Heterochromatin and its Relationship to Cell Senescence and Cancer Therapy

Our goal is to understand the impact of chromatin structure on cell proliferation, cell and tissue aging, cancer and cancer therapies. To this end, we have investigated the formation of specialized domains of facultative heterochromatin, called Senescence Associated Heterochromatin Foci (SAHF), in senescent human cells. A complex of histone chaperones, HIRA and ASF1a, drives formation of SAHF. Remarkably, although SAHF are highly compacted domains of heterochromatin, these domains of facultative heterochromatin largely exclude other domains of chromatin at telomeres and pericentromeres, which are themselves thought to be constitutively heterochromatic. The relationship between SAHF formation and these other domains of heterochromatin is discussed. Also, in the course of our studies, we have obtained evidence that points to a novel function for the widely-studied but poorly-understood family of heterochromatin proteins, HP1 proteins. We propose that HP1 proteins are essential components of a dynamic nuclear response that senses and rectifies defects in epigenetic information, encoded in chromatin through histone modifications and DNA methylation. We further propose that defects in this essential "chromatin repair" response in transformed human cells contributes to the preferential killing of cancer cells by the epigenetic cancer therapies that are currently in clinical development.     

M33 condenses chromatin through nuclear body formation and methylation of both histone H3 lysine 9 and lysine 27

Heterochromatin, a type of condensed DNA in eukaryotic cells, has two main categories: Constitutive heterochromatin, which contains H3K9 methylation, and facultative heterochromatin, which contains H3K27 methylation. Methylated H3K9 and H3K27 serve as docking sites for chromodomain-containing proteins that compact chromatin. M33 (also known as CBX2) is a chromodomain-containing protein that binds H3K27me3 and compacts chromatin in vitro. However, whether M33 mediates chromatin compaction in cellulo remains unknown. Here we show that M33 compacts chromatin into DAPI-intense heterochromatin domains in cells. The formation of these heterochromatin domains requires H3K27me3, which recruits M33 to form nuclear bodies. G9a and SUV39H1 are sequentially recruited into M33 nuclear bodies to create H3K9 methylated chromatin in a process that is independent of HP1α. Finally, M33 decreases progerin-induced nuclear envelope disruption caused by loss of heterochromatin. Our findings demonstrate that M33 mediates the formation of condensed chromatin by forming nuclear bodies containing both H3K27me3 and H3K9me3. Our model of M33-dependent chromatin condensation suggests H3K27 methylation corroborates with H3K9 methylation during the formation of facultative heterochromatin and provides the theoretical basis for developing novel therapies to treat heterochromatin-related diseases.     

Remodeling of chromatin structure in senescent cells and its potential impact on tumor suppression and aging

Cellular senescence is an important tumor suppression process, and a possible contributor to tissue aging. Senescence is accompanied by extensive changes in chromatin structure. In particular, many senescent cells accumulate specialized domains of facultative heterochromatin, called Senescence-Associated Heterochromatin Foci (SAHF), which are thought to repress expression of proliferation-promoting genes, thereby contributing to senescence-associated proliferation arrest. This article reviews our current understanding of the structure, assembly and function of these SAHF at a cellular level. The possible contribution of SAHF to tumor suppression and tissue aging is also critically discussed.     

The other chromatin

Current understanding of heterochromatin, thanks to molecular data, focuses on its performing several functions in evolution and development. Heterochromatin shows characteristic distribution patterns in karyotypes and contributes to the broad scattering of genome sizes through biological taxa. Heterochromatin remains compacted and thus different from properly stained euchromatin during somatic interphase. A minimum amount of heterochromatin, however, is required for it to be visible in light microscopy. It may further escape notice during the dynamic processes of embryogenesis and gametogenesis. Present-day biology is in search of specific proteins and DNA sequences that comprise heterochromatin. The data that result from overcoming the threshold of visibility will support understanding of interference by heterochromatin in ontogeny and evolution. The contributions of Sigrid and Wolfgang Beermann to the study of heterochromation diminution (DNA elimination) are recalled, and we also discuss the functions and effects of heterochromatin on differential DNA endoreplication and in speciation.     

芽殖酵母和裂殖酵母中异染色质形成机制

芽殖酵母(Saccharomyces cerevisiae)和裂殖酵母(Schizosaccharomyces pombe)是用来研究异染色质形成、细胞周期、DNA复制等重要细胞功能的理想单细胞真核生物.本文主要介绍这2种酵母中异染色质形成的机制.异染色质是一种抑制基因转录和DNA重组的特殊染色质结构.尽管在芽殖酵母和裂殖酵母中异染色质形成都需要组蛋白修饰,但异染色质建立的机制不同.在芽殖酵母中参与异染色质形成的主要蛋白是Sir1-4蛋白（其中Sir2为组蛋白H3去乙酰化酶）,而组蛋白H3赖氨酸9甲基化酶Clr4和异染色质蛋白Swi6在裂殖酵母异染色质形成中起关键的作用.在这两个酵母中,参与异染色质形成的组蛋白修饰蛋白由DNA结合蛋白招募到异染色质.此外,裂殖酵母也利用RNA干扰系统招募组蛋白修饰蛋白.     

Heterochromatin,repetitive DNS und Nukleolen in Leberzellen von Microtus agrestis

Zusammenfassung Die Zellstruktur von Leberzellen der Erdmaus, Microtus agrestis, wurde nach Giemsafärbung, Feulgenbehandlung, Behandlung mit Ribonuklease und nach Färbung des konstitutiven Heterochromatins untersucht. Das konstitutive Heterochromatin ist in Leberzellen nicht heteropyknotisch, das fakultative Heterochromatin ist im weiblichen Geschlecht als Sexchromatinkörperchen sichtbar. Bestimmungen des relativen DNS-Gehalts ergaben, daß die Zahl der Sexchromatinkörperchen der Ploidie der Zellkerne proportional ist. Die Nukleolen liegen in Hepatozyten oft randständig; in 59% der diploiden Zellkerne sind 2 Nukleolen enthalten. Nach Anfärbung der repetitiven DNS werden oft auch die Nukleolen gefärbt, nach Ribonukleasebehandlung tritt dieser Effekt nicht auf. Das konstitutive Heterochromatin wird in Form von 2 langen fädigen Strukturen sichtbar.

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Heterochromatin, repetitive DNA and nucleoli in liver cells of Microtus agrestis

Summary The nuclear structure of parenchymal liver cells of embryo and adult Microtus agrestis was studied in smear and section preparations after staining with Giemsa solution and treatment according to Feulgen, after treatment with ribonuclease and after specific staining of constitutive heterochromatin. In liver cell nuclei only the facultative heterochromatin is heteropycnotic, a sex chromatin body is observable in female but not in male animals. Constitutive heterochromatin is not heteropycnotic in liver cells. Measurements of the relative DNA content showed that nuclei with one sex chromatin body are diploid; tetraploid nuclei possess two and octoploid nuclei four sex chromatin bodies. Solely in the diploid cell nuclei of the intrahepatic gall ducts two large chromocenters are found. The nucleoli in hepatocytes often lie at the perimeter of the nucleus. 17% of the diploid nuclei contain one nucleolus, 59% two nucleoli, 23% three and 1% four. After staining of repetitive DNA, the nucleoli often become stained as well; after treatment with ribonuclease this effect does not occur. The constitutive heterochromatin becomes visible in form of two long, threadlike structures. After longer periods of dissociation the sex chromatin body ceases to be visible. Sex chromatin and constitutive heterochromatin are contiguous to the nucleoli.

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Mit dankenswerter Unterstützung durch das Bundesministerium für Bildung und Wissenschaft der Bundesrepublik Deutschland.     

Mapping Simple Repeated DNA Sequences in Heterochromatin of Drosophila Melanogaster

Heterochromatin in Drosophila has unusual genetic, cytological and molecular properties. Highly repeated DNA sequences (satellites) are the principal component of heterochromatin. Using probes from cloned satellites, we have constructed a chromosome map of 10 highly repeated, simple DNA sequences in heterochromatin of mitotic chromosomes of Drosophila melanogaster. Despite extensive sequence homology among some satellites, chromosomal locations could be distinguished by stringent in situ hybridizations for each satellite. Only two of the localizations previously determined using gradient-purified bulk satellite probes are correct. Eight new satellite localizations are presented, providing a megabase-level chromosome map of one-quarter of the genome. Five major satellites each exhibit a multichromosome distribution, and five minor satellites hybridize to single sites on the Y chromosome. Satellites closely related in sequence are often located near one another on the same chromosome. About 80% of Y chromosome DNA is composed of nine simple repeated sequences, in particular (AAGAC)(n) (8 Mb), (AAGAG)(n) (7 Mb) and (AATAT)(n) (6 Mb). Similarly, more than 70% of the DNA in chromosome 2 heterochromatin is composed of five simple repeated sequences. We have also generated a high resolution map of satellites in chromosome 2 heterochromatin, using a series of translocation chromosomes whose breakpoints in heterochromatin were ordered by N-banding. Finally, staining and banding patterns of heterochromatic regions are correlated with the locations of specific repeated DNA sequences. The basis for the cytochemical heterogeneity in banding appears to depend exclusively on the different satellite DNAs present in heterochromatin.     

Heterochromatin as an incubator for pathology and treatment non-response: implication for neuropsychiatric illness

Heterochromatin is a higher order assembly that is characterized by a genome-wide distribution, gene-repression, durability and potential to spread. In this light, it is an appealing mechanism to interpret the neurobiology of complex brain disorders such as schizophrenia where downregulation of expression appears to be the norm. H3K9 methylation (H3K9me) can initiate the seeding of a heterochromatin assembly on an inactive or poorly coordinated promoter as a consequence of a decline in transactivators either from disuse or from misuse. H3K9me can extend its influence by spatial spreading through the mechanism of recursively recruiting adapters, such as heterochromatin protein 1 (HP1) homodimers. HP1 itself serves as a platform for other repressive proteins such as DNA methyltransferases. In full color, heterochromatin can occupy genome-wide gene networks, tissue specific ontologies and even rearrange the nuclear architecture. Heterochromatin in the brain is modified by small molecule pharmacology and serves a physiological role in the functioning of dopamine neurons and the construction of memory. From a therapeutic perspective, the durable nature of heterochromatin implies that it may require disassembly before the full genomic-potential of standard pharmacotherapies is achieved, especially in treatment resistant patients.     

Functions of chromatin remodeling factors in heterochromatin formation and maintenance

Heterochromatin is characteristically more compact than euchromatin in the eukaryotic genome. The establishment of heterochromatin is mediated by special histone modifications, recruitment and propagation of heterochromatin specific proteins, as well as formation of special primary and high order structures of chromatin. Chromatin remodeling factors are ATPases that can alter the conformation and/or positioning of nucleosomes along DNA in an ATP-dependent manner. There is increasing evidence implicating chromatin remodeling activities in heterochromatin in various organisms ranging from yeasts to humans. Chromatin remodeling factors play roles in the establishment, maintenance and epigenetic inheritance of heterochromatin, but the underlying molecular mechanisms have just begun to be investigated.     

Giemsa banding of a human metacentric chromosome number 9

Summary Giemsa staining procedures have been used on human lymphocyte preparations to locate constitutive heterochromatin (C-bands) and to produce distinct banding patterns for each individual chromosome (G-bands). A metacentric C group chromosome has been shown by both techniques to be chromosome number 9.

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Zusammenfassung An menschlichen Lymphocyten wurde eine Giemsafärbung durchgeführt, mit dem Ziel, konstitutives Heterochromatin (C-Banden) zu lokalisieren und für jedes einzelne Chromosom besondere Bandmuster herauszuarbeiten (G-Banden). Beide Techniken erlaubten, ein metazentrisches C-Chromosom als Nr. 9 zu identifizieren.

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Supported by PHS grants RR-62 and 5-SO1-RRO-5411.     

Polymorphismus des konstitutiven Heterochromatins bei menschlichen A1-Metaphasechromosomen

Zusammenfassung Nach Anwendung der Giemsa C-Färbetechnik können bei A1-Metaphasechromosomen 3 Typen von zentromernahem Heterochromatin unterschieden werden: Typ I, Typ II und Typ III. Der Heterochromatin-Typ III des A1-Chromosoms wurde bei 4 Mitgliedern einer Familie gefunden. Dieser Typ kommt auch in Prophase- und Interphasekernen deutlich zur Darstellung. Fluorescenzmikroskopisch ist das zentromernahe Heterochromatin nicht nachweisbar.

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Polymorphism of human constitutive heterochromatin in metaphase chromosome A1

Summary 3 types of human chromosome A1 centromeric heterochromatin stained by Giemsa-C banding technique are described — Type I, Type II and Type III. The Type III heterochromatin block was found in 4 members of one family. This type of heterochromatin can also be shown in prophase and interphase. The centromeric heterochromatin is not stained by fluorochromes.

     

The role of heterochromatin in centromere function

Chromatin at centromeres is distinct from the chromatin in which the remainder of the genome is assembled. Two features consistently distinguish centromeres: the presence of the histone H3 variant CENP-A and, in most organisms, the presence of heterochromatin. In fission yeast, domains of silent "heterochromatin" flank the CENP-A chromatin domain that forms a platform upon which the kinetochore is assembled. Thus, fission yeast centromeres resemble their metazoan counterparts where the kinetochore is embedded in centromeric heterochromatin. The centromeric outer repeat chromatin is underacetylated on histones H3 and H4, and methylated on lysine 9 of histone H3, which provides a binding site for the chromodomain protein Swi6 (orthologue of Heterochromatin Protein 1, HP1). The remarkable demonstration that the assembly of repressive heterochromatin is dependent on the RNA interference machinery provokes many questions about the mechanisms of this process that may be tractable in fission yeast. Heterochromatin ensures that a high density of cohesin is recruited to centromeric regions, but it could have additional roles in centromere architecture and the prevention of merotely, and it might also act as a trigger for kinetochore assembly. In addition, we discuss an epigenetic model for ensuring that CENP-A is targeted and replenished at the kinetochore domain.     

HP1 controls genomic targeting of four novel heterochromatin proteins in Drosophila

Heterochromatin is important for the maintenance of genome stability and regulation of gene expression; yet our knowledge of heterochromatin structure and function is incomplete. We identified four novel Drosophila heterochromatin proteins (HPs). Three of these proteins (HP3, HP4 and HP5) interact directly with HP1, whereas HP6 in turn binds to each of these three proteins. Immunofluorescence microscopy and genome-wide mapping of in vivo binding sites shows that all four proteins are components of heterochromatin. Depletion of HP1 causes redistribution of all four proteins, indicating that HP1 is essential for their heterochromatic targeting. Finally, mutants of HP4 and HP5 are dominant suppressors of position effect variegation, demonstrating their importance in heterochromatic gene silencing. These results indicate that HP1 acts as a docking platform for several mediator proteins that contribute to heterochromatin function.     

Giemsa C-banded karyotypes in Serupius L. (Orchidaceae)

Giemsa C-banding is utilized for the first time to characterize eight taxa of the genus Serapias . Heterochromatin distribution indicated that the Serapias species form a very homogeneous group. All the species possess chromosome pairs with similar heterochromatin patterns. C-banding showed conspicuous bands located around the centromeres, with some het-erochromatic short arms. There was more heterochromatin in S. apulica and S. nurrika than in the other taxa. Extensive centromeric heterochromatin may indicate recent structural rearrangements in the chromosome complement. Taken altogether, karyomorphology indicates a rather recent origin for the genus Serapias , which might also account for the small amount of interspecific variation observed.     

Heterochromatic differentiation in barley chromosomes revealed by C- and N-banding techniques

Summary Heterochromatin distribution in barley chromosomes was investigated by analyzing the C- and N-banding patterns of four cultivars. Enzymatic maceration and air drying were employed for the preparation of the chromosome slides. Although the two banding patterns were generally similar to each other, a clear difference was observed between them at the centromeric sites on all chromosomes. Every centromeric site consisted of N-banding positive and C-banding negative (N⁺ C^–) heterochromatin in every cultivar examined. An intervarietal polymorphism of heterochromatin distribution was confirmed in each of the banding techniques. The appearance frequencies of some bands were different between the two banding techniques and among the cultivars. The heterochromatic differentiation observed is discussed with respect to cause.