THE BASE COMPOSITION OF NUCLEIC ACIDS IN CHROMOSOMES, PUFFS, NUCLEOLI, AND CYTOPLASM OF CHIRONOMUS SALIVARY GLAND CELLS

The base composition of RNA from individually isolated giant chromosomes, puffed chromosome segments, nucleoli, and samples of cytoplasm from Chironomus salivary gland cells was determined by microelectrophoresis. Data on the adenine: guanine quotient of the chromosomal DNA were also obtained. The results show that: 1) Chromosomal, nucleolar, and cytoplasmic RNA's differ significantly from each other in base composition. 2) Nucleolar and cytoplasmic RNA's, in spite of the difference, show great similarities with regard to the base composition and are both rich in adenine and uracil. 3) The RNA extracted from chromosome I differs significantly from the RNA's extracted from different segments of chromosome IV, and the latter differ significantly from each other. 4) The values for the RNA: DNA quotients of chromosome segments parallel the development of synthetically active genes, so-called Balbiani rings. 5) The chromosomal RNA does not show a base symmetry in any of the investigated cases, nor is the content of guanine + cytosine the same as that for DNA. The first of these two facts excludes the possibility that the chromosomal RNA is a complete copy of both strands of the chromosomal DNA. In spite of the difference in guanine + cytosine content between the two nucleic acids the RNA may still partly or completely be a single strand copy depending upon how representative the DNA values are for the synthetically active DNA.     

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.     

THE BASE COMPOSITION OF RIBONUCLEIC ACID IN LAMPBRUSH CHROMOSOMES, NUCLEOLI, NUCLEAR SAP, AND CYTOPLASM OF TRITURUS OOCYTES

The base composition of RNA's extracted from chromosomes, nucleoli, nuclear sap, and cytoplasm of Triturus oocytes has been determined by microelectrophoresis. The chromosomal RNA has a content of guanine+cytosine equal to that of DNA, but there is no complementarity in the composition as for DNA. Nuclear sap contains a highly variable RNA with a tendency towards high uracil values. Nucleolar and cytoplasmic RNA's are similar in composition and both are of the guanine-cytosine rich type. The chromosomes and nucleoli contain roughly equivalent amounts of RNA, somewhat less than is present in the nuclear sap. The RNA/DNA ratio of the whole chromosomes is about 10. However, the ratio in the synthetically active regions, the loops, is much higher, since the loops contain all the chromosomal RNA but only a small fraction of the DNA.     

Cytogenetical and biochemical characterization of a dG + dC-rich satellite DNA in the primate Cebus capucinus

A very abundant and dG + dC rich DNA satellite from primate Cebus capucinus has been characterized in its cytogenetic and biochemical properties with the purpose of studying the correlation between the staining properties of heterochromatin and the base composition of the corresponding very repetitive DNA. The staining techniques, as well as incorporation of base analogues, show that the heterochromatin segments of C. capucinus chromosomes correspond to a dG + dC-rich satellite. This satellite was detected and isolated by centrifugation in density gradient, radioactively labelled and localized by in situ hybridization on heterochromatin segments.     

Chromosome polymorphisms close to the cm-ADE1 locus of Candida maltosa

The imperfect yeast Candida maltosa has an ill-defined genetic constitution; it is nominally diploid, but probably highly aneuploid, in nature. We report on polymorphisms specifically affecting those chromosomes which bear the cm-ADE1 gene. This gene encodes phosphoribosylaminoimidazole-succinocarboxamide synthetase, an enzyme in the adenine biosynthetic pathway. By electrophoretic karyotype analysis, three differently sized chromosomes were demonstrated to carry cm-ADE; the size (but not the number) of these chromosomes was also found to vary, both between strains and during the mitotic growth of a single strain. Four different alleles of cm-ADE1 have been cloned and sequenced from one prototrophic strain. DNA sequence divergence between these different alleles is as high as 8%, with the greatest divergence being found in the upstream region. Mitotic recombination events that led to changes in the karyotype were followed by using cm-ADE1 DNA as an hybridization probe. A recombination hot-spot in the neighbourhood of the gene appears to be responsible for the instability of the chromosomes on which it resides.     

Characterization of the most rapidly renaturing sequences in mouse main-band DNA

The most rapidly renaturing sequences in the main-band DNA of Mus musculus, isolated on hydroxyapatite, are found to consist of two discrete families: a presumed “foldback” DNA fraction and a fraction renaturing bimolecularly. The latter family, which we call “main-band hydroxyapatite-isolated rapidly renaturing DNA”, has a kinetic complexity about an order of magnitude greater than that of mouse satellite DNA. It shows about twice as much mismatching as renatured mouse satellite, as judged by its thermal denaturation curve. In situ hybridization localizes the sequences to all chromosomes in the mouse karyotype, and to at least several regions of each chromosome. The in situ result and solution hybridization studies eliminate the possibility that the main-band rapidly renaturing DNA is composed of mouse satellite sequences attached to sequences of higher buoyant density. Nuelease S₁ digestion experiments disclose that even at low molecular weight there are unrenatured “tails” attached to the rapidly renaturing sequences. When the main-band DNA fragment size is increased the amount of rapidly renaturing sequences remains constant, but the amount of attached tails of unrenatured DNA increases as judged by S₁ nuclease digestibility, hyperchromicity and buoyant density. It is concluded that at least 5% of the mouse genome is composed of segments of the rapidly renaturing sequences averaging about 1500 base pairs, alternating with segments of more complex DNA averaging about 2200 base pairs. This interspersion of sequences is compared to that found in several other organisms. The properties of the foldback DNA are similarly investigated as a function of DNA fragment size.     

Microsatellites that violate Chargaff's second parity rule have base order-dependent asymmetries in the folding energies of complementary DNA strands and may not drive speciation

Models for meiotic recombination based on Crick's “unpairing postulate” require symmetrical extrusion of stem-loop structures from homologous DNA duplexes. The potential for such extrusion is abundant in many species and, for a given single-strand segment, can be quantitated as the “folding of natural sequence” (FONS) energy value. This, in turn, can be decomposed into base order-dependent and base composition-dependent components. The FONS values of top and bottom strands in most Caenorhabditis elegans segments are close, as are the corresponding base order-dependent and base composition-dependent components; any discrepancies are in the base composition-dependent component. This suggests that the strands would extrude with similar kinetics. However, interspersed among these segments and at the ends of chromosomes (telomeres) are segments containing short tandem repeats (microsatellites) which, by virtue of their high variability, have been postulated to inhibit the pairing of homologous chromosomes and hence drive speciation. In these segments, there are usually wide discrepancies between the FONS values of top and bottom strands, mainly attributable to differences in base order-dependent components. Analyses of artificial microsatellites of different unit sizes and base compositions show that this asymmetrical distribution of folding potential is greatest for microsatellites when the units are short and violate Chargaff's second parity rule. It is proposed that when there is folding asymmetry, recombination proceeds by special, strand-biased, somatic mechanisms analogous to those operating with Chi sequences in Escherichia coli. If meiotic recombination in the germ-line requires extrusion symmetry, then a general inhibitory influence of microsatellite-containing segments could mask the antirecombinational influence of their variability. Thus, microsatellites may not have driven speciation.     

Cytofluorometry and visualisation of DNA base composition in the chromosomes of Drosophila melanogaster

The DNA base composition determined cytofluorometrically with the dyes CMA and DAPI in individual mitotic chromosomes of Drosophila melanogaster agrees very well with reference data obtained by hybridisation. Measurements in polytene chromosomes showed: (1) The base composition in the chromocenter, in chromosome 4 and bands X 1 and 3R 81 is lower than would be expected if they consisted of satellite DNAs only. (2) In the chromosome arms, bands with deviating base composition were found also where no satellite DNAs have been localized. With two visualisation methods — a photographic technique and image analysis — a complex pattern of base composition heterogeneity in the arms of the polytene chromosomes was established. In part this pattern may reflect the intercalary heterochromatin shown by weak point behaviour, ectopic pairing, and late replication.     

Parallel polymorphism for supernumerary segments inChorthippus parallelus (zetterstedt)

A complex and parallel pattern of polymorphism for heterochromatic supernumerary segments in the M₇ and S₈ chromosomes has been found in 14 populations of the meadow grasshopperChorthippus parallelus. Nine distinct karyotype classes for these two chromosome pairs occur though they are not equally represented in different populations. Populations differ also with respect to the frequency of supernumerary segments they contain. In all populations the presence of supernumerary segments leads to a significant elevation of mean cell chiasma frequency compared to individuals from the same population lacking such segments. The extent of the effect appears to differ in different populations. The observed frequencies of S₈ karyotypes conform to the expectations of a Hardy-Weinberg distribution. Those of the M₇, however, do not, and in all but one of the 14 populations there is a significant excess of homokaryotypes. In the Ashurst population 26% of the individuals sampled were characterised by germ-line polysomy for the M₄ chromosome, either in the form of entire tetrasomics or more usually as mosaics ranging from tri- to hepta-somics. In all these polysomics the M₄ chromosomes in excess of two were regularly heteropycnotic at first meiotic prophase from zygotene to diakinesis. As a consequence of this multivalents are rare. Extra M₄ chromosomes do not modify the chiasma characteristics of the other chromosomes in the complement. Nor do they modify the action of the supernumerary segments in any way.     

De novo telomere addition to spacer sequences prior to their developmental degradation in Euplotes crassus

During sexual reproduction, Euplotes crassus precisely fragments its micronuclear chromosomes and synthesizes new telomeres onto the resulting DNA ends to generate functional macronuclear minichromosomes. In the micronuclear chromosomes, the macronuclear-destined sequences are typically separated from each other by spacer DNA segments, which are eliminated following chromosome fragmentation. Recently, in vivo chromosome fragmentation intermediates that had not yet undergone telomere addition have been characterized. The ends of both the macronuclear-destined and eliminated spacers were found to consist of six-base, 3′ overhangs. As this terminal structure on the macronuclear-destined sequences serves as the substrate for de novo telomere addition, we sought to determine if the spacer DNAs might also undergo telomere addition prior to their elimination. Using a polymerase chain reaction approach, we found that at least some spacer DNAs undergo de novo telomere addition. In contrast to macronuclear-destined sequences, heterogeneity could be observed in the position of telomeric repeat addition. The observation of spacer DNAs with telomeric repeats makes it unlikely that differential telomere addition is responsible for differentiating between retained and eliminated DNA. The heterogeneity in telomere addition sites for spacer DNA also resembles the situation found for telomeric repeat addition to macronuclear-destined sequences in other ciliate species.     

Analysis of genomic characters reveals that four distinct gene clusters are correlated with different functions in Burkholderia cenocepacia AU 1054

Possessing three circular chromosomes is a distinct genomic characteristic of Burkholderia cenocepacia AU 1054, a clinically important pathogen in cystic fibrosis. In this study, base composition, codon usage and functional role category were analyzed in the B. cenocepacia AU 1054 genome. Although no bias in the base and codon usage was detected between any two chromosomes, function differences did exist in the genes of each chromosome. Similar base composition and differential functional role categories indicated that genes on these three chromosomes were relatively stable and that a proper division of labor was established. Based on variations in the base or codon usage, four small gene clusters were observed in all of the genes. Multivariate analysis revealed that protein hydrophobicity played a predominant role in shaping base usage bias, while horizontal gene transfer and the gene expression level were the two most important factors that affected the codon usage bias. Interestingly, we also found that these gene clusters were correlated with different biological functions: (i) 45 pyrimidine-leading-codon preferred genes were predominantly involved in regulatory function; (ii) most drug resistance-related genes involved in 826 genes that coding for hydrophobic proteins; (iii) most of the 111 horizontal transfer genes were responsible for genomic plasticity; and (iv) 73 highly expressed genes (predicted by their codon adaptation index values) showed environmental adaptation to cystic fibrosis. Our results showed that genes with base or codon usage bias were affected by mutational pressure and natural selection, and their functions could contribute to drug assistance and transmissible activity in B. cenocepacia.     

Next Generation Sequencing-Based Analysis of Repetitive DNA in the Model Dioceous Plant Silene latifolia

Background

Silene latifolia is a dioceous plant with well distinguished X and Y chromosomes that is used as a model to study sex determination and sex chromosome evolution in plants. However, efficient utilization of this species has been hampered by the lack of large-scale sequencing resources and detailed analysis of its genome composition, especially with respect to repetitive DNA, which makes up the majority of the genome.

Methodology/Principal Findings

We performed low-pass 454 sequencing followed by similarity-based clustering of 454 reads in order to identify and characterize sequences of all major groups of S. latifolia repeats. Illumina sequencing data from male and female genomes were also generated and employed to quantify the genomic proportions of individual repeat families. The majority of identified repeats belonged to LTR-retrotransposons, constituting about 50% of genomic DNA, with Ty3/gypsy elements being more frequent than Ty1/copia. While there were differences between the male and female genome in the abundance of several repeat families, their overall repeat composition was highly similar. Specific localization patterns on sex chromosomes were found for several satellite repeats using in situ hybridization with probes based on k-mer frequency analysis of Illumina sequencing data.

Conclusions/Significance

This study provides comprehensive information about the sequence composition and abundance of repeats representing over 60% of the S. latifolia genome. The results revealed generally low divergence in repeat composition between the sex chromosomes, which is consistent with their relatively recent origin. In addition, the study generated various data resources that are available for future exploration of the S. latifolia genome.     

Characterization of a leaf rust-resistant wheat–Thinopyrum ponticum partial amphiploid BE-1, using sequential multicolor GISH and FISH

In situ hybridization (multicolor GISH and FISH) was used to characterize the genomic composition of the wheat–Thinopyrum ponticum partial amphiploid BE-1. The amphiploid is a high-protein line having resistance to leaf rust (Puccinia recondita f. sp. tritici) and powdery mildew (Blumeria graminis f. sp. tritici) and has in total 56 chromosomes per cell. Multicolor GISH using J, A and D genomic probes showed 16 chromosomes originating from Thinopyrum ponticum and 14 A genome, 14 B genome and 12 D genome chromosomes. Six of the Th. ponticum chromosomes carried segments different from the J genome in their centromeric regions. It was demonstrated that these alien chromosome segments did not originate from the A, B or D genomes of wheat, so the translocation chromosomes were considered to be J^s type chromosomes carrying segments similar to the S genome near the centromeres. Rearrangements between the A and D genomes of wheat were detected. FISH using Afa family, pSc119.2 and pTa71 probes allowed the identification of all the wheat chromosomes present and the determination of the chromosomes involved in the translocations. The 4A and 7A chromosomes were identified as being involved in intergenomic translocations. The replaced wheat chromosome was identified as 7D. The localization of these repetitive DNA clones on the Th. ponticum chromosomes of the amphiploid was described in the present study. On the basis of their multicolor FISH patterns, the alien chromosomes could be arranged in eight pairs and could also be differentiated unequivocally from each other.     

DNA-Replikation und Chromosomenstruktur von Mesostoma (Turbellaria)

During meiosis in M. ehrenbergi (2n=10) and M. lingua (2n=8) male certain chromosomes never pair completely. In these bivalents only terminal pairing appears, crossing over could not be proved by ³H-thymidine autoradiography. DNA amounts of the M. ehrenbergi and M. lingua genomes are in a proportion of 10∶1. The mitotic S-phase of spermatogonia in M. ehrenbergi is twice as long as in M. lingua. In metaphase of spermatogonia a differentiated DNA replication pattern can be identified in M. ehrenbergi as late-pulse-replicating segments. After incorporation of ³H-thymidine X₂-metaphase chromosomes can be found, which show single chromatid labeling, terminal and intercalary isolabeling as well as kinds of chromosome labeling, which can only result from sister strand exchange. After treating the chromosomes with low temperature, colchicine or by hydrolysis (60° C) substructures of the chromatin become visible in both spezies which however are evaluated as artefacts. — Formation of the different isolabeling types is discussed on the basis of a two-strand model of the chromosome fibril. A hypothesis is formulated that the surplusage of DNA in M. ehrenbergi is distributed over all the length of the chromatids as small parts of heterochromatin. This hypothesis is supported by investigations of the DNA replication and the contractility of the chromosomes. Furthermore, a pattern of small DNA particles can be demonstrated after partial destruction of the DNA in metaphase chromosomes of M. ehrenbergi, which could represent this intercalary heterochromatin.     

Chromosome regions containing DNAs of known base composition,specifically evidenced by 2,7-di-t-butyl proflavine

After staining by a new proflavine derivative (2,7-di-t-butyl proflavine, DBP), which specifically binds to the A-T base pairs of DNA by an external process, the constrictions of the human chromosomes 1, 16 and to a lesser extent 9 and the centromeric regions of the chromosomes (except the Y) of Mus musculus are brightly fluorescent. These chromosome regions are known to contain repetitive DNAs rich in A-T. On the contrary, the centromeric regions of the autosomes of Bos taurus, which contain a G-C rich DNA, are faintly fluorescent. The arms of the chromosomes of the three species display a banding similar to, but fainter than, the Q-banding. These results are discussed in correlation with physico-chemical studies on the binding and fluorescence processes of the dye bound to DNA and to nucleohistone. The staining properties of DBP are compared to those of quinacrine, quinacrine mustard and proflavine, three intercalative dyes which are also supposed to reveal the A-T base pairs along the chromosomes, but are faintly fluorescent on the human and murine A-T rich regions. This comparison leads us to discuss the mechanisms responsible for the chromosomal banding in relation to DNA base composition and repetitiveness, protein distribution and packing of the chromatin fibers, along the chromosomes.     

DNS-Gehalt und Chromosomenstruktur bei Amphibien

Comparative karyotype analysis and cytophotometric DNA measurements on further amphibian species (Hyla arborea, Bombina variegata, B. bombina, Triturus vulgaris, T. alpestris, and Salamandra salamandra) were carried out. The relative DNA values of the genomes determined for these species and other amphibians investigated earlier (Ullerich, 1966, 1967), already do nearly exclude the hypothesis that the interspecific differences in DNA content in frogs, toads, and salamanders are caused by differential polynemy of their chromosomes. Electron microscopic investigations on the DNA axes of lampbrush chromosomes of Bufo calamita, B. viridis, B. bufo, Rana esculenta, Bombina variegata, and Triturus alpestris treated with trypsin and ribonuclease confirm that the chromosomes of these species are not polynemic; in all species analysed the lampbrush chromosomes consist of the same number of DNA strands. The double-strandedness observed regularly in several segments of the chromatid axes in the loops as well as in the interchromomeric regions of all species suggest that the chromatids possibly are divided into half-chromatids. The minimum diameter of these two deoxyribonuclease-sensitive fibrills is 20–35 Å, whereas the chromatid axes in those segments which do not show double-strandedness mostly measure 40–65 Å. The high DNA amounts and interspecific differences in DNA content in the amphibian species analysed, probably in all amphibians, therefore must be caused during evolutionary processes by local increase (perhaps in a smaller extent also by-local decrease) in DNA in the chromosomes.     

Isolation,fractionation and biochemical analysis of the metaphase chromosomes of Microtus agrestis

A method has been developed for isolating metaphase chromosomes from Microtus agrestis fibroblasts in relatively large quantities with recovery of about 50% of the chromosomes present in the metaphase cells. The method employs pressure homogenisation to release the chromosomes from the cells. The average chemical composition of the Microtus chromosome preparations is 24.6% DNA, 19.9% RNA and 55.5% protein. The isolated chromosomes were fractionated by sedimentation velocity in a density gradient into three size groups in one of which 75–80% of the chromosomes were the large sex-chromosomes. The relative composition of this fraction containing most of the heterochromatin of the cell was DNA: 100, RNA: 59, acid-soluble protein: 54, acid-insoluble protein: 178. — Disc electrophoresis studies revealed no significant difference in the histone patterns between the euchromatic and heterochromatic chromosomes of the three chromosome size-groups. Metaphase chromosomes appear to have a lower lysine-rich histone content than interphase nuclei.     

Rapid determination of nucleotide content and its application to the study of genome structure.

We have developed a sensitive, reliable and accurate procedure for estimating the base composition of small samples of DNAs. This method has been applied to the analysis of genomic DNAs from several sources including large regions of human DNA cloned as yeast artificial chromosomes. To determine whether the human genome is compartmentalized into large segments of homogeneous base composition, we examined the GC content of a 1.2 megabase contig spanning the cystic fibrosis gene.     

Mating variation by DNA inversions of shufflon in plasmid R64

Gene organization of the 54-kb transfer region of IncI1 plasmid R64 was deduced from the DNA sequence. Forty-eight ORFs were found in this region. A unique DNA rearrangement designated shufflon is located at the downstream region of an operon responsible for synthesis of thin pilus. The shufflon of R64 consists of four DNA segments, designated as A, B, C, and D, which are flanked and separated by seven 19-bp repeat sequences. Site-specific recombination mediated by the product of the rci gene between any two inverted repeats results in a complex DNA rearrangement. An analysis of open reading frames revealed that the shufflon is a biological switch to select one of seven C-terminal segments of the pilV genes. The products of pilV genes were shown to be components of thin pilus which was required for liquid mating.Seven R64 derivatives where the pilV genes were fixed in the seven C-terminal segments were constructed and their transfer frequencies in liquid mating were measured using various bacterial strains as recipients. Transfer frequencies of R64 in liquid mating strongly depended on the combination of C-terminal segments of the pilV genes in donor cells and bacterial strains of recipient cells, suggesting that the shufflon determines the recipient specificity in liquid mating of plasmid R64.