Interphase and metaphase resolution of different distances within the human dystrophin gene

Simultaneous visualization of chromosome bands and hybridization signal using colloidal-gold labeling in electron microscopy

Electron microscopy (EM) is seldom used with in situ hybridization to localize DNA sequences because banding methods for chromosome identification could not be coupled to EM techniques. We have applied an immunochemical replication-banding method specific for EM to solve this problem. A thymidine synchronization/BrdUrd release protocol allows BrdUrd incorporation only into late replicating bands. A biotinylated DNA probe is hybridized in situ to its complementary sequence. The biotinylated probe and the BrdUrd-substituted DNA are simultaneously localized by different reporter/detection systems using different-sized colloidal gold particles as electron-dense tags. We demonstrate the high precision of this mapping procedure by localizing on long prophase chromosomes (greater than 1000 bands per haploid set) the pXBR-1 sequence to a small subregion of the centromeric subband Xp11.1-Xq11.1. This localization to a part of an individual prophase subband is the most precise localization ever reported on human banded mitotic chromosomes.

Discrete nuclear domains of poly(A) RNA and their relationship to the functional organization of the nucleus

The functional organization of the nucleus was studied using a fluorescence microscopy approach which allowed integration of positional information for RNA, DNA, and proteins. In cells from sea urchin to human, nuclear poly(A) RNA was found concentrated primarily within several discrete "transcript domains" which often surrounded nucleoli. Concentrations of poly(A) RNA were coincident with snRNP antigen clusters, providing evidence for the localization of pre-mRNA splicing at these sites. The spatial relationship of transcript domains with respect to various classes of DNA was established, in that the poly(A) RNA-rich regions coincided with discrete regions of low DNA density and were non-randomly distributed with respect to specific DNA sequences. Centromeric DNA and late-replicating DNA did not overlap transcript domains, whereas a subset of early-replicating DNA may. Results indicate that transcript domains do not result directly from a simple clustering of chromatin corresponding to metaphase chromosomes bands. Finally, observations on the reassembly of these domains after mitosis suggest that the clustering of snRNP antigens may be dependent on the reappearance of pol II transcription. Implications of these findings for overall nuclear structure and function are considered, including a discussion of whether transcript domains may be sites of polymerase II transcription reflecting a clustering of active genes.

Relative order determination of four Yp cosmids on metaphase and interphase chromosomes by two-color competitive in situ hybridization

Two-color competitive in situ hybridization was used to cytogenetically order four Yp cosmid probes, located in the pseudo-autosomal and TDF regions. The probes were hybridized by pairs to metaphase and interphase chromosomes. On metaphase chromosomes, determination of order between sequences separated by 3 Mb from each other was possible on a statistical basis, whereas the relative position of sequences 0.6 Mb apart could not be determined. On interphase chromosomes the complete order between sequences separated by 0.6-6 Mb was obtained rapidly by measuring the distances between two cosmid spots of every cosmid pair used in 28 to 60 nuclei. Results demonstrate the potential power of fluorescent in situ hybridization at interphase for high resolution cosmid mapping.

Multicolor fluorescence in situ hybridization and pulsed field electrophoresis dissect CMT1B gene region

We have used multicolor fluorescence in situ hybridization of banded chromosomes to orient Fc gamma RII and clone 1054 on a single early metaphase chromosome band (1q22) representing about 2% of the physical map of chromosome 1 in the Charcot-Marie-Tooth (CMT1B) gene region. These two cloned fragments are on the same partially digested 900-kb MluI fragment detected by pulsed field gel electrophoresis. When applied to data from an earlier study, multicolor in situ hybridization results further refined the CMT1B genetic location from an 18 cM interval to a 6 cM interval and the physical map from 15% of chromosome 1 to 3% of chromosome 1. Occasionally the three Fc gamma RII immunoglobulin receptor genes within the 200-kb region are resolved in individual metaphase chromatids.

Recent advances in dystrophin research

Evidence suggesting that dystrophin is a component of the membrane cytoskeleton of excitable cells continues to accumulate. Whereas the specific mechanisms leading to muscle pathology in Duchenne muscular dystrophy are still being debated it is apparent that the progressive weakness that occurs in this disease is the result of a chronic process that is initiated by dystrophin deficiency.

DNA and RNA within the nucleus: how much sequence-specific spatial organization?

Spatial organization of various nuclear components is often proposed as a means by which nuclei more efficiently carry out their various tasks. Such functional compartmentalization may involve a sequence-specific packaging and placement of DNA and RNA. Here we review recent insights, allowed primarily by advances in fluorescent in situ hybridization methodology, into the organization of nucleic acids within individual nuclei.

Molecular cloning, chromosomal mapping, and expression of the cDNA for p107, a retinoblastoma gene product-related protein

p107 is a cellular protein that forms specific complexes with adenovirus E1A and SV40 large T antigen (T). The genetics of the p107-T/E1A interaction as well as other features of this protein suggests that p107 shares functional properties with the tumor suppressor product, RB. A partial cDNA for human p107 has been cloned. Its sequences map to 20q11.2 and encode a 936 residue protein. Comparison analysis of the p107 protein sequence reveals a major region of RB homology extending over 564 residues. This region in RB is essential to its growth-controlling function. Sequences outside of these two regions are largely unique to each protein. The p107 and RB homology regions can independently bind to T and E1A. Thus, these two proteins display similarities of structure that may, at least in part, explain their known functional similarities and suggest a generic function for p107 in cell cycle regulation.

Fine mapping of probes in the adenomatous polyposis coli region of chromosome 5 by in situ hybridization

The gene for adenomatous polyposis coli has been localized to 5q21-22. We have mapped six probes from this region using isotopic or nonisotopic in situ hybridization. Using tritium-labeled probes we localized II227 (D5S37) to 5q14-15 and ECB27 (D5S98) to 5q21. Following hybridization with biotin-labeled probes, the positions of signals along the chromosomes were measured as fractional length relative to the length of the chromosome arm from centromere to qter (FLcen-qter). Ninety-five percent confidence limits, compared with standard karyotypes, provided the corresponding band localization. By this method we localized Cllpll (D5S71) to FLcen-qter 0.407-0.452 (5q21.1-21.3), ECB27 to FLcen-qter 0.426-0.473 (5q21.3), YN5.48 (D5S81) to FLcen-qter 0.459-0.496 (5q21.3-22.2), and ECB134 (D5S97) to FLcen-qter 0.509-0.533 (5q22.3-23.1). ECB220 had three sites of hybridization, a major site at FLcen-qter 0.460-0.492 (5q21.3-22.1) and minor sites at FLcen-qter 0.299-0.339 (5q14.3-15) and FLcen-qter 0.629-0.691 (5q23.3-31.2). We have shown that the chromosome 5 breakpoint in a t(5;15) translocation from a patient with Gardner's syndrome (GM03314) is between Cllpll and ECB27. Linkage data are presented suggesting that ECB27 is located on the same side of the APC locus as II227. These and published results including data on several constitutional deletions (M, SD, and brothers PW and ND) give a probable order of [cen] - [II227, proximal SD breakpoint] - [Cllpll] - [proximal PW/ND, M breakpoint(s), GM03314 breakpoint] - [ECB27] - [APC] - [YN5.48] - [distal PW/ND breakpoint] - [ECB134] - [distal M breakpoint] - [qter]. The major site of ECB220 appears to be between ECB27 and the distal PW/ND breakpoint; the distal SD breakpoint is distal to YN5.48.

Gene mapping in cancer

Observation of genetic alterations that appear consistently in specific types and stages of cancer provides a strong impetus to cancer geneticists to focus their investigations on the exploration of such volatile regions of the human genome. Introduction of powerful molecular cytogenetic and molecular genetic methods in recent years permits more detailed analysis, which will help researchers in their efforts to determine if such areas of the human genome have a functional role in the initiation and progressive development of leukemias and solid tumors. This discussion will focus on several provocative molecular cytogenetic tools that are currently available to localize potential cancer-associated genes and on how these methods are being used in conjunction with the current modes of analysis, including cytogenetics and somatic cell genetics. In addition, we will explore how these methods will help to isolate and dissect recently discovered cancer-associated genes within the human genome. All of these methods used in combination with each other will provide essential DNA markers for future diagnostic and prognostic evaluation of cancer.

Assignment of the human granulocyte colony-stimulating factor receptor gene (CSF3R) to chromosome 1 at region p35-p34.3

The gene for the granulocyte colony-stimulating factor (G-CSF) receptor (CSF3R) was localized on the p35-p34.3 region of human chromosome 1 by in situ hybridization using human G-CSF receptor cDNA as the probe. Polymerase chain reaction using oligonucleotides specific for the human CSF3R produced a specifically amplified DNA fragment with DNA from mouse A9 cells that contained human chromosome 1 but not other human chromosomes. Localization of the CSF3R on chromosome 1 was further confirmed by the spot-blot hybridization of sorted human chromosomes.

Linkage mapping and fluorescence in situ hybridization of TCTE1 on human chromosome 6p: analysis of dinucleotide polymorphisms on native gels

Highly informative dinucleotide repeat polymorphisms were identified at the T-complex-associated-testes-expressed-1 (TCTE1) locus on human chromosome 6p. Electrophoresis of single-stranded DNA on native gels facilitated the analysis of the dinucleotide polymorphisms. Linkage mapping positions this marker midway between the centromere and HLA with recombination fractions as follows: D6Z1-0.21-TCTE1-0.24-HLA. Two-color fluorescence in situ hybridization places TCTE1 proximal to CRIL171 (D6S19). Together, linkage and in situ hybridization indicate that the order of the loci is D6Z1-D6S4-D6S90-TCTE1-D6S19-D6S29-HL A-telomere. A sequence tagged site (STS) was established, and three yeast artificial chromosome (YAC) clones were identified for the TCTE1 locus.

DNA duplication associated with Charcot-Marie-Tooth disease type 1A

Charcot-Marie-tooth disease type 1A (CMT1A) was localized by genetic mapping to a 3 cM interval on human chromosome 17p. DNA markers within this interval revealed a duplication that is completely linked and associated with CMT1A. The duplication was demonstrated in affected individuals by the presence of three alleles at a highly polymorphic locus, by dosage differences at RFLP alleles, and by two-color fluorescence in situ hybridization. Pulsed-field gel electrophoresis of genomic DNA from patients of different ethnic origins showed a novel SacII fragment of 500 kb associated with CMT1A. A severely affected CMT1A offspring from a mating between two affected individuals was demonstrated to have this duplication present on each chromosome 17. We have demonstrated that failure to recognize the molecular duplication can lead to misinterpretation of marker genotypes for affected individuals, identification of false recombinants, and incorrect localization of the disease locus.

The Barr body is a looped X chromosome formed by telomere association

We examined Barr bodies formed by isodicentric human X chromosomes in cultured human cells and in mouse-human hybrids using confocal microscopy and DNA probes for centromere and subtelomere regions. At interphase, the two ends of these chromosomes are only a micron apart, indicating that these inactive X chromosomes are in a nonlinear configuration. Additional studies of normal X chromosomes reveal the same telomere association for the inactive X but not for the active X chromosome. This nonlinear configuration is maintained during mitosis and in a murine environment.

In situ hybridization with fluoresceinated DNA

We have used fluorescein-11-dUTP in a nick-translation format to produce fluoresceinated human nucleic acid probes. After in situ hybridization of fluoresceinated DNAs to human metaphase chromosomes, the detection sensitivity was found to be 50-100 kb. The feasibility and the increase in detection sensitivity of microscopic imaging of in situ hybridized, fluoresceinated DNA with an integrating solid state camera for rapid cosmid mapping is illustrated. Combination of fluoresceinated DNA with biotinated and digoxigeninated DNAs allowed easy performance of triple fluorescence in situ hybridization. The potential of these techniques for DNA mapping, cytogenetics and biological dosimetry is briefly discussed.

Physical mapping of the human genome by pulsed field gel analysis

Detailed physical maps of large regions of the human genome are important for locating and cloning genes responsible for human hereditary diseases, as well as for obtaining a more detailed understanding of chromosome structure and evolution. Pulsed field gel electrophoresis provides one method for generating physical maps of non-methylated rare restriction endonuclease sites. This review summarizes recent progress in the isolation of region-specific mapping probes and in their application for the physical mapping of selected regions of the human genome.

Gene mapping by in situ hybridization

Genome maps with a resolution of approximately 50kb can now be produced by applying the technique of two-color fluorescence in situ hybridization to chromatin targets in varying stages of condensation, such as metaphase chromosomes, interphase nuclei and sperm pronuclei.

Mapping nonisotopically labeled DNA probes to human chromosome bands by confocal microscopy

A method for mapping nonisotopically labeled probes to human metaphase chromosomes that can be used with laser scanning confocal microscopy has been developed. Only a limited number of wavelengths are available from the argon ion lasers used in most commercial instruments and therefore a method that allowed the visualization of bands on human chromosomes stained with propidium iodide and, simultaneously, the detection of hybridization signals using FITC-labeled antibodies was developed. The confocal microscope was used to map single-copy probes to chromosome bands and the positions of the probes on the R-banded chromosomes corresponded to map positions previously determined on Hoechst 33258-stained chromosomes (G-banded). A comparison of confocal imaging of single-copy hybridization signals with conventional fluorescence microscopy and high-sensitivity video cameras revealed little difference in sensitivity but greater resolution of chromosome bands with the confocal microscope. The polymerase chain reaction was used to prepare nonisotopically labeled probes for in situ hybridization and to amplify Alu and KpnI family repeats from cloned DNA to be used to suppress hybridization of these repeat sequences so that a cosmid probe could be mapped to a chromosome band.

A new system for high-resolution DNA sequence mapping interphase pronuclei

Cosmid clones containing human or hamster inserts have been hybridized in situ and localized with fluorescent reporter molecules in interphase nuclei (pronuclei) obtained after fusion of hamster eggs with either human or hamster sperm. Hamster egg cytoplasm processes the tightly packaged sperm DNA into large diffuse networks of chromatin fiber bundles, providing hybridization targets more extended than those available in somatic interphase cell nuclei. Pronuclear physical distances between hybridization signals were measured in micrometers and correlated to genomic distances determined by restriction fragment analyses, using cosmids from the Chinese hamster DHFR region and from the human Factor VIII/color vision pigment gene region (Xq28). The mean pronuclear distances between hybridization sites were about three times as large as those measured in somatic interphase cells for equivalent genomic distances. The relationship between physical and genomic distances was linear from less than 50 kb to at least 800 kb. The results show that physical distance in the sperm-egg system promises to extend the mapping range obtainable in somatic interphase nuclei below 50 kb and up to at least 800 kb.

In situ hybridization banding of human chromosomes with Alu-PCR products: a simultaneous karyotype for gene mapping studies

Polymerase chain reaction products generated from a single Alu primer and human genomic DNA produce a distinct and highly reproducible R-banding pattern when hybridized to metaphase chromosome spreads. Individual chromosomes can be readily identified and karyotyped. Compared to conventional fluorescence banding on heat-denatured chromosomes, the in situ hybridization banding (ISHB) shows high contrast and definition. We demonstrate that this banding method can be employed effectively in double-labeling experiments for the rapid and simultaneous assignment of probes to specific chromosomal bands. Since virtually any fluorochrome can be used to delineate chromosomal bands, ISHB should provide added flexibility for multicolor mapping strategies.

Chromosomal in situ hybridization using yeast artificial chromosomes

Large DNA fragment cloning methods using yeast artificial chromosomes (YACs) have vastly improved the strategies for constructing physical maps of regions of complex genomes, as well as for isolating and cloning genes important for human disease. We present here a simple and rapid method for carrying out in situ hybridization to metaphase chromosomes using isolated YAC clones by labeling DNA directly in agarose gel slices. Nonisotopic labeling and chromosomal in situ hybridization can be used to determine the chromosomal localization of individual YAC clones on human metaphase chromosomes. This method can also be used to characterize YAC clones consisting of single fragments from those that contain concatamerized, and thus artifactual, inserts. This technique also offers a valuable tool to study consistent translocations in neoplastic diseases by identifying YACs that span a specific chromosomal breakpoint.

Localizing DNA and RNA within nuclei and chromosomes by fluorescence in situ hybridization

The enormous potential of in situ hybridization derives from the unique ability of this approach to directly couple cytological and molecular information. In recent years, there has been a surge of success in powerful new applications, resulting from methodologic advances that bring the practical capabilities of this technology closer to its theoretical potential. A major advance has been improvements that enable, with a high degree of reproducibility and efficiency, precise visualization of single sequences within individual metaphase and interphase cells. This has implications for gene mapping, the analysis of nuclear organization, clinical cytogenetics, virology, and studies of gene expression. This article discusses the current state of the art of fluorescence in situ hybridization, with emphasis on applications to human genetics, but including brief discussions on studies of nuclear DNA and RNA organization, and on applications to clinical genetics and virology. Although a review of all of the literature in this field is not possible here, many of the major contributions are summarized along with recent work from our laboratory.

Molecular localization of the t(11;22)(q24;q12) translocation of Ewing sarcoma by chromosomal in situ suppression hybridization

Chromosome translocations are associated with a variety of human leukemias, lymphomas, and solid tumors. To localize molecular markers flanking the t(11;22) (q24;q12) breakpoint that occurs in virtually all cases of Ewing sarcoma and peripheral neuroepithelioma, high-resolution chromosomal in situ suppression hybridization was carried out using a panel of cosmid clones localized and ordered on chromosome 11q. The location of the Ewing sarcoma translocation breakpoint was determined relative to the nearest two cosmid markers on 11q, clones 23.2 and 5.8, through the analysis of metaphase chromosome hybridization. By in situ hybridization to interphase nuclei, the approximate physical separation of these two markers was determined. In both Ewing sarcoma and peripheral neuroepithelioma, cosmid clone 5.8 is translocated from chromosome 11q24 to the derivative chromosome 22 and a portion of chromosome 22q12 carrying the leukemia inhibitory factor gene is translocated to the derivative chromosome 11. The physical distance between the flanking cosmid markers on chromosome 11 was determined to be in the range of 1000 kilobases, and genomic analysis using pulsed-field gel electrophoresis showed no abnormalities over a region of 650 kilobases in the vicinity of the leukemia inhibitory factor gene on chromosome 22. This approach localizes the Ewing sarcoma breakpoint to a small region on chromosome 11q24 and provides a rapid and precise technique for the molecular characterization of chromosomal aberrations.

Analysis of genes and chromosomes by nonisotopic in situ hybridization

Nonisotopic in situ hybridization is a powerful tool to analyze the organization of complex genomes. Current approaches utilizing this technique for the analysis of linear and spatial genome organizations are presented. Clinical applications of these approaches, which open new avenues for diagnosis of disease-related chromosomal changes, are also discussed.

Homologous ribosomal protein genes on the human X and Y chromosomes: escape from X inactivation and possible implications for Turner syndrome

We have isolated two genes on the human sex chromosomes, one on the Y and one on the X, that appear to encode isoforms of ribosomal protein S4. These predicted RPS4Y and RPS4X proteins differ at 19 of 263 amino acids. Both genes are widely transcribed in human tissues, suggesting that the ribosomes of human males and females are structurally distinct. Transcription analysis revealed that, unlike most genes on the X chromosome, RPS4X is not dosage compensated. RPS4X maps to the long arm of the X chromosome (Xq), where no other genes are known to escape X inactivation. Curiously, RPS4X maps near the site from which the X-inactivating signal is thought to emanate. On the Y chromosome, RPS4Y maps to a 90 kb segment that has been implicated in Turner syndrome. We consider the possible role of RPS4 haploinsufficiency in the etiology of the Turner phenotype.

Human type II collagen gene (COL2A1) assigned to chromosome 12q13.1-q13.2 by in situ hybridization with biotinylated DNA probe

We have made a regional assignment of the type II collagen gene (COL2A1) on human chromosome 12 by means of an in situ hybridization technique with a biotinylated DNA probe. The precise localization of the signal was mapped to the band 12q13.1-q13.2. This result was in agreement with the previous mapping by isotopic in situ hybridization technique (12q13.1-q13.2), but not with the result of Southern hybridization analysis using somatic cell hybrids (12q14.3).