Satellite DNA Sequences in Canidae and Their Chromosome Distribution in Dog and Red Fox

Satellite DNA is a characteristic component of mammalian centromeric heterochromatin, and a comparative analysis of its evolutionary dynamics can be used for phylogenetic studies. We analysed satellite and satellite-like DNA sequences available in NCBI for 4 species of the family Canidae (red fox, Vulpes vulpes, VVU; domestic dog, Canis familiaris, CFA; arctic fox, Vulpes lagopus, VLA; raccoon dog, Nyctereutes procyonoides procyonoides, NPR) by comparative sequence analysis, which revealed 86-90% intraspecies and 76-79% interspecies similarity. Comparative fluorescence in situ hybridisation in the red fox and dog showed signals of the red fox satellite probe in canine and vulpine autosomal centromeres, on VVUY, B chromosomes, and in the distal parts of VVU9q and VVU10p which were shown to contain nucleolus organiser regions. The CFA satellite probe stained autosomal centromeres only in the dog. The CFA satellite-like DNA did not show any significant sequence similarity with the satellite DNA of any species analysed and was localised to the centromeres of 9 canine chromosome pairs. No significant heterochromatin block was detected on the B chromosomes of the red fox. Our results show extensive heterogeneity of satellite sequences among Canidae and prove close evolutionary relationships between the red and arctic fox.

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Sequence Analysis and FISH Mapping of Four Satellite DNA Families among Cervidae

Genes ◽

10.3390/genes11050584 ◽

2020 ◽

Vol 11 (5) ◽

pp. 584

Author(s):

Miluse Vozdova ◽

Svatava Kubickova ◽

Halina Cernohorska ◽

Jan Fröhlich ◽

Natália Martínková ◽

...

Keyword(s):

Dna Sequences ◽

Satellite Dna ◽

Phylogenetic Trees ◽

In Situ Hybridisation ◽

Gc Content ◽

Copy Number Variations ◽

Binding Motif ◽

Fluorescence In Situ Hybridisation ◽

Chromosomal Distribution ◽

Satellite Dnas

Centromeric and pericentromeric chromosome regions are occupied by satellite DNA. Satellite DNAs play essential roles in chromosome segregation, and, thanks to their extensive sequence variability, to some extent, they can also be used as phylogenetic markers. In this paper, we isolated and sequenced satellite DNA I-IV in 11 species of Cervidae. The obtained satellite DNA sequences and their chromosomal distribution were compared among the analysed representatives of cervid subfamilies Cervinae and Capreolinae. Only satI and satII sequences are probably present in all analysed species with high abundance. On the other hand, fluorescence in situ hybridisation (FISH) with satIII and satIV probes showed signals only in a part of the analysed species, indicating interspecies copy number variations. Several indices, including FISH patterns, the high guanine and cytosine (GC) content, and the presence of centromere protein B (CENP-B) binding motif, suggest that the satII DNA may represent the most important satellite DNA family that might be involved in the centromeric function in Cervidae. The absence or low intensity of satellite DNA FISH signals on biarmed chromosomes probably reflects the evolutionary reduction of heterochromatin following the formation of chromosome fusions. The phylogenetic trees constructed on the basis of the satellite I-IV DNA relationships generally support the present cervid taxonomy.

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Sequencing of Supernumerary Chromosomes of Red Fox and Raccoon Dog Confirms a Non-Random Gene Acquisition by B Chromosomes

Genes ◽

10.3390/genes9080405 ◽

2018 ◽

Vol 9 (8) ◽

pp. 405 ◽

Cited By ~ 9

Author(s):

Alexey Makunin ◽

Svetlana Romanenko ◽

Violetta Beklemisheva ◽

Polina Perelman ◽

Anna Druzhkova ◽

...

Keyword(s):

Cell Cycle ◽

Red Fox ◽

B Chromosome ◽

Mendelian Inheritance ◽

B Chromosomes ◽

Nyctereutes Procyonoides ◽

Segmental Duplications ◽

Raccoon Dog ◽

Gene Acquisition ◽

Genomic Regions

B chromosomes (Bs) represent a variable addition to the main karyotype in some lineages of animals and plants. Bs accumulate through non-Mendelian inheritance and become widespread in populations. Despite the presence of multiple genes, most Bs lack specific phenotypic effects, although their influence on host genome epigenetic status and gene expression are recorded. Previously, using sequencing of isolated Bs of ruminants and rodents, we demonstrated that Bs originate as segmental duplications of specific genomic regions, and subsequently experience pseudogenization and repeat accumulation. Here, we used a similar approach to characterize Bs of the red fox (Vulpes vulpes L.) and the Chinese raccoon dog (Nyctereutes procyonoides procyonoides Gray). We confirm the previous findings of the KIT gene on Bs of both species, but demostrate an independent origin of Bs in these species, with two reused regions. Comparison of gene ensembles in Bs of canids, ruminants, and rodents once again indicates enrichment with cell-cycle genes, development-related genes, and genes functioning in the neuron synapse. The presence of B-chromosomal copies of genes involved in cell-cycle regulation and tissue differentiation may indicate importance of these genes for B chromosome establishment.

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A new family of satellite DNA sequences as a major component of centromeric heterochromatin in owls (Strigiformes)

Chromosoma ◽

10.1007/s00412-004-0283-7 ◽

2004 ◽

Vol 112 (7) ◽

pp. 372-373 ◽

Cited By ~ 1

Author(s):

Kazuhiko Yamada ◽

Chizuko Nishida-Umehara ◽

Yoichi Matsuda

Keyword(s):

Dna Sequences ◽

Satellite Dna ◽

Centromeric Heterochromatin ◽

New Family

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Survey on viral pathogens in wild red foxes (Vulpes vulpes) in Germany with emphasis on parvoviruses and analysis of a DNA sequence from a red fox parvovirus

Epidemiology and Infection ◽

10.1017/s0950268898001319 ◽

1998 ◽

Vol 121 (2) ◽

pp. 433-440 ◽

Cited By ~ 57

Author(s):

U. TRUYEN ◽

T. MÜLLER ◽

R. HEIDRICH ◽

K. TACKMANN ◽

L. E. CARMICHAEL

Keyword(s):

Dna Sequence ◽

Dna Sequences ◽

Vulpes Vulpes ◽

Red Fox ◽

Canine Parvovirus ◽

Domestic Dog ◽

Interspecies Transmission ◽

Red Foxes ◽

Feline Panleukopenia Virus ◽

Free Ranging

The seroprevalence of canine parvovirus (CPV), canine distemper virus (CDV), canine adenovirus (CAV) and canine herpesvirus (CHV) infections in red foxes (Vulpes vulpes) was determined in fox sera collected between 1991 and 1995. A total of 500 sera were selected and the seroprevalences were estimated to be 13% (65 of 500 sera) for CPV, 4·4% (17 of 383 sera) for CDV, 3·5% (17 of 485 sera) for CAV, and 0·4% (2 of 485 sera) for CHV, respectively. No statistically significant differences were observed between the two (rural and suburban) areas under study.Parvovirus DNA sequences were amplified from tissues of free-ranging foxes and compared to those of prototype viruses from dogs and cats. We report here a parvovirus sequence indicative of a true intermediate between the feline panleukopenia virus-like viruses and the canine parvovirus-like viruses. The red fox parvoviral sequence, therefore, appears to represent a link between those viral groups. The DNA sequence together with a significant seroprevalence of parvovirus infections in foxes supports the hypothesis that the sudden emergence of canine parvovirus in the domestic dog population may have involved the interspecies transmission between wild and domestic carnivores.

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Telomere dysfunction in prostatic carcinogenesis

Journal of Clinical Oncology ◽

10.1200/jco.2006.24.18_suppl.10021 ◽

2006 ◽

Vol 24 (18_suppl) ◽

pp. 10021-10021

Author(s):

A. M. Joshua ◽

B. Vukovic ◽

I. Braude ◽

A. Evans ◽

J. Srigley ◽

...

Keyword(s):

Telomere Length ◽

Dna Sequences ◽

Specific Binding ◽

In Situ Hybridisation ◽

Intraepithelial Neoplasia ◽

Great Promise ◽

Fluorescence In Situ Hybridisation ◽

Telomere Shortening ◽

Prostate Intraepithelial Neoplasia ◽

Prostatic Epithelium

10021 Background: Telomeres are composed of tandemly repeated DNA sequences (TTAGGG) and specific binding proteins located at the ends of eukaryotic chromosomes. They stabilize chromosomal ends; telomere shortening is an important mechanism of genomic instability and can lead to end-to-end chromosomal fusion, rearrangements and cell death. Here we evaluate the hypothesis that telomere shortening contributes to the development of prostate cancer (CaP). Methods: We used telomeric, centromeric and chromosome specific peptide-nucleic acid probes with z-stacked quantitative fluorescence in-situ hybridisation analysis to initially analyse 15 radical prostatectomy specimens and then subsequently sextant core biopsies from 80 men obtained in 1998–2001 containing high-grade prostate intraepithelial neoplasia (HPIN) only. The biopsy cohort outcome is blinded to prevent experimental bias and has a minimum follow-up of 2 years with 41 men diagnosed subsequently with CaP and 39 men without CaP on rebiopsy. Regions of interest were identifying with an overlying haematoxylin and eosin slide. Results: We found a significant decrease in telomere length in both HPIN and CaP in comparison to normal prostatic epithelium accompanied by elevated rates of aneusomy. Telomere erosion in HPIN was more common in regions of the prostate-containing CaP. We now have analyzed ∼4000 cells of matching HPIN and surrounding stroma. Preliminary analysis demonstrated that the median telomere length in HPIN is approximately 27% of the surrounding stroma with upper and lower quartiles being 16% and 38% respectively. Logistic regression analysis is in progress to determine whether the length of the shortest telomeres or the average telomeric length in a sample predicts for subsequent diagnosis of CaP. Secondary analyses are examining the effect of telomere length on the interval to the diagnosis of CaP, the effect of age on telomere length and the eventual Gleason score. Conclusions: Analysis of telomere length holds great promise for developing improved prognostic markers in prostatic carcinogenesis. This is a first of its kind study in the field. No significant financial relationships to disclose.

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Comparative Study of the Bush Dog (Speothos venaticus) Karyotype and Analysis of Satellite DNA Sequences and Their Chromosome Distribution in Six Species of Canidae

Cytogenetic and Genome Research ◽

10.1159/000503082 ◽

2019 ◽

Vol 159 (2) ◽

pp. 88-96 ◽

Cited By ~ 1

Author(s):

Miluse Vozdova ◽

Svatava Kubickova ◽

Halina Cernohorska ◽

Jan Fröhlich ◽

Roman Vodicka ◽

...

Keyword(s):

Dna Sequences ◽

Comparative Sequence Analysis ◽

Domestic Dog ◽

Nyctereutes Procyonoides ◽

Grey Wolf ◽

Raccoon Dog ◽

Satellite Dnas ◽

Fusion Site ◽

Bush Dog ◽

Speothos Venaticus

The bush dog (Speothos venaticus, 2n = 74) is a near threatened species taxonomically classified among South American canids. We revised the bush dog karyotype and performed a comparative sequence analysis of satellite and satellite-like DNAs in 6 canids: the bush dog, domestic dog (Canis familiaris, 2n = 78), grey wolf (C. lupus, 2n = 78), Chinese raccoon dog (Nyctereutes procyonoides procyonoides, 2n = 54+B), red fox (Vulpes vulpes, 2n = 34+B), and arctic fox (V. lagopus, 2n = 48-50) to specify the species position among Canidae. Using FISH with painting and BAC probes, we found that the distribution of canid evolutionarily conserved chromosome segments in the bush dog karyotype is similar to that of the domestic dog and grey wolf. The bush dog karyotype differs by 2 acrocentric chromosome pairs formed by tandem fusions of the canine (29;34) and (26;35) orthologues. An interstitial signal of the telomeric probe was observed in the (26;35) fusion site in the bush dog indicating a recent evolutionary origin of this rearrangement. Sequences and hybridisation patterns of satellite DNAs were compared, and a phylogenetic tree of the 6 canid species was constructed which confirmed the bush dog position close to the wolf-like canids, and apart from the raccoon dog and foxes.

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The role of cytokines in immunological tolerance: potential for therapy

Expert Reviews in Molecular Medicine ◽

10.1017/s1462399400001940 ◽

2000 ◽

Vol 2 (7) ◽

pp. 1-14 ◽

Cited By ~ 10

Author(s):

Nicole McNeil ◽

Thomas Ried

Keyword(s):

Chromosomal Aberrations ◽

Dna Sequences ◽

In Situ Hybridisation ◽

Comparative Genomic ◽

Chromosomal Anomalies ◽

Neoplastic Disease ◽

Fluorescence In Situ Hybridisation ◽

Metaphase Chromosomes ◽

Molecular Cytogenetic ◽

Molecular Cytogenetic Techniques

Molecular cytogenetic techniques that are based on fluorescence in situ hybridisation (FISH) have become invaluable tools for the diagnosis and identification of the numerous chromosomal aberrations that are associated with neoplastic disease, including both haematological malignancies and solid tumours. FISH can be used to identify chromosomal rearrangements, by detecting specific DNA sequences with fluorescently labelled DNA probes. The technique of comparative genomic hybridisation (CGH) involves two-colour FISH. It can be used to establish ratios of fluorescence intensity values between tumour DNA and control DNA along normal reference metaphase chromosomes, and thereby to detect DNA copy-number changes such as gains and losses of specific chromosomal regions and gene amplifications. Spectral karyotyping (SKY) is a novel molecular cytogenetic method for characterising numerical and structural chromosomal aberrations. SKY involves the simultaneous hybridisation of 24 differentially labelled chromosome-painting probes, followed by spectral imaging and chromosome classification, and produces a colour karyotype of the entire genome. The use of SKY has contributed significantly to the identification of chromosomal anomalies that are associated with constitutional and cancer cytogenetics, and has revealed many aberrations that go undetected by traditional banding techniques. In this article, we have reviewed these new molecular cytogenetic techniques and described their various applications in molecular medicine.

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Scaffold attachments within the human genome

Journal of Cell Science ◽

10.1242/jcs.110.21.2673 ◽

1997 ◽

Vol 110 (21) ◽

pp. 2673-2682 ◽

Cited By ~ 2

Author(s):

J.M. Craig ◽

S. Boyle ◽

P. Perry ◽

W.A. Bickmore

Keyword(s):

Dna Sequences ◽

Constitutive Heterochromatin ◽

In Situ Hybridisation ◽

Fluorescence In Situ Hybridisation ◽

Loop Size ◽

Inactive X Chromosome ◽

Attachment Sites ◽

The Matrix ◽

Eukaryotic Chromatin

It is generally agreed that, above the level of the 30 nm fibre, eukaryotic chromatin is constrained into loops, but there is disagreement about the nature of the substructure that serves to anchor loops and the DNA sequences that act as the attachment sites. This problem may stem from the very different methods that all purport to separate loop and attached DNAs. We have tested ideas about how the genome is arranged into loops by analysing the average loop size over different cytologically resolvable regions of human chromosomes using fluorescence in situ hybridisation with loop and attached DNA fractions. Variations in average loop size, along and between chromosomes, measurable at this level of resolution were small but significant and were dependent on the extraction method. This emphasises the fundamental differences between the nuclear substructure probed by different protocols. DNA attached to the nuclear ‘scaffold’ or ‘matrix’ hybridises preferentially to gene-poor regions of the genome (G-bands). Conversely, fractions attached to the nuclear ‘skeleton’ hybridise preferentially to gene-rich R-bands and sites of high levels of transcription. The inactive X chromosome has a deficit of associations with the nuclear skeleton but not with the matrix or scaffold. A large excess of attached sequences is found at some sites of constitutive heterochromatin, but not at centromeres.

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