Chromosome banding analysis by slit-scan flow cytometry

We have investigated the use of fluorescence banding patterns for the resolution of metaphase chromosomes by slit-scan flow cytometry. Fluorescence scans of R-banded chromosomes have been obtained for the entire human karyotype. Metaphase chromosomes were R-banded in suspension by staining with chromomycin A3 after hypotonic treatment in Ohnuki's buffer. Specific fluorescent landmark bands were detected for human chromosomes 1-12. Scans obtained for chromosomes 13-22 did not contain sufficient information for classification. Characteristic fluorescence patterns for human chromosomes 1 and 3 provided the clearest evidence for the detection of R-bands by slit-scan flow cytometry. Specific patterns were detected for human chromosomes 9-12 in which the number and placement of the fluorescent bands served as classifiers.     

Identification of human chromosomes by DNA-binding fluorescent agents

The distribution of DNA along metaphase chromosomes that are not excessively contracted can be visualized in the fluorescence microscope with the aid of fluorescent DNA-binding agents. Additional, characteristic details in the fluorescence patterns are obtained with fluorochromes that bind preferentially to certain chromosomal regions. The highly fluorescent alkylating agent quinacrine mustard (QM) effects discrete, fluorescent labeling of both plant and mammalian metaphase chromosomes, presumably by selective binding to guanine residues in DNA, and is also capable of intercalation in the DNA double helix. Chromosome regions fluorescing particularly strongly with QM have been demonstrated in human metaphase chromosomes 3, 13–15 and Y.A convenient measuring technique has been developed for the rapid and accurate recording of fluorescence patterns in human metaphase chromosomes. These photoelectric recordings of the fluorescence patterns contain far greater detail than can be seen by the human eye.The fluorescence patterns described are based on measurements of about 1,000 human metaphase chromosomes. This new technique of determining fluorescence patterns in human chromosomes should be particularly valuable for the identification of chromosomes 4–5 and the individual types in the 6–12 group. Individual, typical patterns also occur within the groups 13–15, 17–18, and 21–22.     

Complex high-resolution linkage disequilibrium and haplotype patterns of single-nucleotide polymorphisms in 2.5 Mb of sequence on human chromosome 21.

One approach to identify potentially important segments of the human genome is to search for DNA regions with nonrandom patterns of human sequence variation. Previous studies have investigated these patterns primarily in and around candidate gene regions. Here, we determined patterns of DNA sequence variation in 2.5 Mb of finished sequence from five regions on human chromosome 21. By sequencing 13 individual chromosomes, we identified 1460 single-nucleotide polymorphisms (SNPs) and obtained unambiguous haplotypes for all chromosomes. For all five chromosomal regions, we observed segments with high linkage disequilibrium (LD), extending from 1.7 to>81 kb (average 21.7 kb), disrupted by segments of similar or larger size with no significant LD between SNPs. At least 25% of the contig sequences consisted of segments with high LD between SNPs. Each of these segments was characterized by a restricted number of observed haplotypes,with the major haplotype found in over 60% of all chromosomes. In contrast, the interspersed segments with low LD showed significantly more haplotype patterns. The position and extent of the segments of high LD with restricted haplotype variability did not coincide with the location of coding sequences. Our results indicate that LD and haplotype patterns need to be investigated with closely spaced SNPs throughout the human genome, independent of the location of coding sequences, to reliably identify regions with significant LD useful for disease association studies.     

应用涂染技术研究人和猕猴染色体的同源性

用２４种人类染色体探针对人和猕猴Ｇ－显带染色体进行涂染。结果显示：人类所有染色体在猕猴的染色体组里都有其同源染色体或染色体片段。     

Cytological mapping of human chromosomes: results obtained with Quinacrine fluorescence and the Acetic-Saline-Giemsa techniques

The similarities and differences between the banding patterns obtained in human chromosomes with the Quinacrine fluorescence and the Acetic-Saline-Giemsa (ASG) techniques are described. The use of these techniques to identify each chromosome pair in the human karyotype is discussed, as also is the use of the methods to identify aberrant chromosomes and to map points of exchange in translocations and inversions. A number of examples are used to illustrate the resolution permitted by these new methods. Seven polymorphic regions on normal chromosomes are described, which include four identified by fluorescence on chromosomes 3,4, 13, and 22. The secondary constrictions on chromosomes 1, 9, and 16, which had previously been observed in conventionally stained preparations from favourable material, are particularly clear in all cells treated with the Giemsa techniques. The new methods make it possible to detect small differences in size between the heterochromatic blocks at these regions in homologous chromosomes. The benefit to human genetics of studying the familial segregation of both structurally rearranged and normal, but polymorphic chromosomes, where the chromosomes or parts of chromosomes can be unambiguously identified is stressed.     

Simultaneous identification and banding of human chromosome material in somatic cell hybrids

We have developed a method that identifies human chromosomes in human x hamster somatic cell hybrids and simultaneously bands these same metaphases. Other methods generally require separate slides for banding and detection of human chromosome material, making the precise characterization of human material difficult. Our procedure involves denaturing metaphase chromosomes, followed by in situ hybridization of biotinylated whole human DNA. Fluoresceinated avidin is then bound to the biotinylated DNA, staining the human chromosomes yellow-green when excited with UV light. Chromosome banding is achieved by staining the slides with DAPI and actinomycin D. The fluorescein and DAPI excite maximally at 488 and 355 nm and emit at 520 and 450 nm, respectively. This permits identification of the human material at one excitation wavelength and visualization of the banding patterns at another wavelength. With this procedure, we have successfully identified both intact and broken human chromosomes, as well as human material involved in human x hamster translocations. The results indicate that this procedure is more accurate and considerably more rapid than previous methods and can be routinely employed for the cytogenetic analysis of human x rodent hybrids.     

Chromosome banding and compaction

Summary We have described a characteristic substructure of mitotic chromosomes, the chromosomal unit fibre, with lengths about five times the length of the corresponding metaphase chromosomes and a uniform diameter of 0.4 m. In order to study the relationship of chromosome banding to chromosome compaction, methods have been devised to obtain banding patterns on chromosomal unit fibres, similar to G-band patterns of intact mitotic chromosomes. The total number of bands plus interbands per haploid human karyotype is estimated at about 3000. The banding pattern of chromosomal unit fibres indicates a certain resemblance to the normal G-banding pattern of human chromosomes even if the details indicate a short-range random distribution.     

A comparison of the fluorescent karyotypes of the chimpanzee (Pan troglodytes) and man

Individual chimpanzee chromosomes have been identified by their characteristic banding revealed by quinacrine fluorescent staining. A fluorescent karyotype of this species was set up to be compared with the standard human fluorescent karyotype. It was found that chromosomes 1, 3, 11, 12, 14 and X-chromosome of the chimpanzee appear to have banding patterns similar to the equivalent human chromosomes. Chromosomes 6, 7, 8, 10 and 13 also had a fluorescent pattern corresponding to the human chromosomes of the same number, particularly in the long arm. Remarkable variation in intensity and/or size of fluorescent regions was frequently found in the short arm of satellited acrocentric chromosomes 13, 14, 15, 22 and 23. Variations occurred between homologues and between individuals. Such variable fluorescence in a specific chromosomal region of an individual animal is a reproducible characteristic. Unlike its human counterpart, the distal segment in the long arm of the chimp's Y-chromosome is not brightly fluorescent. An earlier report is thus confirmed.     

Bulk separation of Purkinje cells and granular cells from small amounts of cerebellar tissue

BUdR-sensitive fluorescence of the dye 33258 Hoechst allows microfluorometric analysis of replication in human chromosomes. Comparison of the fluorescence patterns of male and female X chromosomes obtained with this technique reveals differences that may reflect regional alterations in DNA synthesis kinetics.     

Comparative mapping of a gorilla-derived alpha satellite DNA clone on great ape and human chromosomes

We have isolated an alpha satellite DNA clone, pG3.9, from gorilla DNA. Fluorescence in situ hybridization on banded chromosomes under high stringency conditions revealed that pG3.9 identifies homologous sequences at the centromeric region of ten gorilla chromosomes, and, with few exceptions, also recognizes the homologous chromosomes in human. A pG3.9-like alphoid DNA is present on a larger number of orangutan chromosomes, but, in contrast, is present on only tow chromosomes in the chimpanzee. These results show that the chromosomal subsets of related alpha satellite DNA sequences may undergo different patterns of evolution.by J.B. Rattner     

Combination of silver and fluorescent staining for metaphase chromosomes.

A convenient and reliable method for simulatneous visualization of silver staining (Ag-NOR) of the nucleolus organizers and fluorescent bandings in metaphase chromosomes is described. Studies employing this combined procedure on human chromosomes revealed that the Ag-NOR patterns may be characteristic for each chromosome of each individual.     

Interchromatidal central ridge and transversal symmetry in early metaphasic human chromosome one

The topographic structure of Giemsa-banded (G-banded) early metaphase human chromosomes adsorbed on glass was analyzed by atomic force microscope using amplitude modulation mode (AM-AFM). Longitudinal height measurements for early metaphasic human chromosomes showed a central ridge that was further characterized by transversal height measurements. The heterochromatic regions displayed a high level of transversal symmetry, while the euchromatic ones presented several peaks across the transversal height measurements. We suggest that this central ridge and symmetry patterns point out a transitional arrangement of the early metaphase chromosome and support evidence for interchromatidal interactions prior to disjunction.     

Protein composition of human metaphase chromosomes analyzed by two-dimensional electrophoreses

A large amount of metaphase chromosomes were isolated from synchronized human cell lines by a polyamine procedure. All the chromosomal proteins extracted by an acetic acid extraction method were fully dissolved into the sample solutions for isoelectric focusing (IEF) or radical free and highly reduced (RFHR) two-dimensional electrophoreses (2-DEs). As a result, well-separated and highly reproducible 2-DE patterns were obtained. This could not be attained by an ordinary acetone precipitation method. The 2-DE patterns visualized using Coomassie Brilliant Blue (CBB) staining indicated that more than one hundred proteins were involved in the isolated metaphase chromosomes, although the most abundant proteins, histones, occupied a greater part of the chromosomal proteins. It was also shown that colcemid treatment for cell cycle synchronization had little effect on the 2-DE pattern compared to that obtained without the treatment. Furthermore, no significant differences were observed in the 2-DE patterns among the chromosomal proteins prepared from two different human cell lines, BALL-1 and K562. However, 2-DE analysis of isolated metaphase chromosomes from HeLa cells apparently showed a smaller number of proteins than the BALL-1 and K562 cell lines at a neutral pI range. The present study paves the way for elucidating protein composition of human metaphase chromosomes.     

X chromosome inactivaton and SV40 transformation of mammalian cells.

Five embryonic mouse cultures and one human fibroblast culture were transformed with SV40. The cultures were studied cytologically to see if the normal pattern of sex chromosome replication was maintained in SV40 transformed cells. Characteristic late replication patterns were observed for both the X and Y chromosomes, and there was no evidence for loss of the inactive X chromosome, even in cells with 4 or more X chromosomes. The human line was heterozygous at two X-linked loci and a clonal analysis showed that the expression of X-linked genes was not affected by SV40 transformation.     

Presence of abundant heterochromatin in the karyotype of Cebus: C. cappucinus and C. nigrivittatus]

The karyotypes of Cebus capucinus and C. nigrivittatus (Primates, Platyrrhini) are compared after applying several banding techniques. The chromosomes have abundant intercallary heterochromatin which can be stained by R-, T- and C-band techniques and which are late replicating. The X chromosome resembles that of man and of numerous primates. However, the late replicating pattern of the X in female lymphocytes resembles that of the late replicating X of human fibroblasts rather than of human lymphocytes. Banding patterns of certain chromosomes appear analogous in Cebus and Cattarhini, including Man.     

Isolabeling of the long arm of the human Y chromosome demonstrated by the FPG technique

Isolabeling segments were found in the distal region of the long arm of Y chromosomes derived from human leukocytes grown through two replication cycles in medium containing BrdU and stained by the FPG technique. Three main types of Y chromosome staining patterns were demonstrated: I-Y chromosome with typical SCD, II-Y chromosome with weakly stained distal regions of long arms (isolabeling segments), III-Y chromosome with both terminal regions displaying SCD interrupted by one isolabeled segment. The existence of different types of Y chromosome staining patterns was explained on the basis of the previously described hypothesis of unequal distribution of thymine residues between two DNA polynucleotide chains in the distal part of the long arms of human Y chromosomes.     

限制酶AluI显带和CA_3/DA/DAPI染色表达的家猪染色体结构异染色质

采用限制酶AluI显带、CA_(?)/DA/DAPI荧光染色和常规C带技术研究了家猪染色体着丝粒结构异染色质,结果表明:着丝粒结构异染色质至少可被区分为3类,并且在染色体组内各有其特异的染色体分布。将家猪染色体DA/DAPI荧光带和限制酶AluI显带与人类染色体比较,发现家猪13—18号端着丝粒染色体显带特征与人染色体1,9、16、Y一致。提示家猪13—18号端着丝粒区结构异染色质存在与人类随体DNA相似的DNA组成。     

A possible correlation between DA-DAPI counterstaining and alu I-induced bands in fixed human chromosomes

DA-DAPI counterstaining is a technique which reveals the heterochromatic areas of chromosomes 1, 9, 15, 16 and Y in humans; a result which may be related to the peculiar characteristics of these chromosomal regions, particularly regarding their DNA content. The present report describes a different DA-DAPI stain reaction. Obtained under standard conditions, it shows positive, bright staining in a large number of chromosomes. Such a result is discussed in relation to the banding pattern produced by Alu I in human metaphase chromosomes, in view of the high degree of overlapping of the two patterns.     

Characterization of human heteroploid cell line J-111: Reverse banding patterns of marker chromosomes

The karyotype of the human cell line, J-111, has been studied employing R-banding by fluorescence using acridine orange technique (RFA). The model chromosome number of this line was 112. All human chromosomes except the Y were present in each metaphase. Twenty-one marker chromosomes were distinguished and their possible origins were investigated. Of these, twelve were consistently present in all cells. Nine markers were highly variable. Four typical marker chromosomes of HeLa cells were found and their origins were identified, indicating that the line is a HeLa contaminant. The reverse banding patterns of all marker chromosomes are presented and the value of the RFA technique is discussed.