Further Studies on the Ribosomal RNA Cistrons of SCIARA COPROPHILA (Diptera)

Additional experiments with homologous as well as heterologous hybridization confirmed our previous finding in Sciara coprophila that XX females have nearly twice the number of ribosomal RNA cistrons as XO males. A comparison between two different X' chromosomes revealed that only the one carrying the irradiation-induced Wavy mutation has a deletion of 70% of its ribosomal RNA cistrons as compared to the standard X. The deletion is relatively stable, and the remaining ribosomal RNA cistrons donot appear to undergo disproportionate replication or magnification as in Drosophila. Homologous hybridization experiments revealed an unusually low reiteration of ribosomal RNA cistrons in this fly, 45 gene copies per X chromosome. The question is raised as to whether such a low number of cistrons may be related to the unusual nucleolar condition encountered in the Sciaridae.     

A molecular and cytogenetic survey of major repeated DNA sequences in tomato (Lycopersicon esculentum)

Summary The major families of repeated DNA sequences in the genome of tomato (Lycopersicon esculentum) were isolated from a sheared DNA library. One thousand clones, representing one million base pairs, or 0.15% of the genome, were surveyed for repeated DNA sequences by hybridization to total nuclear DNA. Four major repeat classes were identified and characterized with respect to copy number, chromosomal localization by in situ hybridization, and evolution in the family Solanaceae. The most highly repeated sequence, with approximately 77000 copies, consists of a 162 bp tandemly repeated satellite DNA. This repeat is clustered at or near the telomeres of most chromosomes and also at the centromeres and interstitial sites of a few chromosomes. Another family of tandemly repeated sequences consists of the genes coding for the 45 S ribosomal RNA. The 9.1 kb repeating unit in L. esculentum was estimated to be present in approximately 2300 copies. The single locus, previously mapped using restriction fragment length polymorphisms, was shown by in situ hybridization as a very intense signal at the end of chromosome 2. The third family of repeated sequences was interspersed throughout nearly all chromosomes with an average of 133 kb between elements. The total copy number in the genome is approximately 4200. The fourth class consists of another interspersed repeat showing clustering at or near the centromeres in several chromosomes. This repeat had a copy number of approximately 2100. Sequences homologous to the 45 S ribosomal DNA showed cross-hybridization to DNA from all solanaceous species examined including potato, Datura, Petunia, tobacco and pepper. In contrast, with the exception of one class of interspersed repeats which is present in potato, all other repetitive sequences appear to be limited to the crossing-range of tomato. These results, along with those from a companion paper (Zamir and Tanksley 1988), indicate that tomato possesses few highly repetitive DNA sequences and those that do exist are evolving at a rate higher than most other genomic sequences.     

Localization of rDNA and giemsa-banded chromosome complement of white-handed gibbon,Hylobates lar

A karyotype based on banding pattern and chromosome length is presented for the white-handed gibbon, Hylobates lar. Little homology with the banding patterns of the chromosomes of the other Hominoidea can be seen, confirming the early evolutionary separation of Hylobatidae and the other apes. Hybridization in situ with ribosomal RNA shows that the secondary constriction of a submetacentric chromosome (15) is the only site of the nucleolar organizer, as in the Cercopithecoidea. The correlation of polymorphic variation in size of this secondary constriction with grain density suggests differences in the number of gene copies per chromosome.     

The Nucleolus Organizer Region of Maize (ZEA MAYS L.): Tests for Ribosomal Gene Compensation or Magnification

Ribosomal gene compensation and magnification that might be detected on a whole-plant basis was not found in maize. Plants monosomic for chromosome 6 (the NOR chromosome) were compared with monosomic-8 and monosomic-10 plants, disomic sibs, and parental lines. Assuming no rDNA compensation, monosomic-6 plants showed approximately the decrease expected in rRNA cistron number. Monosomic-8 had a normal ribosomal gene number, while monosomic-10 showed a decrease; but further documentation is needed. Besides demonstrating the absence of gene compensation, the results document our previous conclusion that maize chromosome 6 carries DNA complementary to ribosomal RNA. Further documentation was provided from studies with trisomic chromosome 6 plants showing proportional increases in ribosomal gene number. Progeny of the monosomic plants crossed as males to a standard singlecross hybrid possessed expected ribosomal gene numbers suggesting the lack of ribosomal gene magnification.—The ragged (rgd) mutant of maize, suspected of being deficient in rRNA cistrons, had a normal number.     

Sequential silver staining and hybridization in situ on nucleolus organizing regions in human cells.

Chromosome preparations from eight individuals were first stained with silver nitrate to reveal the nucleolus organizing regions (NORs) and then hybridized in situ with ribosomal RNA. In six individuals the size of the silver-staining regions was positively correlated with the amount of label present after hybridization in situ. Thus the variation in silver-staining intensity among chromosomes was largely explained by variation in the number of rDNA gene copies per NOR. However, in two individuals this correlation was absent, suggesting that other factors can also influence the size of the silver-staining region.     

Karyotypes of three somaclonal variants and wild plants ofAllium tuberosum by bicolor FISH

Using the fluorescence in situ hybridization (FISH) technique, we conducted karyotype analyses to identify the lost chromosomes in three somaclonal variants obtained from tissue culture of wildAllium tuberosum (2n = 4X = 32). The three lost chromosomes of the At29 variant (2n = 29) were all chromosome 2, the two for At30 (2n = 30) were chromosomes 7 and 8, and At31 was missing chromosome 2. Chromosome compositions of these variants were confirmed as being fixed lines during two years of greenhouse cultivation. The bicolor FISH technique, involving both 5S and 18S–5.8S–26S ribosomal RNA genes as probes, was used to assign chromosomal locations and to confirm whether the lost chromosomes contained any rRNA markers. The 5S rRNA gene signals in all variants as well as the wild type were detected as two sets, one on the intercalary region of the short arm of chromosome 3, the other on the intercalary region of the long arm of chromosome 6. One 18S–5.8S–26S rRNA gene site on the secondary constriction included a flanking satellite and terminal region on the short arm of chromosome 8. Signals of the 18S–5.8S–26S rRNA gene in At30 showpd in only three chromosomes, indicating that one of the lost chromosomes was chromosome 8. Overall, three marker chromosomes were established by FISH, using rRNA multigene families.     

Physical mapping of the 5S ribosomal RNA genes in Arabidopsis thaliana by multi-color fluorescence in situ hybridization with cosmid clones

The 5S ribosomal RNA genes were mapped to mitotic chromosomes of Arabidopsis thaliana by fluorescence in situ hybridization (FISH). In the ecotype Landsberg erecta, hybridization signals appeared on three pairs of chromosomes, two of which were metacentric and the other acrocentric. Hybridization signals on one pair of metacentric chromosomes were much stronger than those on the acrocentric and the other pair of metacentric chromosomes, probably reflecting the number of copies of the genes on the chromosomes. Other ecotypes, Columbia and Wassilewskija, had similar chromosomal distribution of the genes, but the hybridization signals on one pair of metacentric chromosomes were very weak, and detectable only in chromosomes prepared from young flower buds. The chromosomes and arms carrying the 5S rDNA were identified by multi-color FISH with cosmid clones and a centromeric 180 bp repeat as co-probes. The metacentric chromosome 5 and its L arm carries the largest cluster of the genes, and the short arm of acrocentric chromosome 4 carries a small cluster in all three ecotypes. Chromosome 3 had another small cluster of 5S rRNA genes on its L arm. Chromosomes 1 and 2 had no 5S rDNA cluster, but they are morphologically distinguishable; chromosome 1 is metacentric and 2 acrocentric. Using the 5S rDNA as a probe, therefore, all chromosomes of A. thaliana could be identified by FISH. Chromosome 1 is large and metacentric; chromosome 2 is acrocentric carrying 18S-5.8S-25S rDNA clusters on its short arm; chromosome 3 is metacentric carrying a small cluster of 5S rDNA genes on its L arm; chromosome 4 is acrocentric carrying both 18S-5.8S-25S and 5S rDNAs on its short (L) arm; and chromosome 5 is metacentric carrying a large cluster of 5S rDNA on its L arm.     

Quantitative chromosome map of the polyploid Saccharum spontaneum by multicolor fluorescence in situ hybridization and imaging methods

Somatic chromosomes of a wild relative of sugarcane (Saccharum spontaneum L.) anther culture-derived clone (AP 85-361, 2n=32) were identified and characterized by computer-aided imaging technology and molecular cytological methods. The presence of four satellite chromosomes and four nearly identical chromosome sets suggests that the clone is a tetrahaploid with the basic number x=8. A quantitative chromosome map, or idiogram, was developed using image analysis of the condensation pattern (CP) at the prometaphase stage of somatic chromosomes. The 45S and 5S ribosomal RNA gene (rDNA) loci were simultaneously visualized by multi-color fluorescence in situ hybridization (McFISH) and precisely localized to the regions of 3p3.1 and 6q1.3 on the idiogram. The simultaneous visualization of two sets of four ribosomal RNA genes confirms tetraploidy of this clone. This conclusion is consistent with results of molecular marker mapping. The quantitative chromosome map produced will become the foundation for genome analyses based on chromosome identity and structure. Previously impossible identification of small chromosomes and untestable hypotheses about the polyploid nature of plants can now be settled with these two approaches of quantitative karyotyping and FISH.     

Visualization of mitotic chromosomes in filamentous fungi by fluorescence staining and fluorescence in situ hybridization

Mitotic chromosomes of the plant pathogenic filamentous fungi Botrytis cinerea and Alternaria alternata were observed. Chromosomes prepared by the germ tube burst method were stained with the fluorescent dye 4,6-diamidino-2-phenylindole (DAPI) to yield figures with good resolution. Using this method, component chromosomes were clearly distinguished and the chromosome number could be determined. Fluorescence in situ hybridization (FISH) was also successfully applied to the specimens, revealing one ribosomal RNA gene cluster, or nucleolus organizer region (NOR) in the genome of each fungus. A long attenuated chromatid thread expanding from a condensed metaphase chromosome, which had been called a thread-like structure in B. cinerea, was proved to be an NOR. This is the first report of the successful application of FISH to the chromosomes of filamentous fungi.     

Comparative study of molecular characteristics of X and Y nucleolar organizers of various lines of Drosophila melanogaster

We have determined for the X chromosomes of 10 laboratory strains and the Y chromosomes of 4 of them both the total number of ribosomal units and the relative percentages of uninterrupted (ins-), type 1 (ins1: with distinction between small ins1S and large ins1L) and type 2 (ins2) interrupted ribosomal units. These studies were made with the DNA extracted from third instar larval diploid tissues (brains and imaginal discs) of X/X female lines or XNO-/Y male lineages (devoid of X ribosomal genes) whose members possess copies of the same initial X or Y chromosome. Between the X chromosomes as well as the Y chromosomes an approximately equal to 2-fold variation was observed in the total number of ribosomal genes: from approximately equal to 200 to 420 for the X chromosomes and from approximately equal to 150 to 330 for the Y ones. The Y chromosomes are devoid of insertion 1 interrupted units, but one can observe some variation in the percentage and hence the absolute numbers of uninterrupted and insertion 2 interrupted units. Among the X chromosomes a very large variation exists between the percentage and absolute number of all the ribosomal unit types; it is to be noted especially that the number of uninterrupted units, which are the only kind of ribosomal genes actively transcribed, can vary from about 20 to 140 without any differences in the development of the different strains.     

Location of genes coding for 18S and 28S ribosomal RNA within the genome of Mus musculus

Cytological detection of cistrons coding for 18S and 28S ribosomal RNA (rRNA) within the genome of Mus musculus inbred strain SEC/1ReJ was accomplished using the technique of in situ hybridization. Metaphase chromosome spreads prepared from cultured fetal mouse cells were stained with quinacrine-HCl and photographed. After destaining, they were hybridized to Xenopus laevis tritiated 18S and 28S rRNA, specific activity 7.5 X 10(6) dpm/mug. Silver grains clustered over specific chromosomes were readily apparent after 4 months of autoradiographic exposure. The identity of the labelled chromosomes was established by comparing the autoradiographs to quinacrine photographs showing characteristic fluorescent banding of the chromosomes in each metaphase spread. The 18S and 28S rRNA was found to hybridize to chromosomes 12, 18, and 16. Statistical analysis of the grain distribution over 26 spreads revealed that the three chromosomes were significantly labelled. Grains over these chromosomes were concentrated in an area immediately distal to the centromere, a region which in chromosomes 12 and 18 in this particular strain is the site of a secondary constriction. The relative size of the secondary constrictions, long and thus prominent on chromosome 12, obvious but shorter on 18, and indistinguishable on chromosome 16, correlated with the average number of grains observed over the centromeric region of these chromosomes, 2.5, 1.0, and 0.78, respectively.     

The mitotic chromosomes of Notophthalmus (=Triturus) viridescens: Localization of C banding regions and DNA sequences complementary to 18S, 28S and 5S ribosomal RNA

The metaphase chromosomes of Notophthalmus (Triturus) viridescens have been studied by C-banding and in situ hybridization. The chromosomes show the pericentric C-banding seen in many organisms and in addition have interstitial C-bands located a short distance from the pericentric C-bands on each chromosome arm. A few C-bands are seen in telomeric regions. Regions which hybridize in situ with 18S and 28S ribosomal RNA were found on three chromosome pairs. The animals studied fell into three groups with respect to which of the six possible sites showed detectable hybridization with 18S and 28S RNA. Individual animals differed not only in the pattern of in situ hybridization of ribosomal RNA but also in the number of ribosomal RNA cistrons in the genome as measured by saturation hybridization on purified DNA. In situ hybridization showed five pairs of chromosomes which contained DNA complementary to 5S RNA. The four pairs of subtelocentric chromosomes in the N. viridescens karyotype all have 5S DNA in the pericentric regions. The fifth cluster of 5S DNA is in the middle of one arm of the chromosomes in one of the two smallest submetacentric pairs in the genome. The five sites of 5S DNA differ markedly in the level of in situ hybridization with 5S cRNA.     

The location of ribosomal cistrons (rDNA) in chromosomes of the rat

In situ hybridization of ³H-labelled ribosomal RNA to the chromosomes of rat bone marrow cells revealed that clusters of ribosomal cistrons (rDNA) are located in the secondary constrictions of chromosomes No. 3 and 12 and near the centromere of chromosome No. 11, both associated with the late DNA-replicating regions. They were not found in Nos. 1, 2, 13, 19, 20, and the Y chromosome.     

Distribution of 18+28S ribosomal genes in mammalian genomes

In situ hybridization with ³H 18S and 28S ribosomal RNA from Xenopus laevis has been used to study the distribution of DNA sequences coding for these RNAs (the nucleolus organizing regions) in the genomes of six mammals. Several patterns of distribution have been found: 1) A single major site (rat kangaroo, Seba's fruit bat), 2) Two major sites (Indian muntjac), 3) Multiple sites in centromeric heterochromatin (field vole), 4) Multiple sites in heterochromatic short arms (Peromyscus eremicus), 5) Multiple sites in telomeric regions (Chinese hamster). — The chromosomal sites which bind ³H 18S and 28S ribosomal RNA correspond closely to the sites of secondary constrictions where these are known. However, the correlation is not absolute. Some secondary constrictions do not appear to bind ³H ribosomal RNA. Some regions which bind ribosomal RNA do not appear as secondary constrictions in metaphase chromosomes. — Although the nucleolus organizing regions of most mammalian karyotypes are found on the autosomes, the X chromosomes in Carollia perspicillata and C. castanea carry large clusters of sequences complementary to ribosomal RNA. In situ hybridization shows that the Y chromosome in C. castanea also has a large nucleolus organizing region.     

Genetically Induced Mitotic Exchange in the Heterochromatin of DROSOPHILA MELANOGASTER

Multiple copies of the 18S and 28S ribosomal RNA cistrons are present in both the X and Y chromosomes of Drosophila melanogaster. Data are presented here that identify a locus, Rex, that causes exchange-like events between duplicated ribosomal complexes at the ends of an attached-XY chromosome. Rex: (1) is close to or in the basal heterochromatin of the X chromosome; (2) is semidominant and (its effect) is temperature sensitive; (3) acts maternally; and (4) affects behavior of paternally derived attached-XY chromosomes shortly after fertilization. Though, at this point, the existence of Rex is known only from its effects on behavior of a particular compound chromosome, it presents intriguing possibilities for understanding regulation of chromosome behavior and organization of the ribosomal cistrons.