Heterochromatin

 The term heterochromatin was originally used to describe chromatin that stained intensely with particular dyes. This is in contrast to the rest of chromatin, which stained less well and is called euchromatin. Heterochromatin comes in two varieties, constitutive, which is permanently heterochromatic, and facultative, which can change its state. The chromatin regions of centromeres and telomeres are examples of constitutive heterochromatin. In contrast, the inactive X-chromosome and the vast bulk of inactive chromatin in any chromosome are composed of facultative heterochromatin. 

The most common observed consequence of heterochromatin formation is the repression of transcription, either in the heterochromatin itself or in regions of chromatin adjacent to the heterochromatin domain. The variability in gene expression at the border of the heterochromatin is described as “position effect variegation.” Three explanations have been offered for this phenomenon. The first is that special proteins, such as heterochromatin protein 1, cause heterochromatin to adopt its distinct structure and that these proteins can “spill over” into regions of normal chromatin and exert repressive effects on gene expression. The second is that heterochromatin represents the sequestration of chromosomal domains in specialized nuclear compartments from which the transcriptional machinery is excluded, for example, the chromocenter. The third applies only to Drosophila and other insects with polytene chromosomes in that, following placement adjacent to heterochromatin, a gene undergoes fewer rounds of replication than normal. Fewer copies of the gene would cause a concomitant reduction in transcription. Most investigators accept that heterochromatin-specific proteins diffuse onto normal chromatin and thereby influence the gene expression of juxtaposed genes. Although initially defined from work on insects, there is an increasing body of evidence that heterochromatin domains exist in all eukaryotic chromosomes, including those of yeast. Moreover, it is clear that metazoans have used this type of chromosomal organization for the developmental regulation of gene expression.

An approach to the molecular basis of heterochromatin formation has been to look for mutations in Drosophila or more recently in Saccharomyces cerevisiae that enhance or suppress position effects on gene expression (modifiers of position effect variegation). Modifiers of position effect variegation include mutations in the genes encoding the chromosomal proteins involved in forming heterochromatin. Using this approach, the gene encoding a nonhistone protein, HP1, was identified. Mutations of the HP1 gene reduce position effects on gene expression (1). HP1 is preferentially associated with the heterochromatin regions of polytene chromosomes. Other proteins homologous to HP1 include Polycomb, which is also chromatin-associated and from genetic experiments it is known that it influences the expression of many genes in normal chromatin. Neither HP1 nor Polycomb interacts with DNA directly, but they presumably recognize some aspect of nucleosome or chromatin fiber structure. Recent experiments reveal that certain proteins that affect position effect variegation, for example, SUV38H1, are histone methyltransferases that selectively modify lysine #9 in histone H3 (3), and that the resulting modified histone is a preferential target for binding by HP1 (4). Combined with earlier data that overexpression of this enzyme leads to HP1 redistribution from heterochromatin (5), as does the histone hyperacetylation via inhibition of histone deacetylases (6), these data strongly support a model that idiosyncratically modified nucleosomes form a landing pad for HP1. Polycomb and HP1 share a common amino acid sequence known as the chromodomain (chromatin modification). This domain is highly conserved through evolution and can be found even in yeast. For example, the S. pombe SW16 gene encodes a chromodomain protein. The SW16 protein is involved in the assembling the chromosomal domain containing the transcriptionally silent mating type cassettes.

Position effect variegation also depends on the presence of normal levels of the histone proteins and posttranslational modifications of the N-terminal tails of the core histones, such as acetylation. The histones are needed for forming nucleosomes and for subsequently forming higher order structures. Acetylating the N-terminal tails alters the interaction of the histones with DNA and, potentially, the folding of nucleosomal arrays. Position effect variegation also depends on proteins that recognize

nucleosomal arrays, but not naked DNA, such as HP1 and Polycomb. HP1 is associated only with inactive chromosomal regions, but Polycomb interacts with at least 50 different sites within Drosophila chromosomes, including developmentally important loci encoding homeodomain proteins. However, mutations in a second gene family that interacts with the histone proteins allow genes associated with Polycomb to remain active. Thus, Polycomb is likely to exert its effects on gene expression via chromatin structures dependent on the histone proteins (7, 8).

Position effect variegation is recognized now as a universal phenomenon in eukaryotic chromosomes. Genes integrated into yeast chromosomes near the silent mating loci or close to the telomeres are repressed in a way that reflects their proximity to these sites in the chromosome. This silencing effect spreads over at least 5 to 10 kbp of contiguous DNA, but not as much as 20 to 30 kbp in yeast. As in Drosophila, the genes influencing the position effect in yeast encode structural components of chromatin or enzymes associated with the modification of chromatin.

 Examples of mammalian chromosomal regions that contain heterochromatin are also the centromere and the telomere (9). The telomeres of mammalian chromosomes have an unusual chromatin structure in which nucleosomes are closely packed. Mammalian telomeres consist of the sequence (TTAGGG)_n repeated for 10 to 100 kbp. Heterochromatin at the centromere contains tandemly repeated simple sequence “satellite” DNA, for example the a-satellite DNA at the human centromere. This a-satellite heterochromatin plays a structural role by mediating attachment of the kinetochore. In these instances, specialized heterochromatin structures have an important architectural role and protective function in the chromosome.

Occasionally, an entire nucleus becomes heterochromatinized. One example is the inactivation of the erythrocyte nucleus in chicken. Here the special linker histone variant H5, which represses transcription and compacts nucleosomal arrays very effectively, accumulates. Histone H5 is more arginine-rich than the normal linker histone H1 found in somatic cells. This increase in arginine content probably strengthens the interaction of H5 with DNA and stabilizes chromatin structure. In this instance, the assembly of a specialized heterochromatin structure reflects the terminal differentiation of this particular specialized cell type.

References

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