Nucleosomes

Figure 28.11 provides an overall view of the fundamental elements of chromatin structure.

Experimental Evidence - Three experimental observations have revealed that the structure of chromatin is regular and repeating. The repeating element is called a nucleosome. The observations are as follows:

1. If naked DNA (that is, DNA that is not protein-complexed) is partially digested with a nonspecific endonuclease that randomly cuts double strands, a broad smear of polynucleotide fragments is observed in an electrophoresis gel. If the same experiment is conducted with chromatin, or even with whole nuclei (which the nuclease can easily penetrate through the nuclear pores), the random DNA cleavage yields a series of bands that are multiples of approximately 200 base pairs. This indicates that "naked" DNA is present only at regularly spaced points.

2. Electron micrographs of extended chromatin fibers reveal a regular "beaded" pattern in the chromatin structure, with one bead about every 200 bp.

3. If nuclease digestion of chromatin is continued, it slows down and nearly stops when about 30% of the DNA had been consumed. The remaining protected DNA is present in particles corresponding to the beads seen in the electron micrograph.

Nucleosome structure - The bead particles are nucleosomes (or more precisely, nucleosomal core particles). They have a simple, definite composition that is practically invariant over the whole eukaryotic kingdom. Both nucleosomes and nucleosome histone cores have been crystallized.

1. Nucleosomes always contain 146 bp of DNA, wrapped about an octamer of histone molecules--two each of H2A, H2B, H3, and H4. This composition explains the equal amounts of each of the four histones in chromatin.

2. The DNA lies on the surface of the histone octamer and makes about 1.75 left-hand superhelical turns about it. The structure of the octamer provides a helical "ramp" upon which the DNA is bound. Analysis of high-resolution data reveals a common histone structure called the "histone fold."

Other aspects of structure - Although the nucleosome itself is a nearly invariant structure in eukaryotes, the length of DNA between nucleosomes may vary from about 20 bp to over 100 bp. Exactly what determines the arrangement of nucleosomes along the DNA is still not understood completely. However, it is now clear that at least some nucleosomes occupy defined positions. For example, the internucleosomal, or linker, DNA is occupied by the H1-type (very lysine-rich) histones and nonhistone proteins.

1. The Role of Chromatin Structure in Transcription

2. Virtual Tour of the Nucleosome

3. The Nucleus (slow)