Epigenetics of specific chromosome regions

Investigation of protein complexes, various types of protein modifications and the structure of the chromatin of specific chromosome regions, such as centromeres, telomeres, and adjacent heterochromatic regions, considerably complicated the notion on DNA, prevailing five decades ago, as molecules that exclusively control coding and realization of genetic information. Striking plasticity of the primary structure of centromeric and telomeric DNA suggests a variety of molecular mechanisms underlying fundamental and universal functions of these key chromosome regions. The present review is an attempt to consider the current concepts on the structure of the DNA and protein components, as well as the structure of the chromatin of specific chromosome regions in eukaryotes, and the concerted evolution of these components, leading to the formation of a hierarchy of coordinated DNA-protein complexes.     

Epigenetics of specific chromosome regions

Investigation of protein complexes, various types of protein modifications and the structure of the chromatin of specific chromosome regions, such as centromeres, telomeres, and adjacent heterochromatic regions, considerably complicated the notion on DNA, prevailing five decades ago, as molecules that exclusively control coding and realization of genetic information. Striking plasticity of the primary structure of centromeric and telomeric DNA suggests a variety of molecular mechanisms underlying fundamental and universal functions of these key chromosome regions. The present review is an attempt to consider the current concepts on the structure of the DNA and protein components, as well as the structure of the chromatin of specific chromosome regions in eukaryotes, and the concerted evolution of these components, leading to the formation of a hierarchy of coordinated DNA-protein complexes.     

Quinacrine mustard fluorescence of a second Y chromosome in a Y-autosomal translocation

Summary Screening buccal smears from 97 prisoners by the quinacrine mustard technique revealed one XYY-individual and one Y-autosomal translocation of a second Y chromosome with a 46,XY, D-,t (?15q;Yq)+ karyotype. The translocation chromosome could be identified by its intense fluorescence of the short arm in all 75 metaphases examined.

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Zusammenfassung Untersuchungen von Abstrichen der Mundschleimhaut von 97 Gefängnisinsassen mit der Quinacrine-Mustard-Methode führten zur Aufdeckung eines XYY-Karyotyps und einer Y-autosomalen Translokation eines zweiten Y-Chromosoms mit einem Karyotyp von 46,XY,D-,t(?15q;Yq)+. Das Translokationschromosom konnte durch helle Fluorescenz des kurzen Armes in allen 75 Metaphasen identifiziert werden.

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This work was supported in part by grant number Pa 118/8 from the Deutsche Forschungsgemeinschaft and is part of a thesis by S. F.     

The relationship between patterns of DNA replication and of Quinacrine fluorescence in the human chromosome complement

Cultured human peripheral blood lymphocytes were labelled with ³H-thymidine in the early or late S phase prior to mitosis. Quinacrine fluorescence patterns in metaphase chromosomes were then recorded photographically and the slides reprocessed for autoradiography so that the same metaphase cells were examined with the two techniques. The intensity and distribution of ³H-thymidine labelling was compared with the intensity and distribution of Q fluorescence with particular reference to chromosomes 1, 13, 14, 15, 17, 18, 19, 20, 21 and 22. It was found that chromosome regions showing bright fluorescence were also late replicating and that, in general, patterns of late replications reflected the patterns of fluorescence. Exceptions to this generalisation included the late labelling X chromosome in cells of female origin and areas near the centromeres on chromosomes 1, 9, 16 and 22. These centromeric regions show a dull fluorescence but, with exception of chromosome 9, are strongly Giemsa-positive in the ASG staining technique. On the basis of staining reaction, late replicating heterochromatic regions fall into five categories, the relationships and functional significance of these categories is discussed.     

Quinacrine fluorescence and Giemsa banding in trisomy 22

Summary Using quinacrine fluorescence and Giemsa banding techniques we have identified an extra chromosome 22 in three non-mongoloid children with similar phenotypes and 47 chromosomes. In one of the children, the long arm of the extra 22 was shorter than usual. This 22q—chrcmcscme was observed in 4 normal family members with 46 chromosomes. In a fourth child, with similar physical findings, the extra G chromosome was shown to be neither a normal 21 nor 22. It must have arisen from a rearrangement in a parental gamete since it was not present in either parent's karyotype.No constellation of clinical findings, in association with an extra G chromosome, is sufficient evidence for the diagnosis of trisomy 22. The positive identification of the extra chromosome must be made using fluorescence and banding.This paper is dedicated to Professor Marcus M. Rhoades on his 70th birthday in grateful recognition of his friendship, help and advice.Supported in part by U.S. Public Health Service Grants HD1313, RR-75 and TI-HD-66 from the National Institutes of Health. A portion of this paper was presented at the annual meeting of the Society for Pediatric Research, Atlantic City, N.J. May 1, 1971.     

Quinacrine and acridine-R banding without a fluorescence microscope

Summary A technique is described in which a standard fluorescence microscope equipped with a high-pressure mercury lamp is replaced with an ordinary laboratory microscope fitted with a quartz-iodine lamp. A dark field condenser and a set of three filters, including an FITC interference filter, complete a fluorescence microscope.The microscope has proved itself satisfactory in the study of Y-chromatin, chromosome Q-bands including Q-polymorphism, and acridine-R band. It is very easy to operate and does not emit ultraviolet light, which might harm operators. Total cost of the quartz-iodine lamp's outfit, filters, and a dark-field condenser is much less than that of a standard fluorescence microscope. The cost is especially low when a laboratory microscope with a quartz-iodine lamp is already at hand. Spectrofluorometric studies of QM and Q indicate that the present system will show even better performance if an interference filter with a transmission range of about 400 to 440–450 nm is designed and used in combination with a 455–475 nm barrier filter.     

Quinacrine fluorescence of variant and abnormal human Y chromosomes

Quinacrine fluorescence has been used to examine variant and abnormal human Y chromosomes, at interphase and mitosis. The length difference in variant Y chromosomes has been shown to involve the highly fluorescent segment only. Eight abnormalities of the Y chromosome have been positively identified, two isochromosomes of the long arms of the Y, five pericentric inversions, and a dicentric Y chromosome with two long arms. Contributory evidence for two further abnormalities, a ring Y and a dicentric with two short arms, is also given.     

Mechanisms of chromosome banding. V. Quinacrine banding.

A series of biochemical investigations were undertaken to determine the mechanism of Q-banding. The results were as follows: 1. In agreement with previous studies, highly AT-rich DNA, such as poly(dA)-poly(dT), markedly enhanced quinacrine fluorescence while GC containing DNA quenched fluorescence. These effects persisted at DNA concentrations comparable to those in the metaphase chromosome. 2. Studies of quinacrine-DNA complexes in regard to the hypochromism of quanacrine, DNA Tm, DNA viscosity, and equilibrium dialysis, indicated the quinacrine was bound be intercalation with relatively little sid binding. 3. Single or double stranded nucleotide polymers, in the form of complete or partial helices, were 1000-fold more effective in quenching than solutions of single nucleotides, suggesting that base stacking is required for quenching. 4. Studies of polymers in the A conformation, such as transfer RNA and DNA-RNA hybrids, indicated that marked base tilting does not affect the ability of nuclei acids to cause quenching or enhancement of quinacrine fluorescence. 5. Salts inhibit the binding of quinacrine to DNA. 6. Spermine, polylysine and polyarginine, which bind in the small groove of DNA, inhibited quinacrine binding and quenching, while histones, which probably bind in the large groove, had little effect. This correlated with the observation that removal of histones with acid has no effect on Q-banding. 7. Mouse liver chromatin was separated into five fractions. At concentrations of quinacrine from 2 times 10-6 to 2 times 10-5 M all fractions inhibited to varying degrees the ability of the chromatin DNA to bind quinacrine and quench quinacrine fluorescence. At saturating levels of quinacrine two fractions, the 400 g pellet (rich in heterochromatin) and a dispersed euchromatin supernatant fraction, showed a decreased number of binding sites for quinacrine. These two fractions were also the richest in non-histone proteins. 8. DNA isolated from the different fractions all showed identical quenching of quinacrine fluorescenc. 9. Mouse GC-rich, mid-band, AT-rich, and satellite DNA, isolated by CsCL AND Cs-2SO-4-Ag+ centrifugation all showed identical quenching of quinacrine fluorescence, indicating that within a given organism, except for very AT or GC-rich satellites, the variation in base composition is not adequate to explain Q-banding.We interpret these results to indicate that: (a) quinacrine binds to chromatin by intercalation of the three planar rings with the large group at position 9 lying in the small groove of DNA, (b) most pale staining regions are due to a decrease binding of quinacrine, and (c) this inhibition of binding is predominately due to non-histone proteins.     

Quinacrine fluorescence staining of chromosomes and its relationship to DNA base composition

The quinacrine banding patterns of chromosomes of Dipodomys ordii and Mus musculus are described. Satellite and mainband DNA fractions from D. ordii and M. musculus were tested for their ability to quench or enhance the fluorescence of quinacrine dihydrochloride in solution. The relationship between the base composition of a particular DNA fraction, its effect on the fluorescence of quinacrine in solution and its location in chromosomes relative to the quinacrine banding pattern is discussed.     

Enhanced resolution of specific chromosome and nuclear regions by reflectance laser scanning confocal microscopy

 DNA sequences digested by HaeIII and reconstructed by in situ nick translation employing digoxigenin-labelled nucleotides are usually revealed either by horseradish peroxidase or FITC fluorescence. To obtain a significant improvement in terms of resolution, sensitivity and specificity, colloidal gold has been used instead of FITC (as the reporter molecule) to reveal the labelled DNA. Colloidal gold and propidium iodide were visualised by employing the reflectance mode and the 488-nm laser line of a confocal laser scanning microscope. In chromosomes, the fluorescent reaction pattern showed diffuse areas of labelling in which it was impossible to identify any specific kind of banding along the arms. In some chromosomes and, in particular, 1 and 9, a C-negative banding due to the negativity of the centromeric areas was seen. A more accurate localisation on chromosomes, including telomeric regions, often organised in spot pairs that resembled an R-like banding, was detected using 1-nm colloidal gold. A fine labelling was also demonstrated in nuclei, especially at their peripheral heterochromatin. The non-fading properties of colloidal gold combined with visualisation by reflectance confocal laser scanning microscopy demonstrated the possibility of obtaining a higher spatial resolution than when using conventional fluorophores or higher laser wavelength. This improved way to study the localization of HaeIII digestion sites in single chromosomes and in interphase nuclei made the reaction a valuable tool for the detection of antigens or of specific DNA sequences in biological preparations. Accepted: 5 September 1996     

Quinacrine fluorescence analysis of the chromosomes of Dipsacus fullonum L. (Dipsacaceae)

Abstract

Quinacrine fluorescence analysis of the chromosome complement of Dipsacus fullonum L. shows clear heterochromatic regions appearing as brightly fluorescent bands or clusters of fluorescent dots in most chromosomes. The resulting fluorescent pattern is chromosome specific.     

On the Quinacrine fluorescence and Giemsa staining patterns of the chromosomes of Vicia faba

Abstract

A comparison has been made between the Quinacrine fluorescence bands and the bands obtained with a denaturating-reannealing-Giemsa technique in Vicia faba. The results show that some of the bands, particularly on the M and, proximally, on the S chromosomes are visible with both techniques. A complex pattern of bands on the S chromosomes is revealed with the Giemsa technique. Both the similarities and the differences between the banding patterns obtained with the two methods in Vicia faba may indicate various degrees of DNA repetitiousness and other physico-chemical properties in the chromosome segments involved.