Cot-1 banding of human chromosomes using fluorescencein situ hybridization with Cy3 labeling

Wang, Yimin; Minoshima, Shinsei; Shimizu, Nobuyoshi

doi:10.1007/bf01876182

Cited by 8 publications

(5 citation statements)

References 16 publications

(18 reference statements)

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“…Depending on the fraction C o t DNA contains various amounts of satellite DNAs, DNA transposons, and retrotransposons. In some species localization of C o t DNA onto metaphase chromosomes could produce a banding pattern, useful for chromosome identification [ 38 ]. We isolated C o t30 fraction of DNA that includes wide range of repetitive elements.…”

Section: Discussionmentioning

confidence: 99%

Segmental paleotetraploidy revealed in sterlet (Acipenser ruthenus) genome by chromosome painting

et al. 2015

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BackgroundAcipenseriformes take a basal position among Actinopteri and demonstrate a striking ploidy variation among species. The sterlet (Acipenser ruthenus, Linnaeus, 1758; ARUT) is a diploid 120-chromosomal sturgeon distributed in Eurasian rivers from Danube to Enisey. Despite a high commercial value and a rapid population decline in the wild, many genomic characteristics of sterlet (as well as many other sturgeon species) have not been studied.ResultsCell lines from different tissues of 12 sterlet specimens from Siberian populations were established following an optimized protocol. Conventional cytogenetic studies supplemented with molecular cytogenetic investigations on obtained fibroblast cell lines allowed a detailed description of sterlet karyotype and a precise localization of 18S/28S and 5S ribosomal clusters. Localization of sturgeon specific HindIII repetitive elements revealed an increased concentration in the pericentromeric region of the acrocentric ARUT14, while the total sterlet repetitive DNA fraction (C0t30) produced bright signals on subtelomeric segments of small chromosomal elements. Chromosome and region specific probes ARUT1p, 5, 6, 7, 8 as well as 14 anonymous small sized chromosomes (probes A-N) generated by microdissection were applied in chromosome painting experiments. According to hybridization patterns all painting probes were classified into two major groups: the first group (ARUT5, 6, 8 as well as microchromosome specific probes C, E, F, G, H, and I) painted only a single region each on sterlet metaphases, while probes of the second group (ARUT1p, 7 as well as microchromosome derived probes A, B, D, J, K, M, and N) marked two genomic segments each on different chromosomes. Similar results were obtained on male and female metaphases.ConclusionsThe sterlet genome represents a complex mosaic structure and consists of diploid and tetraploid chromosome segments. This may be regarded as a transition stage from paleotetraploid (functional diploid) to diploid genome condition. Molecular cytogenetic and genomic studies of other 120- and 240-chromosomal sturgeons are needed to reconstruct genome evolution of this vertebrate group.

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Section: Discussionmentioning

confidence: 99%

Segmental paleotetraploidy revealed in sterlet (Acipenser ruthenus) genome by chromosome painting

et al. 2015

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“…In the traditional (i.e., qualitative) fish cytogenetics, there are two mutually non-exclusive ways to visualize GC% and rep% even on the same metaphase. These are the CDD-staining combining AT-and GC-specific fluorochromes to the same metaphase [30,31] for GC% and fluorescence in situ hybridization (FISH) with a repetitive DNA fraction, e.g., cot-1, as a probe [32] or a more destructive visualization of constitutive heterochromatin using C-banding [10,33] for rep%. However, application of these methods is limited in fish due to the small size of their chromosomes.…”

Section: Introductionmentioning

confidence: 99%

GC and Repeats Profiling along Chromosomes—The Future of Fish Compositional Cytogenomics

Matoulek

Borůvková

Ocalewicz

et al. 2020

Genes

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The study of fish cytogenetics has been impeded by the inability to produce G-bands that could assign chromosomes to their homologous pairs. Thus, the majority of karyotypes published have been estimated based on morphological similarities of chromosomes. The reason why chromosome G-banding does not work in fish remains elusive. However, the recent increase in the number of fish genomes assembled to the chromosome level provides a way to analyse this issue. We have developed a Python tool to visualize and quantify GC percentage (GC%) of both repeats and unique DNA along chromosomes using a non-overlapping sliding window approach. Our tool profiles GC% and simultaneously plots the proportion of repeats (rep%) in a color scale (or vice versa). Hence, it is possible to assess the contribution of repeats to the total GC%. The main differences are the GC% of repeats homogenizing the overall GC% along fish chromosomes and a greater range of GC% scattered along fish chromosomes. This may explain the inability to produce G-banding in fish. We also show an occasional banding pattern along the chromosomes in some fish that probably cannot be detected with traditional qualitative cytogenetic methods.

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“…It is distributed as dispersed copies or tandem repeats across the genome of most species and is routinely used as a blocking agent in suppressive hybridization (Dugan, Pattee, Williams, Eklund, Sorensen, Bedford & Christian 2005). Cot ‐1 DNA banding has been reported previously in humans (Wang, Minoshima & Shimizu 1995) and plants (Wei et al 2005). The results reported in the present study indicated that the individual homologous chromosome pairs could be stably banded by Cot ‐1 DNA, and non‐homologous chromosome pairs presented different Cot ‐1 DNA banding patterns (Figs 2–4).…”

Section: Discussionmentioning

confidence: 69%

Karyotype analysis of Oreochromis mossambicus, O. urolepis hornorum and their hybrid based on Cot-1 DNA bands by fluorescence in situ hybridization

Zhu

Huang

et al. 2010

Aquaculture Research

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Chromosomal karyotypes of Oreochromis mossambicus and O. urolepis hornorum and their hybrid were analysed by means of Cot-1 DNA bandings through £uorescence in situ hybridization (FISH). To identify all chromosomes, Cot-1DNA^which contains highly and moderately repetitive DNA^was extracted from genomic DNA, labelled as a probe with Dig-11-dUTP, and in situ hybridized to spreads of mitotic chromosomes of the three samples. The hybridized signals were detected by means of Cy3-conjugated antidigoxigenin. The FISH results indicated that the three samples had the same diploid number (2n 5 44) of chromosomes. Speci¢c £uorescence signal bands were detected on all individual chromosome pairs. On the basis of Cot-1 DNA FISH banding patterns and chromosome morphology, the karyotypes of the three samples have been constructed; no remarkable di¡erences were detected between the karyotypes of these species using this method. These resultsŵ hich are similar to those reported previously, with respect to chromosome number, morphology and Cot-1 DNA FISH patterns^suggest chromosomal stasis during speciation and hybridization of tilapia (Oreochromis, Cichlidae). Such a molecular cytogenetic procedure, if used in conjunction with other genomic research methods, could facilitate the study of genomic structure and be adapted for chromosome studies of other animal species.

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Cot-1 banding of human chromosomes using fluorescencein situ hybridization with Cy3 labeling

Cited by 8 publications

References 16 publications

Segmental paleotetraploidy revealed in sterlet (Acipenser ruthenus) genome by chromosome painting

Segmental paleotetraploidy revealed in sterlet (Acipenser ruthenus) genome by chromosome painting

GC and Repeats Profiling along Chromosomes—The Future of Fish Compositional Cytogenomics

Karyotype analysis of Oreochromis mossambicus, O. urolepis hornorum and their hybrid based on Cot-1 DNA bands by fluorescence in situ hybridization

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