Characterization and origin of extrachromosomal DNA granules in Sarcophaga bullata

1987 ◽  
Vol 88 (3) ◽  
pp. 327-334
Author(s):  
H. Bultmann ◽  
R. Mezzanotte
Keyword(s):  
X Chromosome ◽  
Repetitive Sequences ◽  
Buoyant Density ◽  
Restriction Enzymes ◽  
Extrachromosomal Dna ◽  
Mitotic Chromosomes ◽  
Sarcophaga Bullata ◽  
Ethidium Bromide Staining ◽  
Polytene Nuclei

We have used endonuclease treatment in situ, followed by Giemsa or ethidium bromide staining, for mapping repetitive sequences on the chromosomes of the flesh fly Sarcophaga bullata and thus for studying extrachromosomal DNA granules in this species. All three restriction enzymes employed (HaeIII, A1uI and HindIII) show the same cytological effects, except for a single interstitial band. In both polytene and mitotic chromosomes, chromatin resistant to these endonucleases presumably includes at least three endonucleases presumably includes at least three previously unrecognized buoyant density satellites (1.663, 1.670 and 1.692 g ml-1 in neutral CsCl), and is predominantly localized in the pericentric regions of all five autosomes. Mitotic treated chromosomes show that the entire rod-shaped X chromosome, but no part of the dot-like Y chromosome, consists of endonuclease-resistant chromatin. The most unusual heterochromatic component of polytene nuclei in this species, the ‘extrachromosomal DNA granules’, are also entirely resistant to digestion with endonucleases. We think that these DNA granules represent dispersed X chromatin and not, as previously assumed, extruded autosomal heterochromatin.

Analysis of the sex chromosomes of the Mediterranean fruit fly by microdissected DNA probes

Genome ◽  
1998 ◽  
Vol 41 (1) ◽  
pp. 74-78 ◽  
Author(s):  
Ute Willhoeft ◽  
Jutta Mueller-Navia ◽  
Gerald Franz
Keyword(s):  
Y Chromosome ◽  
X Chromosome ◽  
Sex Chromosomes ◽  
Fruit Fly ◽  
Mediterranean Fruit Fly ◽  
Oligonucleotide Primer ◽  
Mitotic Chromosomes ◽  
Degenerate Oligonucleotide ◽  
The Mediterranean

In the Mediterranean fruit fly, Ceratitis capitata, the sex-determining region maps to the long arm of the Y chromosome. DNA from this region of the Y chromosome and, for comparison, from the tip of the long arm of the X chromosome, was isolated by microdissection and amplified by degenerate oligonucleotide primer PCR (DOP-PCR). FISH of the Y-chromosomal microdissection products medY1-medY5 to mitotic chromosomes revealed hybridization signals on most of the long arm of the Y chromosome, including the male-determining region, and on the long arm of the X chromosome, as well as weaker signals on the autosomes, some of which were located in the heterochromatin next to the centromeres. The X-chromosomal microdissected probe medX1 revealed strong signals on the sex chromosomes and randomly distributed signals on the autosomes. Chromosomal in situ suppression hybridization indicates that the Y chromosome contains considerable amounts of Y-enriched and Y-specific sequences and that X-enriched sequences are present on the long arm of the X chromosome. The microdissected probes medY1, medY2, and medX1 hybridize to the sex chromosomes of two closely related species,Ceratitis rosa and Trirhithrum coffeae.

Genomic affinities of Zea luxurians, Z. diploperennis, and Z. perennis: Meiotic behavior of their F1 hybrids and genomic in situ hybridization (GISH)

Genome ◽  
1999 ◽  
Vol 42 (5) ◽  
pp. 993-1000 ◽  
Author(s):  
L Poggio ◽  
V Confalonieri ◽  
C Comas ◽  
G Gonzalez ◽  
C A Naranjo
Keyword(s):  
In Situ Hybridization ◽  
Repetitive Sequences ◽  
Basic Chromosome Number ◽  
Genomic In Situ Hybridization ◽  
F1 Hybrids ◽  
Meiotic Behavior ◽  
Mitotic Chromosomes ◽  
Cytological Evidence ◽  
Zea Luxurians

Since 1987 cytological evidence has arisen in our laboratory, pointing to x = 5 as the original basic chromosome number of maize and its related wild species. This paper deals with the analysis of the meiotic behavior of F1 hybrids Zea luxurians × Z. diploperennis (2n = 20) and Z. luxurians × Z. perennis (2n = 30). In the first hybrid the most frequent configuration was 8ll + 4l and in the latter was 5lll + 5ll + 5l. Applying GISH (genomic in situ hybridization) to mitotic chromosomes of Z. luxurians we found that DAPI (4', 6-diamidino-2-phenylindole) positive bands located in all telomeric regions of this species did not hybridize with either Z. perennis or Z. diploperennis genomic probe. Therefore, Z. luxurians has a repetitive sequence that can be used in fluorescent staining to identify its chromosomes. When GISH was employed on metaphase I of the 2n = 30 hybrid, all the univalents showed distinctive telomeres of Z. luxurians, while the bivalents did not present any signal. These findings show that the formation of bivalent-univalent configurations is not a random event. The bivalents tend to be spatially separated and are very often observed forming an independent group of 5II. Finally, trivalents were composed by one chromosome labeled in its telomeric regions, and two smaller and unlabeled ones. The use of chromosome markers of Z. luxurians demonstrated to be a good step forward in interpreting the nature of meiotic configurations in 2n = 30 Zea spp. hybrids. They can help to clarify the relationship between genomes and provide a useful addition to the taxonomic classification in the genus Zea.Key Words: Zea hybrids, evolution, cytogenetics, repetitive sequences, heterochromatic knobs.

Distribution of highly repeated DNA sequences in species of the genus Lens Miller

Genome ◽  
2003 ◽  
Vol 46 (6) ◽  
pp. 1118-1124 ◽  
Author(s):  
Incoronata Galasso
Keyword(s):  
Dna Sequences ◽  
Lens Culinaris ◽  
Repetitive Sequences ◽  
5S Rdna ◽  
Chromosome Identification ◽  
Mitotic Chromosomes ◽  
Genomic Relationships ◽  
Lens Nigricans ◽  
25S Rdna

Multiple-target fluorescence in situ hybridization (FISH) was applied on mitotic chromosomes of seven Lens taxa using two highly repetitive sequences (pLc30 and pLc7) isolated from the cultivated lentil and the multigene families for the 18S–5.8S–25S (pTa71) and 5S rRNA (pTa794) from wheat simultaneously as probes. The number and location of pLc30 and pLc7 sites on chromosomes varied markedly among the species, whereas the hybridization pattern of 5S rDNA and 18S–5.8S–25S rDNA was less variable. In general, each species showed a typical FISH karyotype and few differences were observed among accessions belonging to the same species, except for the accessions of Lens odemensis. The most similar FISH karyotype to the cultivated lentil is that of Lens culinaris subsp. orientalis, whereas Lens nigricans and Lens tomentosus are the two species that showed the most divergent FISH patterns compared with all taxa for number and location of pLc30 and 18S–5.8S–25S rDNA sites.Key words: chromosome identification, comparative FISH karyotype, wild Lens species, genomic relationships.

Some trends in the evolution of very large chromosomes

1978 ◽  
Vol 283 (997) ◽  
pp. 309-318 ◽  
Keyword(s):  
Molecular Mechanisms ◽  
Repetitive Sequences ◽  
Repeated Sequence ◽  
Lampbrush Chromosomes ◽  
Mitotic Chromosomes ◽  
Rapid Divergence ◽  
Cytological Localization ◽  
Chromosome I ◽  
Heavy Labelling

The general features of the arrangement and cytological distribution of repeated sequences in animal chromosomes are reviewed. These features include internal repetitiveness, conservation of clearly functional sequences, rapid divergence of certain classes of repeated sequence with subsequent fixation of families of diverged sequences, and well defined cytological localization of large blocks of sequences in specific parts of the chromosome set. Moderately or ‘middle’ repetitive (m.r.) sequences constitute a large part of the genomes of higher organisms, they seem to accumulate in a balanced manner within chromosome sets, they are mainly responsible for genome growth, and they are interspersed with sequences of other kinds. Little is known about their cytological distribution. Four experiments are described, each of which aimed to locate middle repetitive sequences in the chromosomes of a salamander and a newt. Tritiated m.r. DNA from Plethodon cinereus binds in a non-random fashion to the meiotic diplotene and mitotic chromosomes of the same species, suggesting a non-random distribution of m.r. sequences on these chromosomes. The same DNA, hybridized in situ to the RNA transcripts on the loops of lampbrush chromosomes, produces light and widespread labelling of many loops, but intense labelling of six pairs of loops, each of which lies near to a centromere. Similar experiments in which newt m.r. DNA was hybridized in situ to newt lampbrush chromosomes showed heavy labelling of about 30 loop pairs on each of the long heteromorphic arms of chromosome I, but very little labelling elsewhere. Autoradiographs of newt mitotic chromosomes hybridized with newt m.r. DNA showed rather even labelling of all chromosomes including chromosome I. The significance of the heavy labelling of lampbrush loops near centromeres and on the heteromorphic arms of the newt chromosome I is discussed in relation to possible cytological and molecular mechanisms for generating and preserving families of tandemly linked and cytologically localized m.r. sequences.

Karyotype variation in the albino rainbow trout (Oncorhynchus mykiss (Walbaum))

Genome ◽  
2009 ◽  
Vol 52 (4) ◽  
pp. 347-352 ◽  
Author(s):  
K. Ocalewicz ◽  
S. Dobosz
Keyword(s):  
Rainbow Trout ◽  
Oncorhynchus Mykiss ◽  
X Chromosome ◽  
5S Rdna ◽  
Mitotic Chromosomes ◽  
Dapi Staining ◽  
Rainbow Trout Oncorhynchus Mykiss ◽  
Rdna Sequences ◽  
Cytogenetic Location

A Robertsonian polymorphism resulting in diploid chromosome number ranging from 59 to 61 and constant chromosome arm number (fundamental number = 104) was observed in the albino rainbow trout ( Oncorhynchus mykiss (Walbaum)) from the yellow color strain. In one individual, 90 mitotic chromosomes and 156 chromosome arms were counted, indicating the fish as a triploid. Morphology of the chromosomes, DAPI staining, and the cytogenetic location of 5S rDNA sequences showed sex-related chromosomal heteromorphism in the specimens. Additionally, length polymorphism of the X chromosome was detected in the studied individuals and two morphs of the X chromosome were described, XL and XS, according to the size of its short arm (p). The XS was observed in the female as well as male albino rainbow trout; however, among females, no XSXS genotype was found. After primed in situ labeling with 5S rDNA primers, the p-arms of both types of the X chromosome showed similar hybridization signals. On the other hand, fluorescence in situ hybridization with telomeric PNA (peptide nucleic acid) probe exhibited weak hybridization spots on the p-arm of the XS chromosome compared with the distinct hybridization spots observed on the XL p-arm. This could reflect a different telomere length on the p-arm of the XS and XL chromosomes. Partial translocation and deletion of the X chromosome p-arm are considered to be responsible for the p-arm length difference between the two morphological variants of X chromosome.

scholarly journals A cookbook for DNase Hi-C

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Maria Gridina ◽  
Evgeniy Mozheiko ◽  
Emil Valeev ◽  
Ludmila P. Nazarenko ◽  
Maria E. Lopatkina ◽  
...  
Keyword(s):  
Rational Design ◽  
Restriction Enzymes ◽  
Nucleotide Exchange ◽  
Computational Tools ◽  
3 Dimensional ◽  
Cultured Human Cells ◽  
Dna Ends ◽  
By Products ◽  
Robust Protocol

Abstract Background The Hi-C technique is widely employed to study the 3-dimensional chromatin architecture and to assemble genomes. The conventional in situ Hi-C protocol employs restriction enzymes to digest chromatin, which results in nonuniform genomic coverage. Using sequence-agnostic restriction enzymes, such as DNAse I, could help to overcome this limitation. Results In this study, we compare different DNAse Hi-C protocols and identify the critical steps that significantly affect the efficiency of the protocol. In particular, we show that the SDS quenching strategy strongly affects subsequent chromatin digestion. The presence of biotinylated oligonucleotide adapters may lead to ligase reaction by-products, which can be avoided by rational design of the adapter sequences. Moreover, the use of nucleotide-exchange enzymes for biotin fill-in enables simultaneous labelling and repair of DNA ends, similar to the conventional Hi-C protocol. These improvements simplify the protocol, making it less expensive and time-consuming. Conclusions We propose a new robust protocol for the preparation of DNAse Hi-C libraries from cultured human cells and blood samples supplemented with experimental controls and computational tools for the evaluation of library quality.

scholarly journals Molecular Characterization of hobo-Mediated Inversions in Drosophila melanogaster

Genetics ◽  
1996 ◽  
Vol 144 (2) ◽  
pp. 647-656
Author(s):  
William B Eggleston ◽  
Nac R Rim ◽  
Johng K Lim
Keyword(s):  
X Chromosome ◽  
Polymerase Chain Reaction Amplification ◽  
Polytene Chromosomes ◽  
Chromosomal Inversions ◽  
Hobo Element ◽  
Reaction Amplification ◽  
Notch Locus ◽  
Polymerase Chain

Abstract The structure of chromosomal inversions mediated by hobo transposable elements in the Uc-1 X chromosome was investigated using cytogenetic and molecular methods. Uc-1 contains a phenotypically silent hobo element inserted in an intron of the Notch locus. Cytological screening identified six independent Notch mutations resulting from chromosomal inversions with one breakpoint at cytological position 3C7, the location of Notch. In situ hybridization to salivary gland polytene chromosomes determined that both ends of each inversion contained hobo and Notch sequences. Southern blot analyses showed that both breakpoints in each inversion had hobo-Notch junction fragments indistinguishable in structure from those present in the Uc-1 X chromosome prior to the rearrangements. Polymerase chain reaction amplification of the 12 hobo-Notch junction fragments in the six inversions, followed by DNA sequence analysis, determined that each was identical to one of the two hobo-Notch junctions present in Uc-1. These results are consistent with a model in which hobo-mediated inversions result from homologous pairing and recombination between a pair of hobo elements in reverse orientation.

Sign in / Sign up

Export Citation Format

Share Document