Higher Order Chromatin Structure

Chromatin compaction - Wrapping DNA about histone cores to form nucleosomes (see here) accomplishes part of the compaction necessary to fit the long eukaryotic DNA into the nucleus. However, much of the chromatin in the nucleus is even more highly compacted. The next stage in compaction involves folding the beaded fiber into a thicker fiber like that shown in Figure 28.12. These fibers may be further folded on themselves to make the thicker chromatin fibers visible in both metaphase chromosomes and the nuclei of nondividing (interphase) cells.

Metaphase scaffolding - Dye staining of metaphase chromosomes from a particular organism gives a reproducible banding pattern. In situ hybridization methods show that particular DNA sequences are always located at the same places in specific chromosomes. Some kind of regular folding must preserve this order. Recent evidence indicates that when metaphase chromosomes are treated with polyanions to strip off the histones and loosely bound nonhistone proteins, the DNA strands emerge as enormous loops from a scaffold of tightly bound protein. Individual loops may range up to 100,000 bp in length--about the size of the globin gene cluster, for example. Approximately 1000 such loops exist in the average chromosome.

Interphase scaffolding - Evidence also exists for a similar but more diffuse scaffold in the interphase nucleus. Removal of histones and weakly bound nonhistone proteins from intact nuclei by high salt concentrations or detergents, together with digestion of most of the DNA by nucleases, leaves a protein structure that has been called the nuclear scaffold, or nuclear matrix (Figure 28.12). It includes the laminar shell that lines the inside of the nuclear membrane, plus a network of fine fibers that seem to extend throughout the nucleus. When the chemical dissection is done gently to remove the histones and most other proteins, the DNA connections to the nuclear matrix are undisturbed. Cleavage of the DNA with restriction endonucleases leaves specific fragments of DNA attached to the nuclear matrix. These fragments are spaced at rather long intervals along the genome and contain characteristic matrix attachment regions (MARs). It appears that groups of coordinately expressed genes often lie between adjacent MARs, as Figure 28.13 illustrates for the repeated histone gene clusters in Drosophila.

Scaffold proteins - Proteins that form the scaffold from which the loops extend include topoisomerases. Topoisomerase molecules at the base of a loop might bring about changes in the supercoiling on that particular loop in addition to the coiling imposed by the nucleosomes. Changes in supercoiling may aid in chromosome condensation and seem to be essential during replication and transcription. The structure of chromatin is likely dynamic, changing locally as the DNA is replicated (see here) or transcribed (see here).

Heterochromatin/Euchromatin - Some loop domains, those involving the nontranscribed genes of a particular cell, may be permanently coiled into 30-nm fibers and perhaps supercompacted into even higher-order coiling. Such regions could correspond to the highly condensed regions of heterochromatin long recognized by cytologists. The more-open chromatin regions, called euchromatin, may then correspond to relaxed domains within which transcription can occur.