In order for an enormous length of DNA to fit into a tiny cell, it must be condensed. This is accomplished in a series of steps. First, the double helix is wound around groups of eight histone protein molecules. The resulting configuration resembles beads on a string, with each histone bundle and its associated DNA representing a bead, and the intervening, unwound DNA representing the string. These beads are called nucleosomes. This beaded structure is then coiled around a scaffolding of non-histone proteins into loops called chromatin. DNA exists during interphase in this state. When the cell is about to enter mitosis, however, the chromatin twists even more tightly upon itself, yielding tight bundles, or chromosomes. When the DNA is tightly wound, transcription factors have no access to the genes; therefore, transcription does not occur during mitosis.
Some parts of the chromosomes, however, remain in this tightly condensed state even during interphase, and are thus transcriptionally inert. These parts of the DNA are called heterochromatin. Heterochromatin stains darkly with Giemsa stain, and is distinguished from euchromatin, which contains the genes that are transcribed during interphase.
There are two classes of heterochromatin. The first, consitutive heterochromatin, is never transcriptionally active. In humans, it is located in the centromeric region of each chromosome. It is also found in the telomeres. It is composed of highly repetitive sequences, and is sometimes called satellite DNA. Constitutive heterochromatin is also found on much of the Y chromosome; in parts of chromosomes 1, 9, and 16; and on the short arms of the acrocentric chromosomes, 13, 14, 15, 21, and 22. These regions of heterochromatin are possibly involved in maintaining a chromosome's structure and in chromosome movement during mitosis.
The other class is called facultative heterochromatin. Unlike constitutive heterochromatin, this type is sometimes active and somemtimes not, depending upon the cell type in an organism and on the organism's stage of development. There is little facultative heterochromatin in embryonic cells; whereas some highly specialized cell types have much more. This may mean that, as cells differentiate and no longer need access to all of their genes, the unnecessary genes are put into the equivalent of long-term storage by taking the form of heterochromatin.
Occasionally, a translocation or inversion of part of a chromosome will reposition an gene. If such a gene, which was transcriptionally active before being repositioned, finds itself in or adjacent to a heterochromatic region, it will not be expressed. Heterochromatin appears to inhibit the expression of genes adjacent to it.
The inactive X chromosome in females is composed almost entirely of facultative heterochromatin. Its DNA is condensed enough that it forms the Barr body visible within the nucleus of female cells in mammals. Only a few of the genes on the inactive X are transcriptionally active. When the germ cells for the next generation are to be formed, however, the condensed X chromosome is reactivated. This demonstrates that no permanent change to the DNA occurs.
Heterochromatin is replicated late in the S period of the cell cycle. For example, the active X chromosome replicates before the inactive X does. The less condensed DNA is, the more accessible it is to the replication machinery. Therefore, less condensed DNA replicates early. The housekeeping genes, which are essential for the moment-to-moment functioning of the cell, are replicated first. If, in a given species, a particular gene is active in one type of cell but not in another type of cell, it will replicate early in the first type, but later in the second type.
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