Natural size classes in DNA from Chinese hamster metaphase chromosomes

DNA from isolated Chinese hamster ovary (CHO) metaphase chromosomes can be obtained in three different molecular weight classes. The two largest forms have sedimentation coefficients of 80 and 120 S at 7,500 rpm. Based on sedimentation and speed dependence analysis these have molecular weights of 220 million and above 5,000 million, and are thought to be analogs of DNA classes observed in a prior study of human metaphase chromosomes. An extract can be converted to primarily the 80 S form through alkaline pH treatment of metaphase DNA. The third class (45 S DNA) is formed as a result of metaphase chromosome exposure to the nuclease Bal31, and has a mass distribution analogous to the CHO replicon.     

The DNA content of Chinese hamster meiotic metaphase chromosomes

DNA values of Chinese hamster male meiotic metaphase chromosomes were measured by slide-based Feulgen cytometry. All the autosomes were distinguishable on the basis of their DNA content. No significant differences were found between the autosomes of the two male animals studied, but a significant difference was found in the DNA content of the sex-chromosome pair between these two animals.     

Chinese hamster metaphase chromosomes isolated under physiological conditions. A partial characterization of associated non-histone proteins and protein cores

In a previous report [2] we have described a non-histone protein core which could be isolated from Chinese hamster metaphase chromosomes. This core structure maintained the overall morphology of the metaphase chromosome even after removal of all of the histones, together with many of the non-histone proteins and the bulk of the DNA. As part of our work on the characterization of these core structures, we have developed a novel procedure for the isolation of metaphase chromosomes which avoids the use of high pH buffers and hexylene glycol, as well as eliminating the numerous centrifugation and resuspension steps previously employed. Chromosome cores prepared by 2 M NaCl extraction and DNase I digestion from metaphase chromosomes isolated under these more gentle, quasi-physiological conditions, are shown to contain a relatively simple subset of non-histone proteins. One-dimensional SDS-polyacrylamide gel electrophoresis shows two major groups of polypeptides having molecular weights 48 000-52 000 and 65 000-72 000 D respectively, with similarities in mobilities to the nuclear pore complex-lamina polypeptides and tubulins. However, more detailed analysis by two-dimensional gel electrophoresis and peptide mapping has failed to detect these proteins. A 52 000 D polypeptide component of the core is tentatively identified as the intermediate filament protein vimentin. The in vivo significance of chromosome cores is discussed.     

Isolated metaphase chromosomes. II. Proteins of Chinese hamster chromosomes.

The proteins on metaphase chromosomes theoretically may be distributed ubiquitously throughout the karyotype, may be present uniquely on individual chromosomes or classes of chromosomes, or may exist in any combination of the above. Separation of chromosomes according to size using sucrose velocity gradients in high capacity zonal centrifuge rotors allows sufficient fractionation of the genome to indicate the distribution of proteins within the karyotype. Flow cytometric analysis and direct microscopic analysis were used to evaluate qualitatively the types of chromosomes present in the fractions obtained. This report is the first quantitative evidence that some of the chromosomal proteins are not distributed ubiquitously on all of the chromosomes of the karyotype.     

S1 nuclease removes DNA from eukaryotic metaphase chromosomes: cytological evidence

Fixed and unfixed human chromosomes, as well as fixed rye chromosomes were treated with S1 nuclease, which specifically cleaves single stranded DNA. Subsequent staining with either acridine orange, ethidium bromide or Giemsa revealed that, contrary to what has previously been reported, S1 digestion extensively altered chromosomal morphology and staining intensity, although the alteration was more pronounced in fixed as compared to unfixed metaphases. A number of mechanisms, which may account for our findings, have been invoked: a) the presence in metaphase chromatin of B-DNA/Z-DNA transitional junctions, b) the induction, by alcohol: acid fixation procedure, of nicks within regular B-DNA conformation and c) the induction of sites available to S1 by torsional stress due to metaphase high condensation degree.     

Distribution of UV-induced unscheduled DNA synthesis in metaphase chromosomes of Chinese hamster cells

Unscheduled DNA synthesis (USD) occurred in metaphase chromosomes of cultured Chinese hamster cells after ultraviolet light (UV) irradiation. When the chromosomes were labeled by UV-induced USD in metaphase, the number of grains was in proportion to the amount of chromosomal DNA and the grain densities were approximately equal all over the segments of chromosomes.     

Chromosome bands and the subunit structure of Chinese hamster metaphase chromosomes

Isolated Chinese hamster chromosomes dissociate into a series of specific chromatin subunits approximately the size of stainable chromosome bands upon reduction of the divalent ion concentration during or after isolation. At high pH the chromatin in some bands is differentially removable during chromosome isolation, leaving a banded chromosome with a pattern typical of most G-band procedures. This provides an alternate molecular mechanism to explain the production of banded chromosomes by a variety of staining procedures. These results also suggest an approach to chromatin fractionation, using metaphase chromosomes as a starting material.     

DNA fragments of 300 base pairs released from metaphase chromosomes by digestion with deoxyribonuclease I

DNase I digestion of metaphase chromosomes, that have been extensively digested with Hae III, further released chromosomal DNA and proteins; 3.3% and 10.8% of the chromosomal DNA and proteins, respectively, remained insoluble. However, digestion of chromosomes first with DNase I followed by Hae III caused most of the proteins to remain in the insoluble fraction. DNase I released DNA fragments of 300 base pairs long which were not released by Hae III digestion. These DNA fragments may be protected by protein components from further fragmentation by DNase I.     

Dansyl chloride-stained nucleolar organizers and core-like structures in Chinese hamster metaphase chromosomes

When chromosomes containing both BrdU-substituted and unsubstituted regions were treated with hot NaH₂PO₄ at high or low pH and then stained with dansyl chloride, brightly fluorescent nucleolar organizer regions (NORs) and core-like structures were apparent in the chromosomes. These structures closely parallel the appearance of the same structures in silver-stained chromosomes. Since dansyl chloride is a protein-specific fluorochrome, the distribution of fluorescence suggests that the NORs and central zone of each chromatid contain higher concentrations of protein relative to other chromosome regions. The fluorescent core structures are interpreted to be artefacts of the NaH₂PO₄ pretreatment induced by changes in the concentration of chromatin (including protein) between the chromatin-dense center and more dispersed peripheral region of each chromatid.     

Nomenclature of the metaphase chromosomes of the djungarian hamster

The proposed nomenclature of G-banded chromosomes of Phodopus sungorus campbelli is based on requisites and principles of the International System for Human Cytogenetic Nomenclature (ISCN).     

Identification of isolated metaphase chromosomes. II. A comparison with the recognizability of chromosomes in metaphase plates

The metaphase chromosomes (MC) isolated from the Chinese hamster cells were identified with the aid of differential staining (G-bands). It was shown that differences in the relative recognizability of MC in metaphase plates and after their isolation are determined by changes in composition of isolated MC, rather than by those in staining capacity of MC after their isolation. The frequencies of identified MC are constant and independent upon the type of MC preparations and relation between identified and unidentified MC in certain preparations. At allows to apply the described method for the analysis of chromosome fractionation, using changes in frequencies of identified MC as a criterion of efficiency of the fractionation method. Possible ways of increasing the recognizability level of isolated MC are discussed.     

Fractionation and initial characterization of the kinetochore from mammalian metaphase chromosomes

We have partially isolated the kinetochore and associated centromeric structures from mammalian metaphase chromosomes. Human autoantibodies from scleroderma CREST (calcinosis, Raynaud's phenomenon, esophageal dysmotility, sclerodactyly, telangiectasia) patients were used as immunofluorescent probes to monitor fractionation. The procedure includes digestion of total chromosomal DNA with micrococcal nuclease, dehistonization with heparin, and dissociation of the remaining material with detergent and urea. We used a density gradient (metrizamide) to obtain an enriched fraction of stained material (kinetochore). When examined by electron microscopy, the kinetochore fraction is seen to contain numerous small immunoperoxidase-positive masses which are morphologically similar to the centromere/kinetochore region of intact metaphase chromosomes. The particulate fraction that contains kinetochore components represents less than 5% of total chromosomal proteins and contains less than 1% of total DNA. Two polypeptides of 18 and 80 kD were identified as kinetochore antigens by immunoblotting with CREST antiserum. In this paper we discuss the distribution of these kinetochore polypeptides with the associated centromeric chromatin.     

The similarity of DNA sequences remaining bound to scaffold upon nuclease treatment of interphase nuclei and metaphase chromosomes.

The fragments of DNA attached to protein skeleton of interphase nuclei or metaphase chromosomes were obtained. Both the method involving restriction endonuclease treatment/1,2/and a novel procedure based on mild staphylococcal nuclease digestion were used. In the latter case, DNA fragments remaining bound to nuclei or chromosomes are not enriched in satellite but only in abundant middle repetitive DNA. The shorter the fragments of attached DNA, the higher the content of middle repetitive DNA in the fraction. It has a slightly higher density in a CsCl gradient comparing to the main DNA. The yield of attached DNA, its distribution in a CsCl density gradient, and its renaturation properties are essentially the same for interphase and metaphase chromosomes. The average size of DNA loops was found to be equal to approximately 60 kb for both metaphase chromosomes and interphase nuclei. The conclusion has been drawn that the bulk of attachment sites of DNP fibrils to axial chromosomal structures remains unchanged during the cell cycle.     

Architecture of the Chinese hamster metaphase chromosome

The development of procedures for the isolation of unfixed metaphase chromosomes has made feasible a direct analysis of their morphology. Wholemount stereo electron microscopy was used to examine intact and partially disrupted chromosomes produced by physical shearing and extraction with salt and urea solutions. A model of chromosome architecture was developed to accommodate evidence from studies using both light and electron microscopy. In the proposed model the chromatid (anaphase chromosome) consists of two half-chromatids; each half-chromatid contains two deoxyribonucleoprotein ribbons wound into a single fiber (termed the core), with many loops of chromatin (termed epichromatin) attached along its length. The core ribbons are each about 50 Å thick by 4000 Å wide and are composed of many parallel deoxyribonucleoprotein strands. The epichromatin loops appear to be 250 Å supercoiled fibers containing about 75 per cent of the chromosomal DNA. The epichromatin can be selectively removed from the core fibers by extraction with 2.0 M NaCl or 6.0 M urea solutions.     

Scaffold attachment of DNA loops in metaphase chromosomes

We have examined the higher-order loop organization of DNA in interphase nuclei and metaphase chromosomes from Drosophila Kc cells, and we detect no changes in the distribution of scaffold-attached regions (SARs) between these two phases of the cell cycle. The SARs, previously defined from experiments with interphase nuclei, not only are bound to the metaphase scaffold when endogenous DNA is probed but also rebind specifically to metaphase scaffolds when added exogenously as cloned, end-labeled fragments. Since metaphase scaffolds have a simpler protein pattern than interphase nuclear scaffolds, and both have a similar binding capacity, it appears that the population of proteins required for the specific scaffold-DNA interaction is limited to those found in metaphase scaffolds. Surprisingly, metaphase scaffolds isolated from Drosophila Kc cells contain both the lamin protein and a pore-complex protein, glycoprotein (gp) 188. To study whether lamin contributes to the SAR-scaffold interaction, we have carried out comparative binding studies with scaffolds from HeLa metaphase chromosomes, which are free of lamina, and from HeLa interphase nuclei. All Drosophila SAR fragments tested bind with excellent specificity to HeLa interphase scaffolds, whereas a subset of them bind to HeLa metaphase scaffolds. The maintenance of the scaffold-DNA interaction in metaphase indicates that lamin proteins are not involved in the attachment site for at least a subset of Drosophila SARs. This evolutionary and cell-cycle conservation of scaffold binding sites is consistent with a fundamental role for these fragments in the organization of the genome into looped domains.