Chromosomal localization of Sau3A repetitive DNA revealed by in situ hybridization

The Sau3A DNA family consists of unique alphoid human repetitive DNA which is prone to be excised from the chromosomes and exhibits restriction fragment length polymorphism. We studied the chromosomal localization of the DNA by in situ hybridization using cultured normal human lymphocytes. Under standard hybridization conditions, the sequence hybridized with the centromeric regions of chromosomes 1, 2, 4, 11, 15, 17, 18, 19 and X, but under high stringency hybridization conditions, it hybridized with the centromeric regions of chromosomes 1, 17 and X, and particularly chromosome 11. Based on these results, we discuss the evolutionary relationship among the sequences of the Sau3A DNA family.     

The pachytene chromosomes of maize as revealed by fluorescence in situ hybridization with repetitive DNA sequences

A repetitive DNA sequence, ZmCR2.6c, was isolated from maize based on centromeric sequence CCS1 of the wild grass Brachypodium sylvaticum. ZmCR2.6c is 309 bp in length and shares 65% homology to bases 421–721 of the sorghum centromeric sequence pSau3A9. Fluorescence in situ hybridization (FISH) localized ZmCR2.6c to the primary constrictions of pachytene bivalents and to the stretched regions of MI/AI chromosomes, indicating that ZmCR2.6c is an important part of the centromere. Based on measurements of chromosome lengths and the positions of FISH signals of several cells, a pachytene karyotype was constructed for maize inbred line KYS. The karyotype agrees well with those derived from traditional analyses. Four classes of tandemly repeated sequences were mapped to the karyotype by FISH. Repeats 180 bp long are present in cytologically detectable knobs on 5L, 6S, 6L, 7L, and 9S, as well as at the termini and in the interstitial regions of many chromosomes not reported previously. A most interesting finding is the presence of 180-bp repeats in the NOR-secondary constriction. TR-1 elements co-exist with 180-bp repeats in the knob on 6S and form alone a small cluster in 4L. 26S and 5S rRNA genes are located in the NOR and at 2L.88, respectively. The combination of chromosome length, centromere position, and distribution of the tandem repeats allows all chromosomes to be identified unambiguously. The results presented form an important basis for using FISH for physical mapping and for investigating genome organization in maize. Received: 29 June 1999 / Accepted: 10 November 1999     

Chromosomal localization of several families of repetitive sequences by in situ hybridization.

Four recombinant DNA clones (H1, H7, H12, and H15) carrying low-repetitive human DNA were previously isolated from a human genomic library based on their specificity for chromosome 21 and were studied for their distribution as determined by in situ hybridization. Clone H7 hybridized to the satellite regions of chromosomes 13, 14, 15, 21, and 22 as well as to the centromere region of chromosome 1. Clone H12 hybridized strongly to chromosomes 11 and 17 and the centromere of the X. Clones H1 and H15 had a very widespread distribution throughout the genome. Clone H15 hybridized significantly more to the short arm of chromosome 18 than to any other chromosomal segment. Clone H1 hybridized strongly to the centromere of chromosome 19 and also showed random distribution on all the other human chromosomes. We conclude that these probes appear to represent four repetitive families that demonstrate in situ hybridization patterns that do not correspond with those of any other repetitive family. Further, the in situ hybridization patterns do not show the strong chromosome 21 specificity originally defined by Southern blot analysis. The nature and chromosomal localization of these repetitive families should be useful in regional mapping and evolutionary studies and give additional insight into chromosomal organization.     

Assignment of human satellite 1 DNA as revealed by fluorescent in situ hybridization with oligonucleotides

We have used a fluorescent in situ hybridization procedure to detect human satellite 1 DNA, the simple sequence family that constitutes the non-male-specific fraction of classical satellite 1 DNA. Satellite 1 appears to be located on pericentromeric regions of chromosomes 3, 4 and 13, and on satellites of each acrocentric chromosome. These results suggest a possible relationship between quinacrine fluorescence of heterochromatin and DNA composition. Furthermore, by means of multicolour in situ hybridization, we have spatially resolved satellite 1 sequences and centromeric -satellite within heterochromatic blocks.     

Highly repetitive sequences in B chromosomes of Secale cereale revealed by fluorescence in situ hybridization.

An analysis of the presence and distribution of the rye and wheat repeated sequences in rye B chromosomes was carried out by fluorescent in situ hybridization. Probes used consisted of three highly repetitive sequences from rye (pSc119.2, pSc74, and pSc34) and the multigene families for the 25S-5.8S-18S and 5S rDNA from wheat (pTa71 and pTa794, respectively). pSc74 and pSc119.2 showed hybridization signals in the telomeric regions of rye B chromosomes. The remaining DNA clones did not hybridize to the B chromosomes.     

Chromosomal localization of human aspartate aminotransferase genes by in situ hybridization

Summary The localization of the human genes for cytosolic and mitochondrial aspartate aminotransferase (AspAT) has been determined by chromosomal in situ hybridization with specific human cDNA probes previously characterized in our laboratory. The cytosolic AspAT gene is localized on chromosome 10 at the interface of bands q241–q251. Mitochondrial AspAT is characterized by a multigene family located on chromosomes 12 (p131–p132), 16 (q21), and 1 (p32–p33 and q25–q31). Genomic DNA from ten blood donors was digested by ten restriction enzymes, and Southern blots were hybridized with the two specific probes. Restriction fragment length polymorphism was revealed in only one case for cytosolic AspAT, with PvuII, while no polymorphism for mitochondrial AspAT was found.     

Homologies in human and Macasa fuscata chromosomes revealed by in situ suppression hybridization with human chromosome specific DNA libraries

We established chromosomal homologies between all chromosomes of the human karyotype and that of an old world monkey (Macaca fuscata) by chromosomal in situ suppression (CISS) hybridization with human chromosome specific DNA libraries. Except for the human chromosome 2 library and limited cross-hybridization of X and Y chromosome libraries all human DNA libraries hybridized to single GTG-banded macaque chromosomes. Only three macaque chromosomes (2, 7, 13) were each hybridized by two separate human libraries (7 and 21, 14 and 15, 20 and 22 respectively). Thus, an unequivocally high degree of synteny between human and macaque chromosomes has been maintained for more than 20 million years. As previously suggested, both Papionini (macaques, baboons, mandrills and cercocebus monkeys, all of which have nearly identical karyotypes) and humans are chromosomally conservative. The results suggest, that CISS hybridization can be expected to become an indispensable tool in comparative chromosome and gene mapping and will help clarify chromosomal phylogenies with speed and accuracy.by E.R. Schmidt     

Quantitative analysis of chromosomal localization of two human cloned satellite DNA III sequences by in situ hybridization

Chromosomal location of two cloned human satellite DNA III sequences pPD9 and pPD18 has been studied in 30 individuals by in situ hybridization. Pericentromeric localization of the DNA subsets studied was found in practically all chromosomes of the set. The majority of label was observed over the pericentromeric region of chromosome 9 (38.3% for pPD18 clone and 26.2% for pPD9), the short arm of chromosome 15 (17.2% - the pPD9 clone and 10.6% - the pPD18 clone) and the distal part of the long arm of Y chromosome (19.6% - the pPD9 clone and 15.4% - the pPD18 clone). Besides significant interchromosomal differences, moderately pronounced interindividual differences were also detected in the number of grains over the regular sites of the chromosomal location. Pretreatment of slides with DA/DAPI induced differences in the results of quantitative analysis is described.     

Characterization of Aegilops uniaristata chromosomes by comparative DNA marker analysis and repetitive DNA sequence in situ hybridization

RFLP analyses were performed on wheat-Aegilops uniaristata Vis. addition and translocation lines to confirm the identity of added N-genome chromosomes. Complete 1N, 3N, 4N, 5N and 7N chromosome additions were identified, while the complete long arm and only part of the short arm was identified for chromosome 2N. There were no wheat-like 4/5 and 4/7 translocations in the Ae. uniaristata chromosomes. Chromosome 3N carried an asymmetric pericentric inversion, and the translocation line was a product of centric fusion between the long arms of chromosomes 3B and 3N. Chromosome-specific RAPD and microsatellite markers were also identified for all the added Ae. uniaristata chromosomes available in this set of addition lines. A new genomic in situ hybridization protocol combining pre-annealing of probe and blocking DNA and prehybridization with blocking DNA was developed to differentiate the very closely related genomes of Ae. uniaristata and wheat. Hybridization sites for the repetitive DNA sequences pAs1, pSc119.2 and pTa71 were identified on the N-genome chromosomes of Ae. uniaristata using the fluorescent in situ hybridization technique. Results showed deviation from the previously published ideogram of this species. A new ideogram, which shows the hybridization sites for the above sequences, was produced in which the chromosomes are arranged according to their homoeologous group. Received: 23 April 1999 / Accepted: 6 August 1999     

Cellular localization of induced human interferon-beta mRNA by non-radioactive in situ hybridization

Induced interferon-beta (IFN-beta) mRNA was localized in human FS-4 fibroblasts by in situ hybridization using biotinylated probes. The hybridization sites were detected by incubation with a nick-translated genomic DNA probe (1.8 kb) via streptavidin-colloidal gold followed by silver contrast enhancement. The positive signals were observed by reflection-contrast light microscopy. IFN-beta mRNA was transiently induced by poly r(I): r(C) in fibroblasts 2-4 h after induction. Induction in the presence of cycloheximide and actinomycin D (superinduction conditions) exhibited an enhanced level of IFN-beta mRNA with a maximum at 4-8 h. The kinetics of the IFN-beta mRNA expression in the cytoplasm as revealed by in situ hybridization proved to be compatible with the results of Northern blotting experiments of total cellular RNA.     

Chromosomal localization of a human myosin heavy-chain gene by in situ hybridization

Summary A cloned rabbit heart muscle myosin heavy-chain cDNA was hybridized in situ with human metaphase chromosomes. The probe was known to have sequence homology with human genomic heavy-chain DNA. Only one site in the human haploid karyotype was labeled with the cDNA, and this site was found on the short arm of chromosome 17. The localization of autoradiographic grains suggests a subregional assignment of the myosin heavy-chain locus to 17p 1,2-pter.     

Localization of repetitive DNA in the chromosomes of Microtus agrestis by means of in situ hybridization

Heterochromatin in the European field vole, Microtus agrestis, was studied using a special staining technique and DNA/RNA in situ hybridization. The heterochromatin composed the proximal 1/4 of the short arm and the entire long arm of the X chromosome, practically the entire Y chromosome and the centromeric areas of the autosomes. By using the DNA/RNA in situ hybridization technique, repeated nucleotide sequences are shown to be in the heterochromatin of the sex chromosomes.Supported in part by Research Grants DRG-1061 and 269 from the Damon Runyon Memorial Fund for Cancer Research, G-373 and G-267 from the Robert A. Welch Foundation.     

More precise localization of the human factor IX gene by in situ hybridization

The location of the human antihemophilic Factor IX has been more specifically assigned from the region Xq27----qter to Xq26----q27 by quantitative in situ hybridization. The present study utilized a complex hybridization probe and prephotographed G-banded human chromosomes to improve analytical sensitivity and accuracy.     

Individual interphase chromosome domains revealed by in situ hybridization

Summary The position and arrangement of individual chromosomes in interphase nuclei were examined in mouse-human cell hybrids by in situ hybridization of biotinylated human DNA probes. Intense and even labeling of human chromosomes with little background was observed when polyethylene glycol and Tween-20 were included in hybridization solutions. Human interphase chromosomes were separated from each other in the nucleus, and were confined to well localized domains. Hybrid cells with a single human chromosome showed a reproducible position of this chromosome in the nucleus. Some chromosomes appeared to have a characteristic folding pattern in interphase. Optical section as well as electron microscopy of labeled regions revealed the presence of 0.2 m wide fibers in each interphase domain, as well as adjacent, locally extended 500 nm fibers. Such fibers are consistent with previously proposed structural models of interphase chromosomes.     

Variation in highly repetitive DNA composition of heterochromatin in rye studied by fluorescence in situ hybridization.

The molecular characterization of heterochromatin in six lines of rye has been performed using fluorescence in situ hybridization (FISH). The highly repetitive rye DNA sequences pSc 119.2, pSc74, and pSc34, and the probes pTa71 and pSc794 containing the 25S-5.8S-18S rDNA (NOR) and the 5S rDNA multigene families, respectively, were used. This allowed the individual identification of all seven rye chromosomes and most chromosome arms in all lines. All varieties showed similar but not identical patterns. A standard in situ hybridization map was constructed following the nomenclature system recommended for C-bands. All FISH sites observed appeared to correspond well with C-band locations, but not all C-banding sites coincided with hybridization sites of the repetitive DNA probes used. Quantitative and qualitative differences between different varieties were found for in situ hybridization response at corresponding sites. Variation between plants and even between homologous chromosomes of the same plant was found in open-pollinated lines. In inbred lines, the in situ pattern of the homologues was practically identical and no variation between plants was detected. The observed quantitative and qualitative differences are consistent with a corresponding variation for C-bands detected both within and between cultivars.     

Chromosomal localization of group-specific component by in situ hybridization

Group-specific component (GC), an alpha 2-globulin plasma protein synthesized primarily in the liver, is the major vitamin D-binding protein in plasma. It has two common phenotypes, GC1 and GC2, which appear in all human populations. Using the cDNA insert containing the entire coding sequence of GC2, the GC gene was mapped to human chromosomal bands 4q13----q21.1 by in situ hybridization.