Nucleosomes
The DNA found inside the eukaryotic nucleus is usually associated with special classes of proteins that form a DNA-protein complex termed chromatin. In turn, chromatin clumps into tightly packed units termed nucleosomes. The structure of nucleosomes can restrict the accessibility of DNA and affect gene regulation.
The nuclei of most eukaryotic cells (cells with a nucleus defined by a nuclear membrane) contain nearly equal amounts of DNA and specialized proteins that bind to the DNA to form chromatin. Approximately half of the proteins associated with DNA are a form of very basic protein termed histones. There are five major classes or forms of histone proteins usually associated with DNA. The histones most commonly associated with DNA are designated H1, H2A, H2B, H3 and H4.
The packaging of DNA with histones and non-histone chromosomal proteins allows bonding to occur in the molecules surrounding the actual DNA nucleotides. This external or cooperative bonding allows chromatin to be packed into clumps and gives chromatin a "beads on a string" appearance under the electron microscope.
Histone H1 molecules play a critical role in the binding of nucleosome together into globular clumps. Although not all nucelosomes are packed the same way, H1 histones tend to bind to DNA in clusters of eight histones. Although bacterial DNA is not normally associated with proteins and histones, studies have demonstrated that histones are capable of binding bacterial DNA.
The nucleosomes (beads) are joined by a thin and tenuous looking short strand of DNA nucleotides that associate with far fewer protein molecules. This string-like strand of DNA is termed spacer DNA or linker DNA and may vary from 20 base pairs (bp) to 120 base pairs in length. The length of the spacer or linker DNA depends upon the organism, and the cell type. Nucleosome and chromatin structure also rapidly and dramatically change during cell division. Accordingly, the in vivo (in living cells) appearance of chromatin is dependant upon the cell's position in the cell cycle.
Scientists use a variety of equipment and a number of techniques to study the detailed structure of nucleosomes. These techniques include electron microscopy, DNA crystallization, neutron diffraction, protein assays and cross linking, x ray diffraction studies, and variety of immunological techniques. Studies of the nucleosome core (nucleosome core particles or NCPs) establish that a nucleosome consists of DNA wrapped around a clump of histones. There are approximately 1.8 turns of DNA per nucleosome. The DNA is not wrapped smoothly, but is wound about the histones in a kinked manner to form superhelical twists that allow as much as eight times the amount of DNA to exist in the same volume.
Chromatin and nucleosome function, especially of subtle biochemical modifications that occur during specific stages of the cell cycle, comprise an active area of genetic research. These changes regulate the accessibility of DNA to the processes of replication, transcription, and repair. Nucleosomes can affect gene expression by limiting the access of DNA regulatory proteins. Some regulatory proteins can only bind to regions of DNA that contain low numbers or that are free of nucleosomes. Nucleosomes are not evenly distributed and a certain level of genetic regulation may be attributed to the non-random distribution of nucleosomes.
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