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Developmental roles for chromatin and chromosomal structure.

Chromosomal architecture is emerging as a key controlling influence in the developmental regulation of gene expression. Recent genetic experiments using Caenorhabditis elegans, Drosophila melanogaster, and the mouse have provided clear evidence for the functional differentiation of chromosomal structures during development. Chromosomes are visualized as highly specialized entities, within which the activity of particular domains is largely determined by defined structural proteins. At a more local level, the mechanisms regulating gene transcription during early embryogenesis in Xenopus and the mouse have been found to be dependent on the biochemical composition of individual nucleosomes. Thus, variation in the type and modification of chromosomal and chromatin structural proteins provides a dominant means of controlling the transcriptional activity of individual genes, individual chromosomal domains, and of entire chromosomes.

Animals↗

Chromosome structures.

Chromosomes are large subcellular structures, visible in the light microscope, that are found in the nuclei of most eukaryotic cells. Each chromosome consists of a single very long DNA molecule that has been compacted approximately 10,000-fold by interactions with proteins, such that the resulting chromosome structure fits within a typical eukaryotic nucleus of only 10 microns in diameter. Several levels of structural organisation are involved in the formation of chromosomes. Most chromosomal DNA is wrapped in left-handed superhelical turns around protein 'spools', called histone octamers, to form nucleosomes. Arrays of these nucleosomes, or 'beads on a string', are further compacted into solenoidal structures, called 30 nm chromatin fibres. The chromatin fibres are, in turn, compacted approximately 250-fold to form topologically independent 'looped' DNA domains, each loop containing about 20,000-100,000 nucleotide pairs of DNA extending from a proteinaceous central scaffold. Some chromosomes, such as lampbrush and polytene chromosomes, can be seen in certain specialised cells during interphase. Metaphase chromosomes, which can be stained to reveal characteristic banding patterns, are formed in most eukaryotic cells during mitosis. Formation of chromosome structures and the nuclei that envelop them involves discrete steps of nucleosome assembly, scaffold assembly, and nuclear envelope assembly, and can be carried out in cell-free extracts of animal eggs. Centromeres, the regions that mediate attachment of a chromosome to a meiotic or mitotic spindle, and telomeres, the natural ends of chromosomes, are structures that ensure that the correct number of full length chromosomes are maintained during the cell cycle. Most chromosome structures (nucleosomes, chromatin fibres, and scaffold loop domains) form from virtually any DNA sequence, but centromeres and telomeres are both composed of specific DNA sequences complexed with specific binding proteins. Recently, complete DNA sequences of entire chromosomes have been determined, and our rapidly emerging knowledge of chromosome structures is beginning to provide insights into the molecular basis of human disease.

Cell Cycle↗

Stability and asymmetric replication of the Bacillus subtilis 168 chromosome structure.

Chromosomal DNAs from a number of strains derived from Bacillus subtilis 168 were digested with restriction endonucleases NotI or SfiI, and the locations of chromosomal alterations were compared with the recently constructed standard NotI-SfiI restriction map (M. Itaya and T. Tanaka, J. Mol. Biol. 220:631-648, 1991). In general, the chromosome structure of B. subtilis 168 was found to be stable, as expected from the genetic stability of this species. DNA alterations, typically deletions, are formed in three limited loci on the chromosome. One of these alterations was characterized as a spontaneous deletion formed between rrn operons, and another occurred as a result of prophage SP beta excision. I found that oriC and terC are not located on precisely opposite sides of the chromosome. Replication in the counter clockwise direction was 196 kb longer than replication in the clockwise direction. The characteristic of length difference is not changed by deletion formation.

Bacillus Phages↗

Analysis of the differences in structural chromosomal aberrations of the gastric mucosa between H. pylori positive and negative gastric cancer patients: involvement of H. pylori in the onset of gastric cancer and examination of the mechanism in gastric carcinogenesis following H. pylori eradication.

Gene mutations are essential to carcinogenesis. If an evident difference is observed in gastric mucosal chromosomal structure aberrations between H. pylori (Hp)-negative and Hp-positive gastric cancer patients, it may be interpreted as suggesting the involvement of Hp in gene mutations. This study was undertaken to compare chromosomal structural aberrations between Hp-negative and Hp-positive gastric cancer patients and to evaluate the effects of Hp eradication on chromosomal structures in clinical cases. The subjects of this study were 40 patients with gastric cancer divided into four groups: Group A was composed of 12 patients with Hp-negative gastric cancer (well-differentiated gastric cancer in 5 cases and poorly-differentiated in 7 cases), Group B of 8 patients with Hp-negative gastric cancer following Hp eradication (well-differentiated in 4 case and poorly-differentiated in 4 cases), Group C of 13 patients with Hp-positive gastric cancer (well-differentiated in 7 cases and poorly-differentiated in 6 cases) and Group D of 7 patients with gastric cancer (well-differentiated in 5 cases and poorly-differentiated in 2 cases) undergoing Hp eradication at subtotal gastrectomy. In each of the groups A, B and C, the structural chromosomal aberration such as loss of heterozygosity (LOH) and microsatellite instability (MSI) was analyzed. In Group D, changes in structural chromosomal aberrations after Hp eradication as compared to the pre-eradication structures were also analyzed. LOH and MSI were examined by PCR, using DNA extracted from the cancer-affected and intact gastric mucosal tissue specimens from each patient. In A, B and C groups, structural chromosomal aberrations were noted, and these aberrations tended to be more marked in cases of poorly-differentiated gastric cancer in each group. In terms of structural chromosomal aberrations, there was no marked difference between Group A and either Group B or C. Hp eradication resulted in no change in chromosomal structure as compared to the pre-eradication structure in Group D. These results suggest the possibility that Hp eradication does not affect chromosomal structures and Hp is involved in gastric carcinogenesis as an additive environmental factor rather than as a factor acting at the gene level.

Anti-Bacterial Agents↗

Premature chromosome condensation, structural chromosome aberrations, and micronuclei in early mouse embryos after treatment of paternal postmeiotic germ cells with triethylenemelamine: possible mechanisms for chemically induced dominant-lethal mutatiions.

Cytogenetic effects in preimplantation 4-8-cell mouse embryos have been investigated after treating paternal postmeiotic germ cells with triethylenemelamine (TEM). Dose-levels of TEM which do not affect fertilization but yield high incidence of dominant-lethal mutations in sperm and spermatids were shown to produce relatively high frequencies of (a) premature chromosome condensation (PCC), (b) structural chromosome anomalies (breakage-reunion phenomena), and (c) micronuclei in these embryos. The results indicate that genetic death of embryos is mainly due to imbalance (i.e. loss) of genetic material, either from breaks leading to lagging fragments and micronuclei, or from the segregation of various types of exchange figures (dicentrics, rings etc.) resulting in mechanical disturbances of cleavage division. It is suggested that PCC, to some extent, is an expression of TEM-induced long-lived lesions which, transmitted into the egg, prevent the chromosomes in question from replicating and/or condensing normally. This phenomenon could well be associated with loss of chromosome material resulting in embryonic death.

Animals↗

A genetic selection for supercoiling mutants of Escherichia coli reveals proteins implicated in chromosome structure.

Chromosomes are divided into topologically independent regions, called domains, by the action of uncharacterized barriers. With the goal of identifying domain barrier components, we designed a genetic selection for mutants with reduced negative supercoiling of the Escherichia coli chromosome. We employed a strain that contained two chromosomally located reporter genes under the control of a supercoiling-sensitive promoter and used transposon mutagenesis to generate a wide range of mutants. We subjected the selected mutants to a series of secondary screens and identified five proteins as modulators of chromosomal supercoiling in vivo. Three of these proteins: H-NS, Fis and DksA, have clear ties to chromosome biology. The other two proteins, phosphoglucomutase (Pgm) and transketolase (TktA), are enzymes involved in carbohydrate metabolism and have not previously been shown to affect DNA. Deletion of any of the identified genes specifically affected chromosome topology, without affecting plasmid supercoiling. We suggest that at least H-NS, Fis and perhaps TktA assist directly in the supercoiling of domains by forming topological barriers on the E. coli chromosome.

Bacterial Proteins↗

Interplay between recombination, cell division and chromosome structure during chromosome dimer resolution in Escherichia coli.

Chromosome dimers form in bacteria by recombination between circular chromosomes. Resolution of dimers is a highly integrated process involving recombination between dif sites catalysed by the XerCD recombinase, cell division and the integrity of the division septum-associated FtsK protein and the presence of dif inside a restricted region of the chromosome terminus, the dif activity zone (DAZ). We analyse here how these phenomena collaborate. We show that (i) both inter- and intrachromosomal recombination between dif sites are activated by their presence inside the DAZ; (ii) the DAZ-specific activation only occurs in conditions supporting the formation of chromosome dimers; (iii) overexpression of FtsK leads to a general increase in dif recombination irrespective of dif location; (iv) overexpression of FtsK does not improve the ability of dif sites inserted outside the DAZ to resolve chromosome dimers. Our results suggest that the formation of an active XerCD-FtsK-dif complex is restricted to when a dimer is present, the features of chromosome organization that determine the DAZ playing a central role in this control.

Bacterial Proteins↗

The human papillomavirus type 16 E6 and E7 oncoproteins independently induce numerical and structural chromosome instability.

The development of genomic instability is a hallmark of high-risk human papillomavirus (HPV) associated cervical carcinogenesis. We have previously shown that the HPV-16 E7 oncoprotein rapidly subverts mitotic fidelity by inducing abnormal centrosome numbers and multipolar mitotic spindles. Here we report that expression of HPV-16 E6 and E7 independently results in various mitotic abnormalities. HPV-16 E6 and E7 were each associated with unaligned or lagging chromosomal material, indicating relaxation of spindle checkpoint control. Moreover, by overwhelming checkpoint control mechanisms that may prevent cells with multiple spindle poles to enter anaphase, expression of HPV-16 E6 and E7 leads to a small but significant number of cells with altered polarity at later stages of the cell division process. In addition to changes that have the potential to give rise to numerical chromosome imbalances, we discovered that expression of HPV-16 E7 could trigger anaphase bridge formation to an extent similar to that of high-risk HPV E6. Anaphase bridges typically develop after chromosomal breaks and alterations of chromosomal structure. Further investigation of mechanisms by which HPV-16 E6 and E7 contribute to the destabilization of the host cell genome revealed that both high-risk HPV oncoproteins induce DNA damage. Moreover, expression of HPV-16 E7 was associated with an increased number of cells exhibiting nuclear foci of phosphorylated histone H2AX as well as activation of cell cycle checkpoints triggered by DNA repair. Our results therefore suggest that HPV oncoproteins are a source for both numerical and structural chromosome instability during HPV-associated carcinogenesis.

Anaphase↗

[Molecular cytogenetic detection of minute chromosomal structural abnormality on the chromosomal terminal regions].

In order to identify those easily overlooked minute chromosomal structural abnormality on the chromosomal regions, and to provide a valuable guidance for pregnancy, fluorescence in situ hybridization (FISH) technique by whole chromosome 7 painting probe, Xq probe and subterminal probe of 7q36-->qter was performed to analyze two cases. Case 1 had a history of recurrence spontaneous abotion and with an uncertain minute translocation on the chromosomal terminal regions. Case 2 was a premature ovarian failure patient with a balanced translocation between chromosome X and chromosome 7 by G banding. The results showed that case 1 was a cryptic minute translocation on the chromosomal terminal regions, and the breakpoint of case 2 was accurately determined, that is, the breakpoint was not on 7q36 but on 7qter. Therefore FISH technique with whole chromosome painting probe and subterminal probe could be used to diagnose the minute chromosomal structural abnormality on the chromosomal regions. It could be used widely in the clinical genetics and was an effective tool for genetic counseling and reproductive guidance.

Abortion, Habitual↗

A high frequency of structural chromosome abnormalities in a south central texas cytogenetics laboratory.

Abnormalities of chromosome number, such as the autosomal trisomies and sex chromosome aneuploidies, are considered to be sporadic events with low and constant recurrence risk across populations. On the other hand, abnormalities of chromosome structure can be generated by environmental agents and also transmitted in families and therefore may accumulate in certain populations. Evidence from several geographically diverse newborn infant screening studies and from clinical cytogenetics laboratories (including our own) supports the hypothesis that the frequency of structural abnormalities varies among populations, whereas the frequency of numerical abnormalities remains relatively constant among populations. The data from our laboratory, based on 1,201 patients over a 6-year period, suggest a two- to nearly fourfold higher frequency of structural defects over that of other populations (8.8% vs 4.2% and 2.5% of samples tested). Some of the problems associated with making comparisons among the published data sets are discussed, along with alternative explanations for the variability in the frequency of structural defects reported in different populations.

Aneuploidy↗

[Structural chromosome organisation and radiation-induced interchromosomal aberrations].

The quantitative prediction of the biological effects of radiation is one of the actual tasks of radiobiology. The experimental study may be impossible under certain conditions (low doses, complex radiation fields, etc). The development of theoretical tools is required to predict biological and medical consequence of the irradiation of cell and organism. The effect under the consideration in the present paper is chromosome aberrations (CA) induced by low and high LET radiation. One of the most uncertain factors in CA prediction is the impact of chromosomal and nuclear architecture. In the present study the quantitative evaluation of the mechanisms of CA induction are discussed in the framework of the biophysical modelling technique taking into account interphase chromosomes structure in the nucleus of living (human) cell. We show that the surface contacts mechanism of interchromosomal aberrations (interchange) formation does not explain the observed ratio of simple/complex interchanges induced by both low and high LET radiation. The chromatin structure repositioning following irradiation is proposed as a possible mechanism involved in the formation of the complex aberrations.

Cell Nucleus↗

[Antenatal diagnosis of structural chromosome anomalies. 226 cases (author's transl)].

A series of 226 antenatal diagnoses of chromosome structural re-arrangements in 181 couples has shown the usefulness of such diagnosis for couples including a genitor carrying a balanced anomaly. Analysis of the data has elicited major variations in the incidence of unbalanced anomalies in foetal cells and has provided information which can usefully be applied to genetic counselling.

Abortion, Spontaneous↗

[SMC (structural maintenance of chromosomes) structural protein family and their role in chromatin reorganization].

Structural chromatin proteins of the SMC (Structural Maintenance of Chromosomes) family play an important role in structural DNA reorganization in pro- and eukaryotes. Eukaryotic SMC proteins are the core components of the cohesin and condensin complexes. The cohesin complex is responsible for sister chromatid and homolog cohesion in mitosis and meiosis. The condensin complex uses ATP energy to induce positive coiled-coils in DNA, which results in compaction of the latter and formation of mitotic chromosome scaffold. In addition, the SMC proteins constitute recombination and recombination repair complexes. In hermaphrodites of nematode Caenorhabditis elegans, the SMC protein-containing complex controls dosage compensation and inactivation of the X chromosome genes.

Adenosine Triphosphate↗

Complete coding sequence, deduced primary structure, chromosomal localization, and structural analysis of murine aggrecan.

We have isolated and sequenced overlapping cDNA clones encoding the entire core protein of aggrecan (the large aggregating chondroitin sulfate/keratan sulfate proteoglycan of cartilage) from three chondrocyte cDNA libraries of BALB/c mice and localized the aggrecan gene in mouse chromosome 7. We determined 7386 bp of the cDNA sequence, including 132 and 854 nucleotides of 5' and 3' untranslated regions, respectively. The core protein precursor is 2132 amino acids long (M(r) 222,008), including a 19-residue secretory signal peptide. The overall amino acid sequence of the mouse aggrecan shows 91.6% identity to rat and 72.5% to human aggrecan. Comparison of the amino acid sequences of various domains and subdomain structures of mouse aggrecan to known sequences of other species and related proteins (versican, neurocan, link protein, and lymphocyte homing receptor CD44) revealed high levels of identity of the G1, G2, and G3 globular domains and relatively less conserved structures in the interglobular and glycosaminoglycan-attachment regions. Epidermal growth factor (EGF)-like module was detected in only a minor fraction of aggrecan clones, while the complement regulatory protein (CRP)-like domain was regularly expressed in all samples.

Aggrecans↗

Chromosome structure. Coiling up chromosomes.

The mechanism by which eukaryotic chromosomes condense as cells enter mitosis has long been inaccessible to molecular biologists. An important clue has now been provided by a ubiquitous protein family, the SMCs.

Amino Acid Sequence↗