5.5: The Nucleosome

Human DNA is almost two meters long. However, it is compressed inside a tiny nucleus measuring only a few microns in diameter. To make this degree of compaction possible, DNA is organized into several sequential levels so that it can fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.

In a chromosome, DNA is wound twice around a protein complex called a histone octamer core, which consists of 8 histone proteins. This DNA and histone protein complex together forms the nucleosome, the fundamental and functional unit of DNA compaction. Nucleosomes can further coil around themselves into higher-order compact structures.

Histones are highly conserved proteins.

The amino acid sequences of core histone proteins are highly conserved even between distantly related species. For example, the amino acid sequence of the H3 histone between a calf thymus and a pea plant has only four amino acid differences.

Non-histone proteins

The nucleosome complex is also bound by a small proportion of non-histone proteins, which help maintain the compaction and organize long chromatin loops. Non-histone proteins are also involved in regulating DNA replication and RNA synthesis.

Histones are small, positively charged proteins that tightly associate with negatively charged DNA, forming structures called nucleosomes.

The nucleosome core particle contains a histone octamer composed of two molecules, each of histones H2A, H2B, H3, and H4. This core particle is wrapped around by a 145 to 147 base-pair section of DNA nearly two times.

Each histone has a small, positively charged tail 11 to 27 amino acids long that aids in keeping the negatively charged DNA wound around the histones. Additionally, the tails of neighboring core particles interact with each other facilitating DNA packaging. 

Adjacent to the core particle, a variable length stretch of linker DNA separates each core particle like beads on a string. Another histone, H1, acts as a clamp to keep the linker DNA in place.

Together, the nucleosome compresses a long DNA molecule into a chromatin thread one-third of its original length.