Heterochromatin

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Overview

Heterochromatin is a tightly packed form of DNA. Its major characteristic is that transcription is limited. As such, it is a means to control gene expression, through regulation of the transcription initiation.

Structure

Chromatin is found in two varieties: euchromatin and heterochromatin.[1] Originally, the two forms were distinguished cytologically by how intensely they stained - the former is less intense, while the latter stains intensely, indicating tighter packing. Heterochromatin is usually localized to the periphery of the nucleus.

Heterochromatin mainly consists of genetically inactive satellite sequences,[2] and many genes are repressed to various extents, although some cannot be expressed in euchromatin at all.[3] Heterochromatin also replicates later in S phase of the cell cycle than euchromatin, and is found only in eukaryotes. Both centromeres and telomeres are heterochromatic, as is the Barr body of the second inactivated X chromosome in a female.

Function

Heterochromatin is believed to serve several functions, from gene regulation to the protection of the integrity of chromosomes; all of these roles can be attributed to the dense packing of DNA, which makes it less accessible to protein factors that bind DNA or its associated factors. For example, naked double-stranded DNA ends would usually be interpreted by the cell as damaged DNA, triggering cell cycle arrest and DNA repair. Some region of chromatin are very densly packed with fibres displaying a condition comparable to that of the chromosome at mitosis. Heterochromatin is generally clonally inherited; when a cell divides the two daughter cells will typically contain heterochromatin within the same regions of DNA, resulting in epigenetic inheritance. Variations cause heterochromatin to encroach on adjacent genes or recede from genes at the extremes of domains. Transcribable material may be repressed by being positioned (in cis) at these boundary domains. This gives rise to different levels of expression from cell to cell,[4] which may be demonstrated by position-effect variegation.[5] Insulator sequences may act as a barrier in rare cases where constitutive heterochromatin and highly active genes are juxtaposed (e.g. the 5'HS4 insulator upstream of the chicken β-globin locus,[6] and loci in two Saccharomyces spp.[7][8]).

Constitutive heterochromatin

All cells of a given species will package the same regions of DNA in constitutive heterochromatin, and thus in all cells any genes contained within the constitutive heterochromatin will be poorly expressed. For example, all human chromosomes 1, 9, 16, and the Y chromosome contain large regions of constitutive heterochromatin. In most organisms, constitutive heterochromatin occurs around the chromosome centromere and near telomeres.

Facultative heterochromatin

Facultative heterochromatin The regions of DNA packaged in facultative heterochromatin will not be consistent within the cell types of a species, and thus a sequence in one cell that is packaged in facultative heterochromatin (and the genes within poorly expressed) may be packaged in euchromatin in another cell (and the genes within no longer silenced). However, the formation of facultative heterochromatin is regulated, and is often associated with morphogenesis or differentiation. An example of facultative heterochromatin is X-chromosome inactivation in female mammals: one X chromosome is packaged in facultative heterochromatin and silenced, while the other X chromosome is packaged in euchromatin and expressed.

Among the molecular components that appear to regulate the spreading of heterochromatin include the Polycomb-group proteins and non-coding genes such as Xist. The mechanism for such spreading is still a matter of controversy.[9]

Yeast heterochromatin

Saccharomyces cerevisiae, or budding yeast, is a model eukaryote and its heterochromatin has been defined thoroughly. Although most of its genome can be characterized as euchromatin, S. cerevisiae has regions of DNA that are transcribed very poorly. These loci are the so-called silent mating type loci (HML and HMR), the rDNA (encoding ribosomal RNA), and the sub-telomeric regions. Fission yeast (Schizosaccharomyces pombe) uses another mechanism for heterochromatin formation at its centromeres. Gene silencing at this location depends on components of the RNAi pathway. Double-stranded RNA is believed to result in silencing of the region through a series of steps.

In the fission yeast Schizosaccharomyces pombe two RNAi complexes, the RNAi-induced transcriptional gene silencing (RITS) complex and the RNA-directed RNA polymerase complex (RDRC), are part of a RNAi machinery involved in the initiation, propagation and maintenance of heterochromatin assembly. These two complexes localize in a siRNA-dependent manner on chromosomes, at the site of heterochromatin assembly. RNA polymerase II synthesizes a transcript that serves as a platform to recruit RITS, RDRC and possibly other complexes required for heterochromatin assembly. Both RNAi and an exosome-dependent RNA degradation process contribute to heterochromatic gene silencing. These mechanisms of Schizosaccharomyces pombe may occur in other eukaryotes.[10]

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References

  1. Elgin, S.C. (1996). "Heterochromatin and gene regulation in Drosophila". Curr. Opin. Genet. Dev. 6: 193–202. doi:10.1016/S0959-437X(96)80050-5. ISSN 0959-437X.
  2. Lohe, A.R.; et al. (1993). "Mapping simple repeated DNA sequences in heterochromatin of Drosophila melanogaster". Genetics. 134 (4): 1149–1174. ISSN 0016-6731. PMID 8375654.
  3. Lu, B.Y.; et al. (2000). "Heterochromatin protein 1 is required for the normal expression of two heterochromatin genes in Drosophila". Genetics. 155 (2): 699–708. ISSN 0016-6731. PMID 10835392.
  4. Fisher, Amanda G. (2002). "Gene silencing, cell fate and nuclear organisation". Curr. Opin. Genet. Dev. 12 (2): 193–197. doi:10.1016/S0959-437X(02)00286-1. ISSN 0959-437X. Unknown parameter |coauthors= ignored (help); Unknown parameter |month= ignored (help)
  5. Zhimulev, I.F.; et al. (1986). "Cytogenetic and molecular aspects of position effect variegation in Drosophila melanogaster". Chromosoma. 94 (6): 492–504. doi:10.1007/BF00292759. ISSN 1432-0886. Unknown parameter |month= ignored (help)
  6. Burgess-Beusse, B; et al. (2002). "The insulation of genes from external enhancers and silencing chromatin". Proc. Natl Acad. Sci. USA. 9 (Suppl 4): 16433–16437. doi:10.1073/pnas.162342499. PMID 12154228. Unknown parameter |month= ignored (help)
  7. Noma, K.; et al. (2001). "transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries". Science. 293 (5532): 1150–1155. doi:10.1126/science.1064150. PMID 11498594. Unknown parameter |month= ignored (help)
  8. Donze, D. & R.T. Kamakaka (2000). "RNA polymerase III and RNA polymerase II promoter complexes are heterochromatin barriers in Saccharomyces cerevisiae". Embo J. 20: 520–31. doi:10.1093/emboj/20.3.520.
  9. Talbert PB, Henikoff S. Spreading of silent chromatin: inaction at a distance. Nat Rev Genet. 2006 Oct;7(10):793-803.
  10. Vavasseur; et al. (2008). "Heterochromatin Assembly and Transcriptional Gene Silencing under the Control of Nuclear RNAi: Lessons from Fission Yeast". RNA and the Regulation of Gene Expression: A Hidden Layer of Complexity. Caister Academic Press. ISBN 978-1-904455-25-7.
  • Z. Avramova Heterochromatin in Animals and Plants. Similarities and Differences. Plant Physiology May 2002, Vol. 129, pp. 40-49.
  • Caron, H.; et al. (2001). "The Human Transcriptome Map: Clustering of Highly Expressed Genes in Chromosomal Domains". Science. 291 (5507): 1289–1292. doi:10.1126/science.1056794. PMID 11181992.

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