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PubMed2005

Chromatin domain boundaries: insulators and beyond.

The eukaryotic genome is organized into functionally and structurally distinct domains, representing regulatory units for gene expression and chromosome behavior. DNA sequences that mark the border between adjacent domains are the insulators or boundary elements, which are required in maintenance of the function of different domains. Some insulators need others enable to play insulation activity. Chromatin domains are defined by distinct sets of post-translationally modified histones. Recent studies show that these histone modifications are also involved in establishment of sharp chromatin boundaries in order to prevent the spreading of distinct domains. Additionally, in some loci, the high-order chromatin structures for long-range looping interactions also have boundary activities, suggesting a correlation between insulators and chromatin loop domains. In this review, we will discuss recent progress in the field of chromatin domain boundaries.

Animals↗
PubMed1987

Chromatin organization in detergent-lysed chicken erythrocyte nuclei.

A method for electron microscopic demonstration of supranucleosomal (20-30 nm chromatin) fiber loops was developed. Chicken erythrocytes were treated with varying concentrations of detergents, such as Joy, sodium N-lauroyl sarcosinate, and sodium laurylsulfate, and then fixed with a formalin solution. The fixed cells were centrifuged onto an electron microscope grid, followed by staining and metal shadowing. Thin-sectioned specimens of the fixed cells were prepared routinely. Although supranucleosomal fiber loops could be observed when any one of these detergents was used, Joy gave the best result. Electron micrographs of rotary-shadowed specimens of erythrocyte ghosts formed by treatment with a low concentration (0.07-0.11 w/w%) of Joy showed a halolike, radial arrangement of supranucleosomal fiber loops around the ghost cells. The width of the halo was about 3 micron. By increasing the detergent concentration (approximately 8% Joy), nucleosome fibers and naked DNA appeared and increased in number, indicating that the supranucleosomal fibers were disassembled by the action of the detergent. Thin-sectioned specimens of cells treated with 0.09% Joy showed granulofibrillar chromatin radially dispersed from the nuclear cage. The fibers were thought to be identical with the supranucleosomal fibers observed in the rotary-shadowed specimens.

Animals↗
PubMed2001

A model for chromosome structure during the mitotic and meiotic cell cycles.

The chromosome scaffold model in which loops of chromatin are attached to a central, coiled chromosome core (scaffold) is the current paradigm for chromosome structure. Here we present a modified version of the chromosome scaffold model to describe chromosome structure and behavior through the mitotic and meiotic cell cycles. We suggest that a salient feature of chromosome structure is established during DNA replication when sister loops of DNA extend in opposite directions from replication sites on nuclear matrix strands. This orientation is maintained into prophase when the nuclear matrix strand is converted into two closely associated sister chromatid cores with sister DNA loops extending in opposite directions. We propose that chromatid cores are contractile and show, using a physical model, that contraction of cores during late prophase can result in coiled chromatids. Coiling accounts for the majority of chromosome shortening that is needed to separate sister chromatids within the confines of a cell. In early prophase I of meiosis, the orientation of sister DNA loops in opposite directions from axial elements assures that DNA loops interact preferentially with homologous DNA loops rather than with sister DNA loops. In this context, we propose a bar code model for homologous presynaptic chromosome alignment that involves weak paranemic interactions of homologous DNA loops. Opposite orientation of sister loops also suppresses crossing over between sister chromatids in favor of crossing over between homologous non-sister chromatids. After crossing over is completed in pachytene and the synaptonemal complex breaks down in early diplotene (= diffuse stage), new contractile cores are laid down along each chromatid. These chromatid cores are comparable to the chromatid cores in mitotic prophase chromosomes. As an aside, we propose that leptotene through early diplotene represent the 'missing' G2 period of the premeiotic interphase. The new chromosome cores, along with sister chromatid cohesion, stabilize chiasmata. Contraction of cores in late diplotene causes chromosomes to coil in a configuration that encourages subsequent syntelic orientation of sister kinetochores and amphitelic orientation of homologous kinetochore pairs on the spindle at metaphase I.

Chromosomes↗
PubMed1982

Extracentromeric connections between sister chromatids demonstrated in human chromosomes induced to condense asymmetrically.

Extracentromeric chromatin fibers were proposed to hold sister chromatids together in mitotic chromosomes examined by electron microscopy, but their existence in living cells has not been demonstrated yet. We have performed an in vitro BrdU-H33258 treatment which induced a differential rate of condensation to each sister chromatid, thus producing asymmetrically condensing chromosomes. The fast condensing chromatid pulled the slower sister one, both bending in parallel. Bent chromatids appeared reciprocally connected by loops of chromatin fibers, suggesting they were the links which permitted the physical interplay between the differently condensing chromatids. When sister chromatid exchanges (SCE) intercalated a fast-condensing fragment in the slow-condensing chromatid or vice versa, the chromosome inverted its curvature at the SCE-point.

Chromatids↗
PubMed1996

Immunofluorescent analysis of the organization of telomeric DNA sequences and their involvement in chromosomal aberrations in hamster cells.

We have investigated the organization of telomeric TTAGGG)n repeats in the extended DNA loops of chromatin of human and hamster cells by immunofluorescent technique. In humans, telomeric repeats which are predominantly localized at the termini of all the chromosomes, have been found associated with nuclear matrix. This distribution pattern did not alter, even after the removal of 90% of the DNA from the nuclear halos by EcoRI digestion. This suggests that the telomeric sequences are tightly associated with nuclear matrix and hence cannot be solubilized by nucleases. In contrast, in Chinese hamster cells (CHO B11), a major proportion of interstitial telomeric repeats are found in the loop regions, like beads on a string, with attachments to the periphery of the nuclear matrix. Unlike in human cells, EcoRI digestion removed most of the telomeric repeats from the loop regions of Chinese hamster cells. This indicates that intrachromosomal sequences are not associated with nuclear matrix, and this finding has been further substantiated by Southern hybridization of matrix associated and loop DNA fractions of hamster cells with the (TTAGGG)n probe. The organizational differences in the telomeric repeat sequences of Chinese hamster and human cells might be due to their chromosomal location as well as their interaction with nucleoprotein complexes specific for the termini of the eukaryotic chromosomes. Furthermore, the interstitial (TTAGGG)n sequences were found to be more frequently involved in the chromosomal aberrations induced by restriction enzymes. This suggests that the intrachromosomal sites of telomeric sequences behave as hot spots for DNA damage.

Animals↗
PubMedDate not supplied

[Electron-microscopic study of the morphology of scaffold-like structures in chromosomes, formed by formamide].

Isolated human metaphase chromosomes treated with formamide and prepared for electron microscopy by protein monolayer technique have an appearance of loop-shaped chromatin fibers coming off the central scaffold-like structures, such chromosomes having approximately the same histone content as those before treatment. The morphology of scaffold-like structures at different formamide concentrations is described. It is shown that during formamide treatment the protein-protein and/or protein-DNA interactions are weakened because of disruption of hydrogen bonds. However, the intermolecular interactions in the chromosomes allow them to preserve their shape and size. The changes in the structure of formamide-treated chromosomes become readily visible after spreading on the hypophase surface. It is shown that after removal of formamide from the incubation solution by dialysis, chromosomes condense drastically. The data obtained are in good agreement with the loop model of chromosome organization. However they evidence also that the scaffold in the form of a rigid characteristic chromosome structure arises as a result of redistribution and/or aggregation of chromosomal proteins during chromosome preparation.

Cell Line↗
PubMed2000

Specification of chromatin domains and regulation of replication and transcription during development.

It is becoming increasingly clear that transcription control is carried out at several interconnecting levels. Besides nucleosomal organization and interaction between transcription factors and gene promoters and other regulatory elements, long-range organization of chromatin in loops or domains seems to play a role in transcriptional regulation. A similar organization is likely to be crucial in the control of the timing and selection of origins of DNA replication. This review considers the implications of domain organization of eukaryotic genome in developmental control of transcription and replication.

Animals↗
PubMed1996

Scanning electron microscopy of C-banding.

The mechanism of C-banding was analyzed on the basis of the structural changes of the 30 nm chromatin fibre using scanning electron microscopy (SEM). SEM of non-banded metaphase spreads of L-cells revealed chromosomes consisting of 30 nm chromatin fibre loops along the entire length. No marked difference in both the dimension and appearance of such looped structures was discernible between the centromeric region and the rest of the chromosome. In contrast, C-banded chromosomes exhibited a conspicuous alteration of the fibre conformation in the centromeric region. The looped, fibrous structures were almost completely lost from this region, while the non-centromeric region still exhibited fibrous structures with slightly different appearances compared with those observed in the control chromosomes. On the other hand, results obtained using fluorescence microscopy showed that more DNA retained in the centromeric region than in the non-centromeric region. Since the analytical experiments exhibited that the characteristic collapsed state of the centromeric region occurred only with the alkali treatment but neither with the 2 x SSC nor acid treatments, the centromeric heterochromatin seemed to contain some specific protein which should be sensitive to alkali. The structurally collapsed but subsequently compact centromeric region may become more, or still, resistant to the DNA extraction due to the 2 x SSC treatment and the centromeric chromatin thus retained may be visualized as the C-band.

Animals↗
PubMed1992

Homeotic protein binding sites, origins of replication, and nuclear matrix anchorage sites share the ATTA and ATTTA motifs.

Nuclear matrix organizes the mammalian chromatin into loops. This is achieved by binding of nuclear matrix proteins to characteristic DNA landmarks in introns as well as proximal and distal sites flanking the 5' and 3' ends of genes. Matrix anchorage sites (MARs), origins of replication (ORIs), and homeotic protein binding sites share common DNA sequence motifs. In particular, the ATTA and ATTTA motifs, which constitute the core elements recognized by the homeobox domain from species as divergent as flies and humans, are frequently occurring in the matrix attachment sites of several genes. The human apolipoprotein B 3' MAR and a stretch of the Chinese hamster DHFR gene intron and human HPRT gene intron shown to anchor these genes to the nuclear matrix are mosaics of ATTA and ATTTA motifs. Several origins of replication also share these elements. This observation suggests that homeotic proteins which control the expression level of many genes and pattern formation during development are components of the nuclear matrix. Thus, the nuclear matrix, known as the site of DNA replication, might sculpture the crossroads of the differential activation of origins during development and S-phase and the control of gene expression and pattern formation in embryogenesis.

Animals↗
PubMed1981

Insights on diplochromosome structure and behaviour.

Diplochromosomes from colchicine-induced endoreduplicated HeLa cells were analyzed by light and electron microscopy. The patterns of C-, G-, NOR-, and late replicating DNA-rich bands obtained clearly indicate that the four chromatids constituting a diplochromosome are structurally identical and behave the same, at least in terms of replication kinetics and r-DNA transcription. Under the electron microscope, whole-mounted diplochromosomes appeared formed by two completely divided chromosomes showing no physical connection at their centromeric regions. The two chromosomes forming a diplochromosome seem to be held together by chromatin fiber loops connecting the two neighbouring chromatids of the sister chromosomes. These connecting loops clearly decrease in number as chromosome condensation progresses.

Bromodeoxyuridine↗
PubMed2005

Chromosome structure: improved immunolabeling for electron microscopy.

To structurally dissect mitotic chromosomes, we aim to position along the folded chromatin fiber proteins involved in long-range order, such as topoisomerase IIalpha (topoIIalpha) and condensin. Immuno-electron microscopy (EM) of thin-sectioned chromosomes is the method of choice toward this goal. A much-improved immunoprocedure that avoids problems associated with aldehyde fixation, such as chemical translinking and networking of chromatin fibers, is reported here. We show that ultraviolet irradiation of isolated nuclei or chromosomes facilitates high-level specific immunostaining, as established by fluorescence microscopy with a variety of antibodies and especially by immuno-EM. Ultrastructural localizations of topoIIalpha and condensin I component hBarren (hBar; hCAP-H) in mitotic chromosomes were studied by immuno-EM. We show that the micrographs of thin-sectioned chromosomes map topoIIalpha and hBar to the center of the chromosomal body where the chromatin fibers generally converge. This localization is defined by many clustered gold particles with only rare individual particles in the peripheral halo. The data obtained are consistent with the view that condensin and perhaps topoIIalpha tether chromatin to loops according to a scaffolding-type model.

Antigens, Neoplasm↗
PubMed1995

The architectural organization of nuclear metabolism.

Nucleic acid metabolism is structurally organized in the nucleus. DNA replication and transcription have been localized to particular nuclear domains. Additional domains have been identified by their morphology or by their composition; for example, by their high concentration of factors involved in RNA splicing. The domain organization of the nucleus is maintained by the nuclear matrix, a nonchromatin nuclear scaffolding that holds most nuclear RNA and organizes chromatin into loops. The nuclear matrix is built on a network of highly branched core filaments that have an average diameter of 10 nm. Many of the intermediates and the regulatory and catalytic factors of nucleic acid metabolism are retained in nuclear matrix preparations, suggesting that nucleic acid synthesis and processing are structure-bound processes in cells. Tissue-specific and malignancy-induced variations in nuclear structure and metabolism may result from altered matrix architecture and composition.

Animals↗
PubMed1999

Competence for assembly of sister chromatid cores is progressively acquired during S phase in mammalian cells.

Condensed sister chromatids possess a protein scaffold or axial core to which loops of chromatin are attached. The sister cores are believed to be dynamic frameworks that function in the organization and condensation of chromatids. Chromosome structural proteins are implicated in the establishment of sister chromatid cohesion and in the maintenance of epigenetic phenomena. Both processes of templating are tightly linked to DNA replication itself. It is a question whether the structural basis of sister chromatid cores is templated during S phase. As cells proceed through the cell cycle, chromatid cores undergo changes in their protein composition. Cytologically, cores are first visualized at the start of prometaphase. Still, core assembly can be induced in G1 and G2 when interphase cells are fused with mitotic cells. In this study, we asked if chromatid cores are similarly able to assemble in S-phase cells. We find that the ability to assemble cores is transiently lost during local replication, then regained in chromosome regions shortly after they have been replicated. We propose that core templating occurs coincident with DNA replication and that the competence for the assembly of the sister chromatid cores is acquired shortly after passage of replication forks.

Animals↗
PubMedDate not supplied

[Structure and function of nuclear matrix associated regions (S/MARs)].

Modern concepts on the chromatin loop-domain organization and the role of the DNA regions specifically binding the nuclear matrix (nuclear scaffold, or S/MARs) in its formation, maintenance, and regulation are discussed. Some S/MAR structural features, properties of binding the nuclear matrix, and probable mechanisms of their involvement in regulation of gene activity are considered. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2004, vol. 30, no. 1; see also http://www.maik.ru.

Amino Acid Sequence↗
PubMed2003

Smad4 and beta-catenin co-activators functionally interact with lymphoid-enhancing factor to regulate graded expression of Msx2.

Recent in vivo evidence suggests that Wnt signaling plays a central role in determining the fate of stem cells in the ectoderm and in the neural crest by modulating bone morphogenetic protein (BMP) levels, which, in turn, influence Msx gene expression. However, the molecular mechanism regulating the expression of the Msx genes as key regulators of cell fate has not been elucidated. Here we show in murine embryonic stem cells that BMP-dependent activation of Msx2 is mediated via the cooperative binding of Smad4 at two Smad binding elements and of lymphoid enhancing factor (Lef1) at two Lef1/TCF binding sites. Lef1 can synergize with Smad4 and Smad1 to activate Msx2 promoter, and this transcriptional complex is assembled on the endogenous promoter in response to BMP2. The Wnt/beta-catenin signaling pathway can activate Msx2 via the binding of Lef1 to its promoter and synergizes with BMP2 to activate Msx2 expression, possibly via enhanced recruitment of the p300/cAMP-response element-binding protein-binding protein co-factor. Interestingly, the Wnt/beta-catenin-dependent activation of Msx2 was defective in Smad4-deficient embryonic stem cells or when Smad binding elements were mutated but persisted in the presence of various BMP antagonists, indicating that Smad4 was involved in transducing the Wnt/beta-catenin signals in the absence of a BMP autocrine loop. A chromatin immunoprecipitation analysis revealed that endogenous Smad4, but not Smad1, was part of the Lef1 transcriptional complex in response to beta-catenin activation, dismissing any implication of BMP signaling in this response. We propose that Wnt signaling pathway could dictate cell fate not only by modulating BMP levels but also by directly regulating cooperatively BMP-target genes.

Animals↗
PubMed1998

The signal model: a possible explanation for the conversion of DNA double-strand breaks into chromatid breaks.

PURPOSE: To present and evaluate the 'signal' model for the formation of radiation-induced chromatid breaks. CONCLUSIONS: Chromatid breaks in human cells represent the apparent interstitial loss of up to about 40 Mbp of DNA, difficult to account for as single lesions under the classical 'breakage-and-reunion' hypothesis. If breakage-first resulted from two interacting DNA double-strand breaks (dsb) with the loss or displacement of the intervening fragment, a dose-squared relationship would be predicted for chromatid breaks. However, the relationship between chromatid break frequency and dose for human cells is linear. The alternative 'exchange' model of Revell is based on the principle of the interaction of two initiating lesions, thus also predicting a dose-squared relationship for chromatid 'breaks'. The signal model explains the conversion of dsb into chromatid breaks on the assumption that a single dsb generates a signal which triggers the cell to initiate a recombinational exchange involving a large loop of chromatin. Incomplete exchanges would be observed as chromatid breaks. Possible candidates for the signalling molecule(s) are DNA protein kinase (DNA PK) and the ATM protein.

Animals↗
PubMed1995

A postprophase topoisomerase II-dependent chromatid core separation step in the formation of metaphase chromosomes.

Metaphase chromatids are believed to consist of loops of chromatin anchored to a central scaffold, of which a major component is the decatenatory enzyme DNA topoisomerase II. Silver impregnation selectively stains an axial element of metaphase and anaphase chromatids; but we find that in earlier stages of mitosis, silver staining reveals an initially single, folded midline structure, which separates at prometaphase to form two chromatid axes. Inhibition of topoisomerase II prevents this separation, and also prevents the contraction of chromatids that occurs when metaphase is arrested. Immunolocalization of topoisomerase II alpha reveals chromatid cores analogous to those seen with silver staining. We conclude that the chromatid cores in early mitosis form a single structure, constrained by DNA catenations, which must separate before metaphase chromatids can be resolved.

Animals↗
PubMed1997

The yeast Red1 protein localizes to the cores of meiotic chromosomes.

Mutants in the meiosis-specific RED1 gene of S. cerevisiae fail to make any synaptonemal complex (SC) or any obvious precursors to the SC. Using antibodies that specifically recognize the Red1 protein, Red1 has been localized along meiotic pachytene chromosomes. Red1 also localizes to the unsynapsed axial elements present in a zip1 mutant, suggesting that Red1 is a component of the lateral elements of mature SCs. Anti-Red1 staining is confined to the cores of meiotic chromosomes and is not associated with the loops of chromatin that lie outside the SC. Analysis of the spo11 mutant demonstrates that Red1 localization does not depend upon meiotic recombination. The localization of Red1 has been compared with two other meiosis-specific components of chromosomes, Hop1 and Zip1; Zip1 serves as a marker for synapsed chromosomes. Double labeling of wild-type meiotic chromosomes with anti-Zip1 and anti-Red1 antibodies demonstrates that Red1 localizes to chromosomes both before and during pachytene. Double labeling with anti-Hop1 and anti-Red1 antibodies reveals that Hop1 protein localizes only in areas that also contain Red1, and studies of Hop1 localization in a red1 null mutant demonstrate that Hop1 localization depends on Red1 function. These observations are consistent with previous genetic studies suggesting that Red1 and Hop1 directly interact. There is little or no Hop1 protein on pachytene chromosomes or in synapsed chromosomal regions.

Cell Nucleolus↗