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Methylation dynamics, epigenetic fidelity and X chromosome structure.

DNA methylation of the X chromosome is reviewed and discussed, with emphasis on the partial methylation seen in the mouse X-linked Pgk1 promoter region. A new study of partial methylation is presented in which the methylation of CpG site H3 in the mouse Igf2 upstream region was quantitatively measured during growth of subcloned cells in tissue culture. Before subcloning the average methylation level was 50%. After subcloning, methylation was highly variable in early stage clones. With continued passage, clones initially having high methylation lost methylation, whereas clones initially having low methylation gained methylation. By about the 25th generation, all clones had returned to a steady-state methylation level of 50%. These findings are discussed in the context of epigenetic mechanisms and epigenetic fidelity. Interpretation of the results is made according to a model that assumes stochastic methylation and demethylation, with rate parameters influenced by local chromatin structure. A second type of study is reported in which we have measured chromatin accessibility differences between the active X chromosome (Xa) and the inactive X chromosome (Xi). We found that Xa/Xi differences in accessibility to DNase I are surprisingly labile. Relatively infrequent DNA nicks rapidly eliminate differential accessibility.

Animals↗

Relation of chromosome structure and gene expression.

We have been able to map specific DNA fragments at the bases of chromatin loops with the help of a novel extraction procedure by using lithium-3',5'-diiodosalicylate. One such scaffold-attached region (SAR) is found in the non-transcribed spacer in each repeat of the histone gene cluster, on a 657 base pair (b.p.) restriction fragment. Exonuclease III digestion has localized two protein-binding domains on the SAR of the histone cluster. Each covers approximately 200 b.p. and they are separated by a nuclease-accessible region of about 100 b.p. These domains are rich in sequences closely related to the topoisomerase II cleavage consensus. We have studied the scaffold association of three developmentally regulated genes of Drosophila melanogaster: alcohol dehydrogenase (Adh), the homoeotic gene fushi tarazu (ftz) and Sgs-4, a gene encoding one of the glue proteins secreted by third-instar larvae. We find regions attached to the nuclear scaffold (SARS) both 5' and 3' of all three genes, defining small domains ranging from 4.5 to 13 kilobases. In the case of Adh, a gene with two promoters, we find two upstream and two downstream SARS. Those 5' of the gene co-map with regulatory regions for the adult and the larval transcripts, respectively. For Sgs-4, the 5' SAR covers 866 b.p. immediately upstream of the transcript, and encompasses the 200 b.p. regulatory region defined by two deletion mutants that produce little or no Sgs-4 protein. In ftz the 5' SAR is found 4.8 kilobases upstream of the start of transcription within a 2.5 kilobase element required for a high level of ftz expression in the early embryo. Sequence analysis of five upstream SARS reveals clusters of sequences closely related to the cleavage consensus of topoisomerase II. In addition, they contain multiple copies of two sequence motifs: a specific 10 b.p. A-rich sequence, and another 10 b.p. T-rich stretch. In conclusion, the intimate association of the SAR with the upstream/enhancer elements, the presence of clustered sequences highly homologous to the topoisomerase II cleavage consensus, and the localization of topoisomerase II in the scaffold, suggest a structure-function relation between chromosome organization and gene expression.

Animals↗

[Chromosomal structures of Pseudomonas testosteroni. I. Isolation and characterization of the chromosomal complexes. (author's transl)].

After lysis of Pseydomonas testosteroni with lysozyme and non-ionic detergents different DNA-protein complexes can be separated in 5-25% (w/v) neutral sucrose gradient. The protein to DNA ratio of these complexes varies between 0.5-4.5 to 1, whereby the faster sedimenting forms contain more protein than the slower sedimenting ones. Different initial rates of DNase digestion may indicate various degrees of DNA packing in these complexes. The chromosomal complexes of Pseudomonas testosteroni are relatively stable towards pronase. Treatment with RNase or sodium dodecylsulphate is accompanied by a dramatic increase in viscosity and decrease in relative density. It suggests that DNA in these complexes is maintained in its supercoiled form by RNA molecule(s) in a similar way as in isolated chromosome of E. coli.

Chromosomes, Bacterial↗

[Frequency of structural chromosome aberrations in the hepatocytes of rats exposed to polymeric 239Pu].

Intravenous injection of polymeric 239Pu(IV) nitrate (166.5, 55.5 and 18.5 kBq/kg body mass) to Wistar rats was shown to produce biphase changes in the frequency of hepatocyte chromosome aberrations. The increase in the structural damages to chromosomes at later times of observation was a pronounced function of radiation dose. The absence of such a dependence at early times was evidently due to the elimination of damaged liver parenchyma cells.

Animals↗

Phosphorylation of non-histone proteins in the regulation of chromosome structure and function.

Non-histone chromosomal proteins are phosphorylated and dephosphorylated within the intact nucleus by two independent sets of reactions, a protein kinase reaction which transfers the terminal phosphate group of a variety of nucleoside and deoxynucleoside triphosphates to serine and threonine residues in the proteins, and a phosphatase reaction which cleaves these phosphoserine and phosphothreonine bonds and releases inorganic phosphate. Several lines of evidence are consistent with the hypothesis that the phosphorylation and dephosphorylation of these proteins is involved in gene control mechanisms, including the findings that phosphorylated non-histone proteins are highly heterogeneous and their phosphorylation patterns are tissue specific, changes in their phosphorylation correlate with changes in chromatin structure and gene acticity, addition of phosphorylated non-histone proteins increases RNA synthesis in vitro. and phosphorylated non-histone proteins bind specifically to DNA. Cyclic AMP has both stimulatory and inhibitory properties on non-histone protein phosphorylation, depending on the enzyme fraction and substrate employed A specific protein component whose phosphorylation is inhibited by cyclic AMP has been found to be associated with RNA polymerase. The cyclic AMP-induced decrease in the phosphorylation of this protein correlates with an enhancement of RNA synthesis in vitro. These results suggest that both phosphorylation and dephosphorylation of chromatin-associated proteins may be involved in the control of gene readout.

Animals↗

Paternally inherited chromosomal structural aberrations detected in mouse first-cleavage zygote metaphases by multicolour fluorescence in situ hybridization painting.

We describe a fluorescence in situ hybridization (FISH) procedure for assessing zygotic risk of paternal exposure to endogenous or exogenous agents. The procedure employs multicolour FISH with chromosome-specific DNA painting probes plus DAPI staining for detecting both balanced and unbalanced chromosomal aberrations in mouse first-cleavage (1-Cl) zygote metaphases. Four composite probes specific for chromosomes 1, 2, 3 or X, each labelled with biotin, plus a composite probe specific for chromosome Y labelled with digoxigenin, were used. We applied this method to evaluate the effects of paternal exposure to acrylamide, a model germ cell clastogen. First-cleavage zygote metaphases, collected from untreated females mated to males whose sperm or late spermatids were treated with acrylamide, were scored for the induction of structural aberrations using both chromosome painting (PAINT analysis) and DAPI analysis. Structural chromosomal aberrations were observed in the sperm-derived, but not in the egg-derived, pronuclei. While 59.4% of the zygotes had structural aberrations by DAPI analysis, 94.1% of the same zygotes had structural aberrations by PAINT analysis (P < 0.001), illustrating the increased sensitivity for detecting translocations and insertions obtained by adding chromosome painting. These findings show that FISH painting of mouse 1-Cl zygotes when used in conjunction with DAPI analysis is a powerful model for investigating the cytogenetic defects transmitted from father to offspring.

Animals↗

Chromosomes with two intact axial cores are induced by G2 checkpoint override: evidence that DNA decatenation is not required to template the chromosome structure.

Here we report that DNA decatenation is not a physical requirement for the formation of mammalian chromosomes containing a two-armed chromosome scaffold. 2-aminopurine override of G2 arrest imposed by VM-26 or ICRF-193, which inhibit topoisomerase II (topo II)-dependent DNA decatenation, results in the activation of p34cdc2 kinase and entry into mitosis. After override of a VM-26-dependent checkpoint, morphologically normal compact chromosomes form with paired axial cores containing topo II and ScII. Despite its capacity to form chromosomes of normal appearance, the chromatin remains covalently complexed with topo II at continuous levels during G2 arrest with VM-26. Override of an ICRF-193 block, which inhibits topo II-dependent decatenation at an earlier step than VM-26, also generates chromosomes with two distinct, but elongated, parallel arms containing topo II and ScII. These data demonstrate that DNA decatenation is required to pass a G2 checkpoint, but not to restructure chromatin for chromosome formation. We propose that the chromosome core structure is templated during interphase, before DNA decatenation, and that condensation of the two-armed chromosome scaffold can therefore occur independently of the formation of two intact and separate DNA helices.

2-Aminopurine↗

A three-dimensional approach to mitotic chromosome structure: evidence for a complex hierarchical organization.

We describe findings on the architecture of Drosophila melanogaster mitotic chromosomes, made using a three-dimensional-oriented structural approach. Using high-voltage and conventional transmission electron microscopy combined with axial tomography and digital contrast-enhancement techniques, we have for the first time visualized significant structural detail within minimally perturbed mitotic chromosomes. Chromosomes prepared by several different preparative procedures showed a consistent size hierarchy of discrete chromatin structural domains with cross-sectional diameters of 120, 240, 400-500, and 800-1,000 A. In fully condensed, metaphase-arrested chromosomes, there is evidence for even larger-scale structural organization in the range of 1,300-3,000-A size. The observed intrachromosomal arrangements of these higher-order structural domains show that both the radial loop and sequential helical coiling models of chromosome structure are over-simplifications of the true situation. Finally, our results suggest that the pathway of chromatin condensation through mitosis consists of concurrent changes occurring at several levels of chromatin organization, rather than a strictly sequential folding process.

Animals↗

The kinetochore of mammalian chromosomes: structure and function in normal mitosis and aneuploidy.

The kinetochore is a structurally differentiated site on mitotic chromosomes to which spindle microtubules (MTs) are attached. In mammalian cells, the kinetochore is organized into a trilamellar plate and is morphologically distinct from the centromere. Although kinetochores and centromeres are morphologically and biochemically distinct regions, they are functionally linked and necessary for normal chromosome movement and segregation. Recent biochemical and immunocytochemical studies suggest that the kinetochore is composed of several polypeptides, DNA, and possibly RNA. The kinetochore plates are composed of tubulin and two antigens of 17 Kd and 80 Kd, as detected by scleroderma CREST antiserum. Colcemid, a MT inhibitor, also causes reversible rearrangements of kinetochore structure. Mitomycin C binds to heterochromatin and causes the trilamellar plates to become detached from the chromosome. Diethylstilbestrol (DES), a synthetic estrogen, inhibits mitosis in mammalian cells and causes chromosome lagging or malorientation during recovery. Electron microscopy indicates that DES causes disruption of the mitotic spindle, centriole elongation, and unusual chromosome associations due to interkinetochore microtubules. No apparent damage to kinetochores was noted in lagging or maloriented chromosomes.

Aneuploidy↗

Report of the committee on structural chromosome changes in neoplasia.

An enormous amount of data on neoplasia-associated chromosome aberrations has accumulated over the past two years. More than 4,000 tumors with a chromosome anomaly identified by banding have been published since HGM9, and the total number of cases contained in the registry on which the Catalog of Chromosome Aberrations in Cancer (Mitelman, 1988) is based is now well above 12,000. The information presently available is, however, still in many respects incomplete. First, the data is heavily biased in favor of hematologic disorders. Solid tumors comprise only 20% of the total data base, which is totally disproportionate to the relative contribution of these disorders to human cancer morbidity and mortality. For example, malignant epithelial tumors (carcinomas), which cause almost 80% of all cancer deaths in man, comprise only 7% of the total. Second, our knowledge about early stage tumors is very limited. For example, the great majority of the solid tumors that have been studied cytogenetically have been metastatic lesions or effusions (advanced tumors usually have a large number of complex structural and numerical chromosome aberrations). Obviously, many more such neoplasms will have to be studied before the primary (pathogenetically essential) changes can be distinguished from the confusing variety of secondary abnormalities that may dominate the karyotype. It should be noted that secondary changes may also be nonrandom, and may be important for tumor progression. Therefore, no attempt has been made in this report to distinguish between primary and secondary changes. All nonrandomly occurring abnormalities that met the criteria for inclusion are listed in Table 1 irrespective of their presumed pathogenetic significance. Results of molecular genetic studies (e.g. the demonstration of loss of heterozygosity or gene amplification) were not considered, although they may be included in the HGM10.5 report. A total of 149 nonrandom chromosome changes were identified (Table 1) in 43 different types of neoplastic disorders, including hematologic diseases and malignant lymphomas, as well as tumors of epithelial, mesenchymal, neurogenic, germ cell, and melanocytic origin. The aberrations comprise a variety of structural chromosome rearrangements (translocations, inversions, insertions, deletions, duplications and isochromosomes), and all chromosomes, except the Y chromosome are involved. The great majority (121 of the 149 identified aberrations) represent well-defined, specific structural changes. More than half of them are consistently associated with a particular morphologic disease characteristic. Twenty-eight of the aberrations, although nonrandom, are not characterized as well. Most are deletions or translocations that only affect a certain chromosome region, often spanning several bands.(ABSTRACT TRUNCATED AT 400 WORDS)

Chromosome Aberrations↗

A chromomeric model for nuclear and chromosome structure.

The basic structural elements of chromatin and chromosomes are reviewed. Then a model involving only three architectural motifs, nucleosomes, chromatin loops and transcription factories/chromomeres, is presented. Loops are tied through transcription factors and RNA polymerases to factories during interphase and to the remnants of those factories, chromomeres, during mitosis. On entry into mitosis, increased adhesiveness between nucleosomes and between factories drives a 'sticky-end' aggregation to the most compact and stable structure, a cylinder of nucleosomes around an axial chromomeric core.

Cell Nucleolus↗

Human cells in suspension. 1 Human lymphoid and granulopoietic cells in primary and secondary cultures: effects of in vitro induction and prolonged methanol acetic acid fixation on metaphase chromosome structure.

Modifications of Hungerford's method (1965) for production of chromosomal slides from human lymphoid cells in culture have been developed. Modified in vitro induction of banding and uncoiling has been used to produce chromosomal slides from human neoplastic cells of granulopoietic origin. The chromosomes are well spread and appear either long, thin and segmented or uncoiled. It is suggested that it is the combined action of the prolonged fixation used, and the in vitro induction, which leads to the observed structural alteration of the chromosomes. A method for increasing the yield of metaphase cells when working with bone marrow has been developed on the basis of culturing the granulopoietic cells in medium containing colony stimulating factor (CSF). Comparative analysis of metaphases from primary and secondary cultures of bone marrow cells showed that the culturing conditions for the secondary cultures do not induce chromosome abnormalities in the cells during the growth period.

Acetates↗