. When chromosomes are stained with dyes, they appear to have alternating lightly and darkly stained regions. The lightly-stained regions are euchromatin and contain single-copy, genetically-active DNA. The darkly-stained regions are heterochromatin and contain repetitive sequences that are genetically inactive.

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