scholarly journals Retrotransposon-Related DNA Sequences in the Centromeres of Grass Chromosomes

Genetics ◽  
1998 ◽  
Vol 150 (4) ◽  
pp. 1615-1623 ◽  
Author(s):  
Joseph T Miller ◽  
Fenggao Dong ◽  
Scott A Jackson ◽  
Junqi Song ◽  
Jiming Jiang
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequences ◽  
Blot Hybridization ◽  
Artificial Chromosome ◽  
Fish Analysis ◽  
Sequence Identity ◽  
Centromere Function ◽  
Eukaryotic Species

Abstract Several distinct DNA fragments were subcloned from a sorghum (Sorghum bicolor) bacterial artificial chromosome clone 13I16 that was derived from a centromere. Three fragments showed significant sequence identity to either Ty3/gypsy- or Ty1/copia-like retrotransposons. Fluorescence in situ hybridization (FISH) analysis revealed that the Ty1/copia-related DNA sequences are not specific to the centromeric regions. However, the Ty3/gypsy-related sequences were present exclusively in the centromeres of all sorghum chromosomes. FISH and gel-blot hybridization showed that these sequences are also conserved in the centromeric regions of all species within Gramineae. Thus, we report a new retrotransposon that is conserved in specific chromosomal regions of distantly related eukaryotic species. We propose that the Ty3/gypsy-like retrotransposons in the grass centromeres may be ancient insertions and are likely to have been amplified during centromere evolution. The possible role of centromeric retrotransposons in plant centromere function is discussed.

Chromosomal localization of two novel repetitive sequences isolated from the Chenopodium quinoa Willd. genome

Genome ◽  
2011 ◽  
Vol 54 (9) ◽  
pp. 710-717 ◽  
Author(s):  
B. Kolano ◽  
B.W. Gardunia ◽  
M. Michalska ◽  
A. Bonifacio ◽  
D. Fairbanks ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Repetitive Sequences ◽  
Chenopodium Quinoa ◽  
5S Rdna ◽  
Rrna Gene ◽  
Fish Analysis ◽  
Rdna Loci

The chromosomal organization of two novel repetitive DNA sequences isolated from the Chenopodium quinoa Willd. genome was analyzed across the genomes of selected Chenopodium species. Fluorescence in situ hybridization (FISH) analysis with the repetitive DNA clone 18–24J in the closely related allotetraploids C. quinoa and Chenopodium berlandieri Moq. (2n = 4x = 36) evidenced hybridization signals that were mainly present on 18 chromosomes; however, in the allohexaploid Chenopodium album L. (2n = 6x = 54), cross-hybridization was observed on all of the chromosomes. In situ hybridization with rRNA gene probes indicated that during the evolution of polyploidy, the chenopods lost some of their rDNA loci. Reprobing with rDNA indicated that in the subgenome labeled with 18–24J, one 35S rRNA locus and at least half of the 5S rDNA loci were present. A second analyzed sequence, 12–13P, localized exclusively in pericentromeric regions of each chromosome of C. quinoa and related species. The intensity of the FISH signals differed considerably among chromosomes. The pattern observed on C. quinoa chromosomes after FISH with 12–13P was very similar to GISH results, suggesting that the 12–13P sequence constitutes a major part of the repetitive DNA of C. quinoa.

Differentiation of triticale cultivars through FISH karyotyping of their rye chromosomes

Genome ◽  
2013 ◽  
Vol 56 (5) ◽  
pp. 267-272 ◽  
Author(s):  
Maia Fradkin ◽  
María Rosa Ferrari ◽  
Shirley Mary Espert ◽  
Víctor Ferreira ◽  
Ezequiel Grassi ◽  
...  
Keyword(s):  
Cluster Analysis ◽  
In Situ Hybridization ◽  
Dna Sequences ◽  
Fish Analysis ◽  
Repetitive Dna Sequences ◽  
Agronomic Characters ◽  
Breeding Programs ◽  
Specific Localization ◽  
Highly Repetitive Dna

The aim of this work was to cytogenetically characterize triticale cultivars through fluorescence in situ hybridization (FISH) analysis of their rye chromosomes. In the present work, we studied six cultivars of triticale (‘Cayú-UNRC’, ‘Cumé-UNRC’, ‘Genú-UNRC’, ‘Ñinca-UNRC’, ‘Quiñé-UNRC’, and ‘Tizné-UNRC’), released by the Universidad Nacional de Río Cuarto (UNRC), Córdoba, Argentina. The cultivars were obtained from the International Center for the Improvement of Maize and Wheat (CIMMYT) and improved for fresh forage, haymaking, and feed grain at UNRC. The distribution and organization of highly repetitive DNA sequences of Secale cereale (pSc74, pSc200, pSc250, and pSc119.2) using FISH analyses revealed a specific localization of the signals for several rye chromosomes, which allowed us to distinguish the cultivars. Cluster analysis showed a great cytogenetic similarity among the rye cultivars used to originate these hybrids. The knowledge of the variability among triticale cultivars is necessary to propose future crosses in breeding programs. This study will also be valuable to identify commercial seeds and to analyze the possible association between agronomic characters and the presence of certain rye chromosomes or specific regions in these chromosomes.

FISH-mapping of rDNAs and Arabidopsis BACs on pachytene complements of selected Brassicas

Genome ◽  
2002 ◽  
Vol 45 (1) ◽  
pp. 189-197 ◽  
Author(s):  
Piotr A Ziolkowski ◽  
Jan Sadowski
Keyword(s):  
In Situ Hybridization ◽  
Physical Mapping ◽  
5S Rdna ◽  
Artificial Chromosome ◽  
Rdna Locus ◽  
Fish Analysis ◽  
45S Rdna ◽  
Fish Mapping ◽  
Rdna Sequences

To improve resolution of physical mapping on Brassica chromosomes, we have chosen the pachytene stage of meiosis where incompletely condensed bivalents are much longer than their counterparts at mitotic metaphase. Mapping with 5S and 45S rDNA sequences demonstrated the advantage of pachytene chromosomes in efficient physical mapping and confirmed the presence of a novel 5S rDNA locus in Brassica oleracea, initially identified by genetic mapping using restriction fragment length polymorphism (RFLP). Fluorescence in situ hybridization (FISH) analysis visualized the presence of the third 5S rDNA locus on the long arm of chromosome C2 and confirmed the earlier reports of two 45S rDNA loci in the B. oleracea genome. FISH mapping of low-copy sequences from the Arabidopsis thaliana bacterial artificial chromosome (BAC) clones on the B. oleracea chromosomes confirmed the expectation of efficient and precise physical mapping of meiotic bivalents based on data available from A. thaliana and indicated conserved organization of these two BAC sequences on two B. oleracea chromosomes. Based on the heterologous in situ hybridization with BACs and their mapping applied to long pachytene bivalents, a new approach in comparative analysis of Brassica and A. thaliana genomes is discussed.Key words: Brassicaceae, pachytene chromosomes, FISH, rDNA, BACs.

scholarly journals Fluorescence in situ hybridization mapping of translocations and deletions involving the short arm of human chromosome 12 in malignant hematologic diseases

Blood ◽  
1994 ◽  
Vol 84 (10) ◽  
pp. 3473-3482 ◽  
Author(s):  
H Kobayashi ◽  
KT Montgomery ◽  
SK Bohlander ◽  
CN Adra ◽  
BL Lim ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Cell Line ◽  
Yeast Artificial Chromosome ◽  
Artificial Chromosome ◽  
Chromosome 12 ◽  
Fish Analysis ◽  
Translocation Breakpoints ◽  
Hybridization Mapping

Translocations and deletions of the short arm of chromosome 12 [t(12p) and del(12p)] are common recurring abnormalities in a broad spectrum of hematologic malignant diseases. We studied 20 patients and one cell line whose cells contained 12p13 translocations and/or 12p deletions using fluorescence in situ hybridization (FISH) with phage, plasmid, and cosmid probes that we previously mapped and ordered on 12p12–13. FISH analysis showed that the 12p13 translocation breakpoints were clustered between two cosmids, D12S133 and D12S142, in 11 of 12 patients and in one cell line. FISH analysis of 11 patients with deletions demonstrated that the deletions were interstitial rather than terminal and that the distal part of 12p12, including the GDI-D4 gene and D12S54 marker, was deleted in all 11 patients. Moreover, FISH analysis showed that cells from 3 of these patients contained both a del(12p) and a 12p13 translocation and that the affected regions of these rearrangements appeared to overlap. We identified three yeast artificial chromosome (YAC) clones that span all the 12p13 translocation breakpoints mapped between D12S133 and D12S142. They have inserts of human DNA between 1.39 and 1.67 Mb. Because the region between D12S133 and D12S142 also represents the telomeric border of the smallest commonly deleted region of 12p, we also studied patients with a del(12p) using these YACs. The smallest YAC, 964c10, was deleted in 8 of 9 patients studied. In the other patient, the YAC labeled the del(12p) chromosome more weakly than the normal chromosome 12, suggesting that a part of the YAC was deleted. Thus, most 12p13 translocation breakpoints were clustered within the sequences contained in the 1.39 Mb YAC and this YAC appears to include the telomeric border of the smallest commonly deleted region. Whether the same gene is involved in both the translocations and deletions is presently unknown.

scholarly journals Fluorescence in situ hybridization mapping of translocations and deletions involving the short arm of human chromosome 12 in malignant hematologic diseases

Blood ◽  
1994 ◽  
Vol 84 (10) ◽  
pp. 3473-3482 ◽  
Author(s):  
H Kobayashi ◽  
KT Montgomery ◽  
SK Bohlander ◽  
CN Adra ◽  
BL Lim ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Cell Line ◽  
Yeast Artificial Chromosome ◽  
Artificial Chromosome ◽  
Chromosome 12 ◽  
Fish Analysis ◽  
Translocation Breakpoints ◽  
Hybridization Mapping

Abstract Translocations and deletions of the short arm of chromosome 12 [t(12p) and del(12p)] are common recurring abnormalities in a broad spectrum of hematologic malignant diseases. We studied 20 patients and one cell line whose cells contained 12p13 translocations and/or 12p deletions using fluorescence in situ hybridization (FISH) with phage, plasmid, and cosmid probes that we previously mapped and ordered on 12p12–13. FISH analysis showed that the 12p13 translocation breakpoints were clustered between two cosmids, D12S133 and D12S142, in 11 of 12 patients and in one cell line. FISH analysis of 11 patients with deletions demonstrated that the deletions were interstitial rather than terminal and that the distal part of 12p12, including the GDI-D4 gene and D12S54 marker, was deleted in all 11 patients. Moreover, FISH analysis showed that cells from 3 of these patients contained both a del(12p) and a 12p13 translocation and that the affected regions of these rearrangements appeared to overlap. We identified three yeast artificial chromosome (YAC) clones that span all the 12p13 translocation breakpoints mapped between D12S133 and D12S142. They have inserts of human DNA between 1.39 and 1.67 Mb. Because the region between D12S133 and D12S142 also represents the telomeric border of the smallest commonly deleted region of 12p, we also studied patients with a del(12p) using these YACs. The smallest YAC, 964c10, was deleted in 8 of 9 patients studied. In the other patient, the YAC labeled the del(12p) chromosome more weakly than the normal chromosome 12, suggesting that a part of the YAC was deleted. Thus, most 12p13 translocation breakpoints were clustered within the sequences contained in the 1.39 Mb YAC and this YAC appears to include the telomeric border of the smallest commonly deleted region. Whether the same gene is involved in both the translocations and deletions is presently unknown.

Repeated DNA sequences isolated by microdissection. I. Karyotyping of barley (Hordeum vulgare L.)

Genome ◽  
1995 ◽  
Vol 38 (6) ◽  
pp. 1082-1090 ◽  
Author(s):  
Winfried Busch ◽  
Regina Martin ◽  
Reinhold G. Herrmann ◽  
Uwe Hohmann
Keyword(s):  
In Situ Hybridization ◽  
Hordeum Vulgare ◽  
Fluorescence In Situ Hybridization ◽  
Dna Sequences ◽  
Fish Analysis ◽  
Hordeum Vulgare L ◽  
Agropyron Elongatum ◽  
D Genome ◽  
In Situ Experiments

We report on microdissection, cloning and sequence, and Southern and fluorescence in situ hybridization (FISH) analysis of one moderately and one highly amplified repetitive DNA element, pHvMWG2314 and pHvMWG2315, respectively, isolated from barley (Hordeum vulgare L.) chromosome arm 3HL. The pHvMWG2315 sequence hybridizes to all 14 telomeric or subtelomeric regions of the barley chromosomes as determined by FISH. The 50 different hybridization sites that include intercalary signals allow the discrimination of all 14 chromosome arms and the construction of a karyotype of barley. The tandemly repeated subtelomeric element of 331 bp exists in all Triticeae species tested (H. vulgare, Agropyron elongatum, Secale cereale, Triticum tauschii, T. turgidum, and T. aestivum). It is AT rich (66%), exhibits 84% sequence homology to subfragments of the D genome "specific" 1-kb element pAsl of T. tauschii and 75% homology to the interspersed genome-specific DNA sequence pHcKB6 from H. chilense. The repetitive sequence pHvMWG2314 is moderately amplified in barley and highly amplified in hexaploid wheat. The in situ experiments revealed no distinct signals on barley chromosomes, indicating a dispersed character for the sequence. The significance of the results for the identification of chromosomes and chromosome aberrations in FISH experiments are discussed.Key words: karyotype, fluorescence in situ hybridization, FISH, DNA sequencing.

scholarly journals Clinical Role of the Detection of Human Telomerase RNA Component Gene Amplification by Fluorescence in situ Hybridization on Liquid-Based Cervical Samples: Comparison with Human Papillomavirus-DNA Testing and Histopathology

2015 ◽  
Vol 59 (4) ◽  
pp. 345-354 ◽  
Author(s):  
Roberta Zappacosta ◽  
Manuel Maria Ianieri ◽  
Danilo Buca ◽  
Elena Repetti ◽  
Alessandra Ricciardulli ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Human Papillomavirus ◽  
Fluorescence In Situ Hybridization ◽  
Fish Analysis ◽  
Dna Testing ◽  
Hpv Dna ◽  
Hpv Dna Testing ◽  
Human Telomerase

Objective: This study was designed to evaluate whether the adjunct of human telomerase RNA component (hTERC) fluorescence in situ hybridization (FISH) analysis to cytological diagnosis and human papillomavirus (HPV)-DNA testing may serve as a predictive marker for distinguishing cervical lesions destined to regress from those at high risk of progression towards invasive cancer. Study Design: hTERC FISH analysis was performed on 54 residual liquid-based cytology specimens obtained from women referred to colposcopy for the detection of atypical squamous cells of undetermined significance or worse (ASCUS+) lesions. Histological diagnosis was considered the gold standard and cervical intraepithelial neoplasia of grade 2 or worse (CIN2+) as the worst outcome. Results: Oncogenic HPV-DNA was found in 96.3% of the specimens. Among these, 38.5% revealed a CIN2+ diagnosis. hTERC gene amplification was detected in 37% of the cases; among these, 70% showed up as CIN2+. hTERC FISH analysis significantly improves the specificity and positive predictive value of HPV-DNA testing, thus differentiating patients with a CIN2+ diagnosis from those with a CIN2- diagnosis. Conclusions: Despite the limitation of a small study sample, our findings provide promising data, indicating the possible role of hTERC analysis in the assessment of the risk of developing cervical cancer. This approach would implement the specificity of DNA testing, avoiding overtreatment at the same time. Prospective follow-up studies are needed with the aim of introducing hTERC FISH into decision-making algorithms.

Fluorescent in situ hybridization and C-banding analyses of highly repetitive DNA sequences in the heterochromatin of rye (Secale montanum Guss.) and wheat incorporating S. montanum chromosome segments

Genome ◽  
1995 ◽  
Vol 38 (4) ◽  
pp. 795-802 ◽  
Author(s):  
Angeles Cuadrado ◽  
Nicolás Jouve
Keyword(s):  
In Situ Hybridization ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Secale Cereale ◽  
Fluorescent In Situ Hybridization ◽  
Fish Analysis ◽  
C Banding ◽  
Translocation Breakpoints ◽  
Secale Montanum

The molecular characterization of C-banded regions of Secale montanum Guss. by means of in situ hybridization was performed in order to provide new information about their chromosome structure relative to cultivated rye, Secale cereale L. Accurate identification of individual chromosomes was achieved using simultaneous and (or) successive fluorescent in situ hybridization (FISH) and C-banding. FISH identification was performed using total rye DNA, three highly repetitive rye DNA sequences (pSc119.2, pSc74, and pSc34), and the ribosomal RNA probes pTa71 (18S, 5.8S, and 26S rDNA) and pTa794 (5S rDNA). FISH was also used to identify the chromosome segment involved in two spontaneous translocation lines recovered from a 'Chinese Spring' – S. montanum wheat–rye addition line. FISH analysis revealed the exact translocation breakpoints and allowed the identification of the transferred rye segments. The value of this type of analysis is discussed.Key words: Secale cereale, Secale montanum, rye, repetitive DNA, fluorescence in situ hybridization.

DNA sequence mapping in interphase and metaphase chromosomes by fluorescence in situ hybridization

1992 ◽  
Vol 50 (1) ◽  
pp. 496-497
Author(s):  
Barbara Trask ◽  
Susan Allen ◽  
Anne Bergmann ◽  
Mari Christensen ◽  
Anne Fertitta ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Dual Band ◽  
Nick Translation ◽  
Metaphase Chromosomes ◽  
Band Pass ◽  
Texas Red ◽  
Fluorescent Spot

Using fluorescence in situ hybridization (FISH), the positions of DNA sequences can be discretely marked with a fluorescent spot. The efficiency of marking DNA sequences of the size cloned in cosmids is 90-95%, and the fluorescent spots produced after FISH are ≈0.3 μm in diameter. Sites of two sequences can be distinguished using two-color FISH. Different reporter molecules, such as biotin or digoxigenin, are incorporated into DNA sequence probes by nick translation. These reporter molecules are labeled after hybridization with different fluorochromes, e.g., FITC and Texas Red. The development of dual band pass filters (Chromatechnology) allows these fluorochromes to be photographed simultaneously without registration shift.

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