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

Genes ◽  
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.

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

2016 ◽  
Vol 150 (2) ◽  
pp. 118-127 ◽  
Author(s):  
Miluse Vozdova ◽  
Svatava Kubickova ◽  
Halina Cernohorska ◽  
Jan Fröhlich ◽  
Jiri Rubes
Keyword(s):  
Dna Sequences ◽  
Satellite Dna ◽  
Red Fox ◽  
In Situ Hybridisation ◽  
B Chromosomes ◽  
Domestic Dog ◽  
Centromeric Heterochromatin ◽  
Arctic Fox ◽  
Nyctereutes Procyonoides ◽  
Fluorescence In Situ Hybridisation

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.

The molecular structure, chromosomal organization, and interspecies distribution of a family of tandemly repeated DNA sequences of Antirrhinum majus L.

Genome ◽  
1996 ◽  
Vol 39 (2) ◽  
pp. 243-248 ◽  
Author(s):  
Thomas Schmidt ◽  
Jörg Kudla
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequences ◽  
Satellite Dna ◽  
Antirrhinum Majus ◽  
Repeated Dna ◽  
Satellite Dnas ◽  
Repeated Dna Sequences ◽  
The North ◽  
Tandemly Repeated Dna

Monomers of a major family of tandemly repeated DNA sequences of Antirrhinum majus have been cloned and characterized. The repeats are 163–167 bp long, contain on average 60% A + T residues, and are organized in head-to-tail orientation. According to site-specific methylation differences two subsets of repeating units can be distinguished. Fluorescent in situ hybridization revealed that the repeats are localized at centromeric regions of six of the eight chromosome pairs of A. majus with substantial differences in array size. The monomeric unit shows no homologies to other plant satellite DNAs. The repeat exists in a similar copy number and conserved size in the genomes of six European species of the genus Antirrhinum. Tandemly repeated DNA sequences with homology to the cloned monomer were also found in the North American section Saerorhinum, indicating that this satellite DNA might be of ancient origin and was probably already present in the ancestral genome of both sections. Key words : Antirrhinum majus, satellite DNA, repetitive DNA, methylation, in situ hybridization.

Satellite DNA in Plants: More than Just Rubbish

2015 ◽  
Vol 146 (2) ◽  
pp. 153-170 ◽  
Author(s):  
Manuel A. Garrido-Ramos
Keyword(s):  
Dna Sequences ◽  
Satellite Dna ◽  
Dna Repeats ◽  
Satellite Dnas ◽  
Factors Affecting ◽  
Functional Roles ◽  
Tandem Repeat Sequences ◽  
Satellite Repeats ◽  
History Of ◽  
Main Components

For decades, satellite DNAs have been the hidden part of genomes. Initially considered as junk DNA, there is currently an increasing appreciation of the functional significance of satellite DNA repeats and of their sequences. Satellite DNA families accumulate in the heterochromatin in different parts of the eukaryotic chromosomes, mainly in pericentromeric and subtelomeric regions, but they also span the functional centromere. Tandem repeat sequences may spread from subtelomeric to interstitial loci, leading to the formation of chromosome-specific loci or to the accumulation in equilocal sites in different chromosomes. They also appear as the main components of the heterochromatin in the sex-specific region of sex chromosomes. Satellite DNA, required for chromosome organization, also plays a role in pairing and segregation. Some satellite repeats are transcribed and can participate in the formation and maintenance of heterochromatin structure and in the modulation of gene expression. In addition to the identification of the different satellite DNA families, their characteristics and location, we are interested in determining their impact on the genomes, by identifying the mechanisms leading to their appearance and amplification as well as in understanding how they change over time, the factors affecting these changes, and the influence exerted by the evolutionary history of the organisms. On the other hand, satellite DNA sequences are rapidly evolving sequences that may cause reproductive barriers between organisms and promote speciation. The accumulation of experimental data collected in recent years and the emergence of new approaches based on next-generation sequencing and high-throughput genome analysis are opening new perspectives that are changing our understanding of satellite DNA. This review examines recent data to provide a timely update on the overall information gathered about this part of the genome, focusing on the advances in the knowledge of its origin, its evolution, and its potential functional roles.

Cloning and expression of a DAX1 homologue in the chicken embryo

2000 ◽  
Vol 24 (1) ◽  
pp. 23-32 ◽  
Author(s):  
CA Smith ◽  
V Clifford ◽  
PS Western ◽  
SA Wilcox ◽  
KS Bell ◽  
...  
Keyword(s):  
Ligand Binding ◽  
In Situ Hybridisation ◽  
Binding Domain ◽  
Cloning And Expression ◽  
Binding Motif ◽  
Fluorescence In Situ Hybridisation ◽  
Orphan Nuclear Receptor ◽  
Sequence Comparisons ◽  
Rnase Protection ◽  
Embryonic Chicken

DAX1 is an unusual member of the orphan nuclear receptor family of transcription factors. Mutations in human DAX1 cause X-linked adrenal hypoplasia congenita, while abnormal duplication of the gene is responsible for male-to-female dosage-sensitive sex reversal. Based on these and other observations, DAX1 is thought to play a role in adrenal and gonadal development in mammals. As DAX1 has not previously been described in any other vertebrate, a putative avian DAX1 clone was isolated from an embryonic chicken (Gallus domesticus) urogenital ridge cDNA library. The expression profile of this cDNA was then examined during gonadogenesis. The clone included the conserved 3' ligand-binding motif identified in humans and mice but the 5' region lacked the repeat motif thought to specify a DNA-binding domain in mammals. Southern blot analysis and fluorescence in situ hybridisation mapping showed that the gene is autosomal, located on chromosome 1q. Sequence comparisons showed that the putative chicken DAX1 protein has 63 and 60% identity with the human and mouse proteins respectively over the region of the conserved ligand-binding domain. However, stronger identity (74%) exists with a putative alligator DAX1 sequence over the same region. Northern blotting detected a single 1.4 kb transcript in late embryonic chicken gonads, while RNase protection assays revealed expression in the embryonic gonads of both sexes during the period of sexual differentiation. Expression increased in both sexes during gonadogenesis, but was higher in females than in males. This is the first description of a DAX1 homologue in a non-mammalian vertebrate.

Molecular Cytogenetic Mapping of Satellite DNA Sequences in Aegilops geniculata and Wheat

2016 ◽  
Vol 148 (4) ◽  
pp. 314-321 ◽  
Author(s):  
Dal-Hoe Koo ◽  
Vijay K. Tiwari ◽  
Eva Hřibová ◽  
Jaroslav Doležel ◽  
Bernd Friebe ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Satellite Dna ◽  
Chromosome Identification ◽  
Genome Chromosome ◽  
Satellite Dnas ◽  
Efficient System ◽  
Aegilops Geniculata ◽  
Alien Gene ◽  
Homoeologous Relationships ◽  
M Genome

Fluorescence in situ hybridization (FISH) provides an efficient system for cytogenetic analysis of wild relatives of wheat for individual chromosome identification, elucidation of homoeologous relationships, and for monitoring alien gene transfers into wheat. This study is aimed at developing cytogenetic markers for chromosome identification of wheat and Aegilops geniculata (2n = 4x = 28, UgUgMgMg) using satellite DNAs obtained from flow-sorted chromosome 5Mg. FISH was performed to localize the satellite DNAs on chromosomes of wheat and selected Aegilops species. The FISH signals for satellite DNAs on chromosome 5Mg were generally associated with constitutive heterochromatin regions corresponding to C-band-positive chromatin including telomeric, pericentromeric, centromeric, and interstitial regions of all the 14 chromosome pairs of Ae. geniculata. Most satellite DNAs also generated FISH signals on wheat chromosomes and provided diagnostic chromosome arm-specific cytogenetic markers that significantly improved chromosome identification in wheat. The newly identified satellite DNA CL36 produced localized Mg genome chromosome-specific FISH signals in Ae. geniculata and in the M genome of the putative diploid donor species Ae. comosa subsp. subventricosa but not in Ae. comosa subsp. comosa, suggesting that the Mg genome of Ae. geniculata was probably derived from subsp. subventricosa.

Telomere dysfunction in prostatic carcinogenesis

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.

Sequence analysis of the cloned cucumis melo highly repetitive satellite dna

1983 ◽  
Vol 38 (11-12) ◽  
pp. 1062-1065 ◽  
Author(s):  
A. Brennicke ◽  
V. Hemleben
Keyword(s):  
Dna Sequences ◽  
Satellite Dna ◽  
Cucumis Melo ◽  
Repeat Unit ◽  
Gc Content ◽  
Direct Repeat ◽  
Open Reading Frames ◽  
Scilla Sibirica ◽  
Highly Repetitive Dna ◽  
Reading Frames

The primary sequence of the prom inent Cucumis melo satellite DNA is presented. The cloned Hind III-repeat unit has a length of 352 bp and a GC-content of 56%. Within this sequence an inverted repeat of 9 bp, including a 286 bp loop, and one direct repeat are shown. Several open reading frames are possible following the sequence in both directions whose significance is not yet clear. The sequence has been compared with other highly repetitive DNA sequences of Sinapis alba and Scilla sibirica. The genomic satellite DNA exhibits an unusual behaviour in actinomycin D-CsCl gradients in comparison to ribosomal D NA

Differential sensitivity of some human alphoid and classical satellite DNA regions from lymphocyte chromosomes to in situ exonuclease III digestion

Genome ◽  
1996 ◽  
Vol 39 (6) ◽  
pp. 1210-1213
Author(s):  
José Luis Fernández ◽  
Carmen López-Fernández ◽  
Jaime Gosálvez ◽  
Vicente Goyanes
Keyword(s):  
Dna Sequences ◽  
Satellite Dna ◽  
Fluorescent In Situ Hybridization ◽  
Human Lymphocytes ◽  
Differential Sensitivity ◽  
Satellite Dnas ◽  
Exonuclease Iii ◽  
Human Cytogenetics ◽  
Structural Differences

Fluorescent in situ hybridization of alphoid and classical satellite III DNA sequences was performed on fixed chromosomes from human lymphocytes that were previously digested in situ with exonuclease III to produce single-stranded DNA motifs. Digital image analysis showed that while labeled alphoid satellite DNAs produced signals of similar strength to thermally denatured chromosomes, those of classical satellite III DNAs of chromosomes 9 and Yq were around 50% weaker. This result shows a differential sensitivity of these satellite DNA regions to in situ exonuclease III digestion and suggests structural differences in the higher-order organization of both subchromosomal constitutive heterochromatic regions. Key words : alphoid sequences, classical satellite, exonuclease III, FISH, human cytogenetics, satellite DNA.

Distribution and complex organization of satellite DNA sequences in Aveneae species

Genome ◽  
1996 ◽  
Vol 39 (6) ◽  
pp. 1045-1050 ◽  
Author(s):  
Bärbel Grebenstein ◽  
Oliver Grebenstein ◽  
Wilhelm Sauer ◽  
Vera Hemleben
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Satellite Dna ◽  
Sequence Similarity ◽  
Satellite Dnas ◽  
A Genome ◽  
Complex Organization ◽  
Dna Elements ◽  
Taxonomic Groups ◽  
Dna Components

Distribution, organization, and molecular analysis of four unrelated satellite DNA components in Aveneae species are described. Highly repeated DNA elements were cloned from Helictotrichon convolutum (CON1 and CON2) and Helictotrichon compression (COM1 and COM2). The lengths of the repeat monomers are 365 bp (CON1), 562 bp (CON2), 346 bp (COM1), and 476 bp (COM2). Similar repeats were detected by dot blots, Southern blots, and by DNA sequencing in other species of the genus Helictotrichon, in Aveneae species, and in species of the tribes Andropogoneae and Oryzeae. All four satellite DNAs are differently distributed in the taxonomic groups mentioned above. Remarkably, the longer elements are built up in a complex pattern of either shorter subrepeats arranged in tandem (COM2) or by duplications inserted into an original 369-bp element (CON2). Shorter representatives, 190 bp, similar to CON1 elements occur in Holcus species. In Koeleria species, COM1-related repeats are only 180 bp in length. No similarity was found among the sequences CON2, COM1, and COM2 or with sequences of other repetitive DNA elements of the grasses, but CON1 shows sequence similarity to an A genome specific repetitive DNA of Oryza (rice). Key words : genome evolution, grasses, Poaceae, repetitive DNA, wild oats.

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