vnewjay

Heterochromatin is as followed.

[ 本帖最后由 vnewjay 于 2008-5-9 22:31 编辑 ]

vnewjay

Nuclear components of eukaryotic cells (later known as chromosomes) were visualized around 1840 using basophilic aniline dyes. Forty years later, Walther Flemming termed this colorable substance within the eukaryotic nuclei “chromatin” ([Flemming, 1878] and [Flemming, 1882]). We now know that chromatin is the complex assemblage of DNA, histone proteins, and other nonhistone protein components. Yet, even with the limited technology of the late 19th century, Flemming and others made remarkable observations through the staining of biological material combined with light microscopy. For instance, chromatin appeared to transform (condense) into chromosomes during mitosis and decondense into lower-ordered chromatin after cell division (Boveri, 1904). Three decades later, Emil Heitz discovered that identical chromatin/chromosome regions in different individuals of the same cell type recurrently stain bright and others scarce. These differentially stained regions corresponded to condensed and decondensed chromatin states that Heitz termed as heterochromatin (HC) and euchromatin (EC), respectively (Heitz, 1928). He also hypothesized that “euchromatin is genicly active, heterochromatin genicly passive. Heterochromatic chromosomes or pieces of chromosomes contain no genes or somehow passive genes” (Heitz, 1929). Although this is not entirely valid, it paved the way for major discoveries in chromatin research.

The following decades were largely dedicated to identifying the nuclear components encoding the information stored in genes. Mutagenesis and subsequent phenotypic analyses were widely used in Drosophila embryos and various plant species to explore gene function. Muller observed that X-ray-irradiated Drosophila embryos exhibited patterns of variegated gene expression (Muller, 1930), evidenced by changes in eye color in a subset of cells. This effect was later directly related to suppression of the gene responsible for red eye pigmentation when juxtaposed close to or within HC. This phenomenon, termed position effect variegation (PEV), represented the first palpable link between the conformational state of chromatin and the transcriptional status of genes. A major conceptual advance in recognizing the dynamic nature of HC came about through extensive studies of transposable elements in plants. Barbara McClintock proposed that “changes in quantity, quality or structural organization of heterochromatic elements may well alter the kind and/or degree of particular exchanges that occur, and in this way control the chromosome organization and the kind and the relative effectiveness of genic action” (McClintock, 1950). With subsequent improvements in staining methods and the development of electron microscopy, it became apparent that HC could be subdivided into constitutive (c) and facultative (f) HC, the latter of which was initially ascribed to developmentally regulated heterochromatinization of only one allele of a homologous chromosome pair (for instance, see Brown, 1966).

This mainly cytological view of fHC was gradually expanded as molecular techniques were devised to explore the mechanisms of gene expression in an unprecedented manner. Studies exploring the molecular mechanisms of cellular differentiation revealed that some genes of multicellular organisms were linked to the differentiation state—for instance, inactive in certain differentiated cell types but transcribed in undifferentiated or other differentiated cell lineages. Based on the prevailing concept that gene activity correlates with EC regions, these genes had to be localized to EC in the undifferentiated cell but somehow transformed into a heterochromatic state upon differentiation. In the following years, cohorts of transcription factors were discovered that control gene expression as a function of the state of differentiation. A model emerged that placed opposing effects of promoter-bound activators and repressors at the heart of gene regulation to explain changes in gene expression during cellular differentiation. This model, however, could not explain gene expression being linked to genomic location, as in the case of PEV of transgenes, or the majority of transposable elements in the mammalian genome being inactive, or that transgenes integrated at random genomic locations have a strong tendency to be silenced over time unless flanked by DNA elements that block the spreading of HC (Mutskov et al., 2002).

vnewjay

The term ‘heterochromatic gene’ is considered to be an oxymoron by some scientists, and there is a historical reason for this confusion. The inclination to equate heterochromatin with a lack of gene expression dates back to none other than Emil Heitz, the cytogeneticist who coined the term heterochromatin in 1928 [1]. Heitz characterized heterochromatin as the chromosomal component that appears darkly staining throughout the cell cycle, to distinguish it from the cycling euchromatin, which appears diffuse in interphase nuclei. He showed that heterochromatin is a common entity in plant and animal cells and imagined it to be the manifestation of functionally inactive regions of the genome. This notion was largely supported by observations of contemporaries of Heitz. When geneticists discovered and mapped the first mutations in Drosophila, they found that most map to euchromatin. Only a few genes mapped to the Y chromosome or near the spindle attachment site of other chromosomes, regions that were classified as ‘constitutive’ heterochromatin because they appeared consistently heterochromatic on both homologs in most if not all cell types in an organism. The ability of these heterochromatic regions to induce variegated expression of euchromatic genes when the two types of chromatin were abnormally juxtaposed by chromosome rearrangements made a striking impression on geneticists. This phenomenon, called position effect variegation (PEV), was discovered by H.J. Muller in 1930 [2]. Subsequent studies revealed that dozens of euchromatic genes are inactivated when placed near or in heterochromatin [3], irrespective of the time or tissue in which the gene is expressed, or the function of its product. The generality of PEV showed that heterochromatin not only lacks gene activity, but could routinely cause gene inactivation. Molecular biologists later showed that constitutive heterochromatin largely comprises highly repetitive satellite sequences and middle-repetitive transposable elements (TEs), so-called ‘junk’ DNA, whose transcription was considered either nonexistent or dispensable. Genetic tests revealed that the silencing effect of heterochromatin was subject to modification by altering the dose of heterochromatin (such as adding an extra Y chromosome) or by mutations in genes that became known as Suppressors (Su(var)s) or Enhancers (E(var)s) of PEV [4].

In the past decade, key insights into the molecular features of heterochromatin have been obtained. It is now widely recognized that heterochromatic domains in diverse organisms are often associated with particular chromosomal proteins and core histone modifications, and with the ability to silence euchromatic gene expression [5]. The discovery of the activities of two key highly conserved proteins, SU(VAR)3-9 and HP1, has been particularly informative and has led to a molecular model of heterochromatin formation [6]. The model proposes that SU(VAR)3-9, a methyltransferase, specifically methylates Lys9 of histone H3 (H3K9me) on heterochromatic DNA. HP1 (heterochromatin protein 1), a chromodomain protein that binds H3K9me as a dimer, is proposed to condense the chromatin fiber through protein–protein interaction, rendering it inaccessible for transcription [6]. Although SU(VAR)3-9 and HP1 are the most extensively studied SU(VAR) proteins, numerous genetic and molecular factors have been found to affect heterochromatin formation or maintenance, including components of the RNA interference (RNAi) machinery. The landmark discovery that small interfering RNAs (siRNAs) have a role in heterochromatin formation in some organisms has highlighted the importance of the transcription of specific repetitive sequences in heterochromatin [7].

The molecular features described above are often considered the hallmarks of heterochromatin; however, none are absolute defining features. Nonetheless, the tendency to equate the term ‘heterochromatin’ with ‘silent chromatin’, ‘H3K9me-enriched chromatin’ or ‘HP1-enriched chromatin’ dominates the field. Like many generalizations, overly simplified views of heterochromatin can be misleading. In reality, some of the earliest geneticists recognized the diverse features and functions of heterochromatin. As we summarize in this review, the existence of active genes that normally reside within heterochromatin has important implications for understanding how chromosomal context and chromatin structure can regulate gene expression. We focus here on heterochromatic genes in Drosophila, plants and mammals that reside in or near constitutive heterochromatin. We refer the reader to other reviews for a discussion of genes expressed from the inactivated X chromosome of female mammals, the classic and best characterized example of facultative heterochromatin 8 and 9.

vnewjay

A defining feature of chromosomes is the centromere, the site for spindle attachment at mitosis and meiosis. Intriguingly, centromeres of plants and animals are maintained by both sequence-specific and sequence-independent (epigenetic) processes. Epigenetic inheritance might enable kinetochores (the structures that attach centromeres to spindles) to maintain an optimal size. However, centromeres are susceptible to the evolution of ‘selfish’ DNA repeats that bind to kinetochore proteins. We argue that such sequence-specific interactions are evolutionarily unstable because they enable repeat arrays to influence kinetochore size. Changes in kinetochore size could affect the interaction of kinetochores with the spindle and, in principle, skew Mendelian segregation. We propose that key kinetochore proteins have adapted to disrupt such sequence-specific interactions and restore epigenetic inheritance.