Proteins in chromosome banding. I. Effect of G-banding treatments on the proteins of isolated nuclei

Unfixed and fixed human chromosomes show different staining patterns after restriction endonuclease digestion

Restriction endonucleases (REs) have been widely used to produce banding patterns on chromosomes, but it remains uncertain to what extent the patterns are due to the sequence specificity of the enzymes, and to what extent chromatin structure influences the pattern of digestion. To throw light on this question, we have digested with restriction endonucleases unfixed chromosomes prepared in two different ways (isolated, and whole metaphase cells spread with a cytocentrifuge) and compared the results with those obtained on conventionally fixed chromosomes. Unfixed isolated chromosomes are easily destroyed by REs; after fixation with cold methanol, which produced minimal alteration to the chromatin structure, the chromosomes are resistant to the action of REs, and conventional methanol-acetic acid fixation is required to permit the induction of banding patterns by REs. Unfixed cytocentrifuge preparations, in which the chromosomes are still surrounded by cytoplasm, are much more resistant to the action of REs, and again banding patterns were only induced after methanol-acetic acid fixation. We conclude that the action of restriction endonucleases on chromosomes is strongly influenced by chromatin organisation, and that methanol-acetic acid fixation is required to permit the induction of conventional banding patterns on chromosomes.

Time-dependent AluI action on human chromosomes

We have analyzed the pattern of AluI digestion over time on human chromosomes in order to monitor the evolution of the in situ enzyme action. Short treatments followed by Giemsa staining produce a G-like banding effect, whereas longer treatments produce a C-like banding pattern. However, when Propidium iodide staining is used, it reveals a uniform bright fluorescence after short AluI digestions and C bands when longer treatments are developed. We propose that C banding is the result of a uniform DNA removal in non centromeric regions taking place after a critical time point, the initial G like banding being produced by changes in the DNA-proteins interactions.

Determination of the electrophoretic mobility of chromosomes by free flow electrophoresis. I. Morphology and stability

Isolated metaphase chromosomes of several fibroblastoid cell lines (Chinese hamster, Chinese hamster x human hybrid) were subjected to free flow electrophoresis (FFE) to study their electrophoretic mobility (EM). The morphology and stability of the chromosomes were unaffected by FFE as examined by cytogenetic methods and flow cytometry. The chromosomes of the complement all showed similar EM under most of the conditions applied. At neutral pH the EM of the chromosomes had the same sign as free DNA and about 2/3 of its magnitude. The variation of EM with buffer parameters such as ionic strength, valence of counterions, buffer capacity and dielectric constant of the solvent were investigated. Thermal denaturation increased the EM of the chromosomes by 20%. Partial denaturation might offer a possibility to separate or enrich large amounts of chromosomes by FFE.

Differential decondensation of mitotic chromosomes during hypotonic treatment of living cells as a possible cause of G-banding: an ultrastructural study

The chromosomal ultrastructure of Chinese hamster cells treated with 0.075 M KCl - a solution ordinarily used for making preparations of spread chromosomes - was studied. The hypotonic treatment was shown to result in differential decondensation of chromosomes which consists in the uneven distribution of deoxyribonucleoprotein (DNP) fibrils along chromatids. Fixation of cells with methanol acetic acid causes an abrupt restructuring of chromosomes. However, the DNP preserves its uneven distribution along chromatids. As seen on ultra-thin sections of marker nucleolus organizer chromosomes, the densely packed regions may correspond to G-bands detected in the selfsame chromosomes by standard methods of differential staining. The results suggest that the capacity of chromosomes for differential staining is based on the different resistance of G- and R-bands to the decondensing action of hypotonic solutions on living cells.

Morphological and biochemical effects of endonucleases on isolated mammalian chromosomes in vitro

Endonuclease digestion of isolated and unfixed mammalian metaphase chromosomes in vitro was examined as a means to study the higher-order regional organization of chromosomes related to banding patterns and the mechanisms of endonuclease-induced banding. Isolated mouse LM cell chromosomes, digested with the restriction enzymes AluI, HaeIII, EcoRI, BstNI, AvaII, or Sau96I, demonstrated reproducible G- and/or C-banding at the cytological level depending on the enzyme and digestion conditions. At the molecular level, specific DNA alterations were induced that correlated with the banding patterns produced. The results indicate that: (1) chromatin extraction is intimately involved in the mechanism of endonuclease-induced chromosome banding. (2) The extracted DNA fragments are variable in size, ranging from 200 bp to more than 4 kb in length. (3) For HaeIII, there appears to be variation in the rate of restriction site cleavage in G- and R-bands; HaeIII sites appear to be more rapidly cleaved in R-bands than in G-bands. (4) AluI and HaeIII ultimately produce banding patterns that reflect regional differences in the distribution of restriction sites along the chromosome. (5) BstNI restriction sites in the satellite DNA of constitutive heterochromatin are not cleaved intrachromosomally, probably reflecting an inaccessibility of the BstNI sites to enzyme due to the condensed nature of this chromatin or specific DNA-protein interactions. This implies that some enzymes may induce banding related to regional differences in the accessibility of restriction sites along the chromosome. (6) Several specific nonhistone protein differences were noted in the extracted and residual chromatin following an AluI digestion.(ABSTRACT TRUNCATED AT 250 WORDS)

Immunofluorescent staining of mammalian nuclei and chromosomes with a monoclonal antibody to triplex DNA

Triplex DNA is an unusual conformation of DNA formed when two pyrimidine nucleotide strands share a common purine strand. A monoclonal antibody, demonstrated by numerous criteria to be specific for triplex DNA, was used to investigate the presence and distribution of this unique DNA configuration in nuclei and chromosomes of mouse LM cells and human lymphocytes. Indirect immunofluorescence microscopy revealed that constitutive heterochromatin in acetic-methanol fixed mouse nuclei was usually, but not always immunofluorescent, suggesting possible cell cycle related variations in the amount of triplex DNA or its accessibility in this condensed chromatin. In fixed mouse and human chromosomes, there was a positive correlation between immunofluorescent staining patterns, Hoechst 33258 banding, and G- and/or C-banding patterns. Unfixed, isolated mouse chromosomes also reacted positively with the antibody, particularly when they were gently decondensed by exposure to low ionic conditions at neutral pH. This result indicates that fixation is not mandatory for antibody staining, suggesting that some mammalian chromosomal DNA may be naturally organized in a triplex configuration. However, there is a possibility that fixation may facilitate the formation of additional triplex DNA complexes in potential sequences or expose previously inaccessible triplex DNA. The precise correspondence between the immunofluorescent patterns produced by anti-triplex DNA antibodies and G- and C-bands known to represent regions of chromatin condensation, suggests a potential role of triplex DNA in chromosome structure and regional chromatin condensation.

Silver staining the chromosome scaffold

Cytological silver-staining procedures reveal the presence of a "core" running along the chromatid axes of isolated HeLa mitotic chromosomes. In this communication we examine the relationship between this "core" and the nonhistone chromosome scaffolding, isolated and characterized in previous publications from this laboratory. When chromosomes on coverslips were subjected to the steps used for scaffold isolation in vitro and subsequently stained with silver, the characteristic "core" staining was unaffected. Control experiments suggested that the "core" does not contain large amounts of DNA. When scaffolds were isolated in vitro, centrifuged onto electron microscope grids, and stained with silver, they were found to stain selectively under conditions where specific "core" staining was observed in intact chromosomes. These results suggest that the nonhistone scaffolding is the principal target of the silver stain in chromosomes.

The effect of chromosome banding techniques on the proteins of isolated chromosomes

Experiments were undertaken to determine the effect of various chromosome banding treatments on the histone and nonhistone proteins of isolated, fixed, air-dried metaphase chromosomes. Chromosome preparations were exposed to G-banding (SSC, urea, NaCl-urea, or trypsin), R-banding (Earle's balanced salt solution), and C-banding (NaOH or Ba(OH)2) treatments, and the extracted and residual proteins were examined by SDS polyacrylamide gel electrophoresis. The results indicate that each of the banding treatments induce characteristic alterations in the chromosomal proteins. The residual proteins left in chromosomes after the diverse G-banding treatments were generally similar to one another, indicating that treatments inducing the same type of banding have similar effects on the chromosomal proteins. This was also true for the two different C-banding treatments. On the other hand, the residual protein patterns seen after the G-banding treatments were strikingly different from those seen after R-banding, which in turn differed from those seen after C-banding. The treatments inducing different types of banding therefore produce markedly different effects on the chromosomal proteins. These protein alterations may have an important influence on the induction of chromosome bands.

Scanning electron microscopy of Giemsa-stained chromosomes and surface-spread chromosomes

Giemsa-stained chromosomes as prepared for light microscopy, and including G-banded, C-banded, and FPG-stained chromosomes, were examined by scanning electron microscopy. Although suitable for light microscopy, these chromosomes were too flat for a close examination of their fine structure by scanning electron microscopy. The surface of Giemsa-positive regions was rough and bright, whereas that of unstained or poorly stained regions was smoother and less bright. Giemsa-staining, therefore, seems to produce the bulkiness of the chromosomes. On topographical examination by scanning electron microscopy, the transparent chromosomes as observed with the light microscope proved to be "footprints". Stereographical examinations of surface-spread chromosomes showed that minimally stretched chromosomes were composed of a mass of nodular and twisted looping fibers with an average diameter of about 300 A. The substructure of these chromosome fibers was not determined. The kinetochore region was discernible as a constriction in the mass of the chromosome fibers, and was distinguishable from gaps by the presence of several chromosome fibers parallel to the axis of the chromatid. The organization of the chromosome fibers, however, was disordered rather than regular.

Differential staining of the X-chromosome during meiosis of orthoptera by a silver impregnation procedure

Differential staining of the X chromosome of Orthoptera, which normally cannot be distinguished from the autosomes during the more condensed stages of meiosis, has been achieved by a silver impregnation procedure involving a pretreatment with 2 x SSC at 60 degrees C. The results suggest that the saline citrate solution preferentially extracts proteins from the X chromosome. This method may be useful for distinguishing chromosome regions composed of facultative heterochromatin in Orthoptera.

Microfluorometric investigations of chromatin structure. I. Evaluation of nine DNA-specific fluorochromes as probes of chromatin organization

The ability of the highly condensed chromatin of small thymocyte nuclei and the more loosely organized chromatin of hepatocyte nuclei to interact with nine DNA-specific fluorochromes was assessed by microfluorometry. Although the results obtained with five of the fluorochromes - mithramycin, 7-aminoactinomycin D, Hoechst 33258, DAPI, and propidium iodide - were found to be virtually unaffected by differences in the degree of condensation of the chromatin, the values obtained with the remaining fluorochromes - proflavine, quinacrine mustard, berberine sulfate, and pyronin Y - appeared to be affected significantly by organizational differences of the chromatin. All of the latter "structural probes," except quinacrine mustard, produced fluorescence values which were higher in the 2c nuclei of hepatocytes than in the nuclei of small thymocytes. Quinacrine mustard yielded higher values in thymocyte nuclei; and in the hepatocyte polyploid series (2, 4, and 8c), it did not produce the expected multiples of the 2c value. Pretreatment of the two types of nuclei with RNase affected their total fluorescence in unpredictable ways. While RNase extraction lessened the differences between thymocyte and 2c hepatocyte nuclei stained with propidium iodide, Hoechst 33258, proflavine, and berberine sulfate, it increased the differences between nuclei stained with mithramycin, quinacrine mustard, pyronin Y, and 7-aminoactinomycin D. The ability of RNA-depleted chromatin to interact with various types of fluorochromes might be a useful parameter in subsequent studies of chromatin organization.

Proteins in chromosome banding. II. Effect of R- and C-banding treatments on the proteins of isolated nuclei

SDS polyacrylamide gel electrophoresis was used to study the proteins extracted from, and those remaining in isolated, fixed, air-dried nuclei subjected to a variety of R- and C-banding techniques. The R-banding procedures, involving exposure to hot Earle's BSS or NaH2PO4, had the least effect of any of the banding techniques on the extraction of proteins from isolated nuclei. Only small amounts of 5 nonhistone proteins were detected in the Earle's BSS extract, and no proteins were found in the NaH2PO4 solution after treatment. The residual proteins remaining in the nuclei after either treatment were virtually identical to those in control nuclei. The C-banding techniques, on the other hand, produced substantial changes in the nuclear proteins. These techniques involve several sequential steps, including HCl treatment, exposure to NaOH or Ba(OH)2, and an incubation in hot SSC. The HCl treatment extracted a large variety of nonhistones and some of each of the remaining histones. No proteins were detected in the SSC solution. Some of the proteins extracted by Ba(OH)2 appeared after the two complete C-banding treatments revealed both similarities and differences. The Ba(OH)2 technique appeared to have a more severe effect on the nuclear proteins than the NaOH technique. Fewer residual nuclear proteins were observed after the former technique, but all of these were also represented in nuclei after the NaOH technique. The results indicate that the different treatments producing a common type of banding generally have similar effects on the nuclear proteins, while the treatments producing different types of banding (G-, R-, C-banding) have substantially different effects on these proteins. Such alterations may have implications for chromosome banding.