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Heredity Jul 2019The human genome is not randomly organised, with respect to both the linear organisation of the DNA sequence along chromosomes and to the spatial organisation of... (Review)
Review
The human genome is not randomly organised, with respect to both the linear organisation of the DNA sequence along chromosomes and to the spatial organisation of chromosomes in the cell nucleus. Here I discuss how these patterns of sequence organisation were first discovered by molecular biologists and how they relate to the patterns revealed decades earlier by cytogeneticists and manifest as chromosome bands.
Topics: Chromosome Banding; Chromosome Mapping; Chromosomes, Human; CpG Islands; DNA Methylation; Genome, Human; Genomics; Humans; In Situ Hybridization, Fluorescence; Oligonucleotide Array Sequence Analysis
PubMed: 31189906
DOI: 10.1038/s41437-019-0220-4 -
Cytogenetic and Genome Research 2021
Topics: Chromosome Aberrations; Chromosome Banding; Cytogenetic Analysis; Cytogenetics; Humans
PubMed: 34407536
DOI: 10.1159/000516654 -
Cytogenetic and Genome Research 2006Chromosome bar codes are multicolor banding patterns produced by fluorescence in situ hybridization (FISH) with differentially labeled and pooled sub-regional DNA... (Review)
Review
Chromosome bar codes are multicolor banding patterns produced by fluorescence in situ hybridization (FISH) with differentially labeled and pooled sub-regional DNA probes. These molecular cytogenetic tools facilitate chromosome identification and the delineation of both inter- and intra-chromosomal rearrangements. We present an overview of the various conceptual approaches which can be largely divided into two classes: Simple bar codes designed for chromosome identification and complex bar codes for high resolution aberration screening of entire karyotypes. We address the issue of color redundancy and how to overcome this limitation by complementation of bar codes with whole chromosome painting probes.
Topics: Chromosome Aberrations; Chromosome Banding; Chromosome Mapping; Chromosome Painting; DNA Probes; Electronic Data Processing; Gene Rearrangement; Humans; In Situ Hybridization, Fluorescence; Karyotyping; Translocation, Genetic
PubMed: 16954661
DOI: 10.1159/000094208 -
Heredity Jan 2012Rodentia is the most species-rich mammalian order and includes several important laboratory model species. The amount of new information on karyotypic and phylogenetic... (Review)
Review
Rodentia is the most species-rich mammalian order and includes several important laboratory model species. The amount of new information on karyotypic and phylogenetic relations within and among rodent taxa is rapidly increasing, but a synthesis of these data is currently lacking. Here, we have integrated information drawn from conventional banding studies, recent comparative painting investigations and molecular phylogenetic reconstructions of different rodent taxa. This permitted a revision of several ancestral karyotypic reconstructions, and a more accurate depiction of rodent chromosomal evolution.
Topics: Animals; Chromosome Banding; Chromosome Painting; Chromosomes, Mammalian; Evolution, Molecular; Genetic Speciation; Karyotype; Phylogeny; Rodentia
PubMed: 22086076
DOI: 10.1038/hdy.2011.110 -
BMC Genomics Nov 2016The unambiguous identification of individual chromosomes is a key part of the genomic characterization of any species. In this respect, the development and application...
BACKGROUND
The unambiguous identification of individual chromosomes is a key part of the genomic characterization of any species. In this respect, the development and application of chromosome banding techniques has revolutionised mammalian and especially, human genomics. However, partly because of the traditional use of chromosome squash preparations, consistent fluorescence banding has rarely been achieved in plants. Here, successful fluorescence chromosome banding has been achieved for the first time in perennial ryegrass (Lolium perenne), a forage and turf grass with a large genome and a symmetrical karyotype with chromosomes that are difficult to distinguish.
RESULTS
Based on flame-dried chromosome preparations instead of squashes, a simple fluorescence Q-banding technique using quinacrine mustard, unambiguously identified each chromosome and enabled the development of a banded karyotype and ideogram of the species. This Q-banding technique was also shown to be compatible with sequential FISH mapping enabling labelled genes and molecular markers to be precisely assigned to specific cytogenetic bands. A technique for DAPI-banding, which gave a similar pattern to Q-banding, was also introduced. This was compatible with FISH mapping and was used to anchor a single copy gene from an earlier mapped linkage group of L. perenne, thus providing a step towards integration of the genetic and cytogenetic maps.
CONCLUSIONS
By enabling the allocation of genes mapped by other methods to physically identified chromosome positions, this work will contribute to a better understanding of genomic structures and functions in grasses.
Topics: Chromosome Banding; Chromosome Mapping; In Situ Hybridization, Fluorescence; Karyotype; Lolium
PubMed: 27887567
DOI: 10.1186/s12864-016-3231-z -
International Journal of Radiation... Jun 2016To examine the influence of α-particle radiation exposure from internally deposited plutonium on chromosome aberration frequencies in peripheral blood lymphocytes of...
PURPOSE
To examine the influence of α-particle radiation exposure from internally deposited plutonium on chromosome aberration frequencies in peripheral blood lymphocytes of workers from the Sellafield nuclear facility, UK.
MATERIALS AND METHODS
Chromosome aberration data from historical single colour fluorescence in situ hybridization (sFISH) and Giemsa banding (G-banding) analyses, together with more recent sFISH results, were assessed using common aberration analysis criteria and revised radiation dosimetry. The combined sFISH group comprised 29 men with a mean internal red bone marrow dose of 21.0 mGy and a mean external γ-ray dose of 541 mGy. The G-banding group comprised 23 men with a mean internal red bone marrow dose of 23.0 mGy and a mean external γ-ray dose of 315 mGy.
RESULTS
Observed translocation frequencies corresponded to expectations based on age and external γ-ray dose with no need to postulate a contribution from α-particle irradiation of the red bone marrow by internally deposited plutonium. Frequencies of stable cells with complex aberrations, including insertions, were similar to those in a group of controls and a group of workers with external radiation exposure only, who were studied concurrently. In a similar comparison there is some suggestion of an increase in cells with unstable complex aberrations and this may reflect recent direct exposure to circulating lymphocytes.
CONCLUSIONS
Reference to in vitro dose response data for the induction of stable aberrant cells by α-particle irradiation indicates that the low red bone marrow α-particle radiation doses received by the Sellafield workers would not result in a discernible increase in translocations, thus supporting the in vivo findings. Therefore, the greater risk from occupational radiation exposure of the bone marrow resulting in viable chromosomally aberrant cells comes from, in general, much larger γ-ray exposure in comparison to α-particle exposure from plutonium.
Topics: Adult; Aged; Alpha Particles; Biological Assay; Cells, Cultured; Chromosome Aberrations; Chromosome Banding; Dose-Response Relationship, Radiation; Humans; In Situ Hybridization, Fluorescence; Lymphocytes; Male; Middle Aged; Nuclear Reactors; Occupational Exposure; Plutonium; Radiation Dosage; Radiometry; Reproducibility of Results; Sensitivity and Specificity; United Nations
PubMed: 27043761
DOI: 10.3109/09553002.2016.1152414 -
Chromosome Research : An International... Jun 2015Rumex hastatulus is the North American endemic dioecious plant with heteromorphic sex chromosomes. It is differentiated into two chromosomal races: Texas (T) race...
Rumex hastatulus is the North American endemic dioecious plant with heteromorphic sex chromosomes. It is differentiated into two chromosomal races: Texas (T) race characterised by a simple XX/XY sex chromosome system and North Carolina (NC) race with a polymorphic XX/XY1Y2 sex chromosome system. The gross karyotype morphology in NC race resembles the derived type, but chromosomal changes that occurred during its evolution are poorly understood. Our C-banding/DAPI and fluorescence in situ hybridization (FISH) experiments demonstrated that Y chromosomes of both races are enriched in DAPI-positive sequences and that the emergence of polymorphic sex chromosome system was accompanied by the break of ancestral Y chromosome and switch in the localization of 5S rDNA, from autosomes to sex chromosomes (X and Y2). Two contrasting domains were detected within North Carolina Y chromosomes: the older, highly heterochromatinised, inherited from the original Y chromosome and the younger, euchromatic, representing translocated autosomal material. The flow-cytometric DNA estimation showed ∼3.5 % genome downsizing in the North Carolina race. Our results are in contradiction to earlier reports on the lack of heterochromatin within Y chromosomes of this species and enable unambiguous identification of autosomes involved in the autosome-heterosome translocation, providing useful chromosome landmarks for further studies on the karyotype and sex chromosome differentiation in this species.
Topics: Chromosome Banding; Chromosomes, Plant; Genetic Markers; In Situ Hybridization, Fluorescence; Karyotype; Rumex; Sex Chromosomes; Translocation, Genetic
PubMed: 25394583
DOI: 10.1007/s10577-014-9446-4 -
Journal of Medical Genetics Aug 1980A 2-month-old female infant with typical features of the 13q-syndrome was found to be a hitherto unreported mosaic consisting of 46,XX,del(13)(q22)-46,XX,r(13)(p13q22)....
A 2-month-old female infant with typical features of the 13q-syndrome was found to be a hitherto unreported mosaic consisting of 46,XX,del(13)(q22)-46,XX,r(13)(p13q22). Both of the 13q- and r(13) chromosomes were Ag N banding positive. Therefore, it was assumed that they had retained the satellite stalks. Two possible mechanisms were proposed for the genesis of the mosaicism. Firstly, the patients started with the 13q- chromosome, which then underwent breakage and reunion at both ends to form the r(13) chromosome. Secondly, the patients started with the r(13) chromosome, which reopened at or close to the joining point to form the 13q- chromosome.
Topics: Abnormalities, Multiple; Chromosome Aberrations; Chromosome Banding; Chromosome Deletion; Chromosome Disorders; Chromosomes, Human, 13-15; Female; Humans; Infant; Karyotyping; Mosaicism
PubMed: 7205909
DOI: 10.1136/jmg.17.4.316 -
Cytometry 1990Stylized chromosome images 1) serve as a format to test effects of preprocessing algorithms used in automated karyotyping; 2) enhance the ability of humans to perform... (Comparative Study)
Comparative Study
Stylized chromosome images 1) serve as a format to test effects of preprocessing algorithms used in automated karyotyping; 2) enhance the ability of humans to perform quantitative analysis of chromosomal aberrations; 3) provide an alternative format for karyotype hard copies produced by automated systems. Stylized chromosomes are two-dimensional computer-generated images based on information extracted from one-dimensional width and density profiles. These profiles correspond to what cytogeneticists observe through the microscope as the shape and banding patterns of stained chromosomes. Stylized presentation sharpens chromosome band boundaries and perimeters, reduces "noise," and enhances gray level variations, which are difficult to distinguish by humans on photographic or computer generated karyotypes. Karyotyping accuracy using stylized images was used to detect difficult areas for automated chromosome identification. Landmark bands sufficient to classify chromosomes were identified; shapes of chromosomes reflected in width profiles were said to aid classification. A two-step automated karyotyping strategy proposed is: 1) classify chromosomes by landmarks, minimum information needed for identification; 2) subsequently employ the full banding pattern with maximum resolution to detect aberrations. Stylized images of abnormal chromosomes have potential for testing hypothesis regarding breakpoints and quantitative analysis, but improvements are needed in homologue normalization and definition of termini of chromosomes.
Topics: Algorithms; Chromosome Aberrations; Chromosome Banding; Humans; Image Processing, Computer-Assisted; Karyotyping
PubMed: 2307061
DOI: 10.1002/cyto.990110106 -
Journal of Medical Genetics Jul 1988High resolution prometaphase chromosome banding has allowed the detection of discrete chromosome aberrations which escaped earlier metaphase examinations. Consistent... (Review)
Review
High resolution prometaphase chromosome banding has allowed the detection of discrete chromosome aberrations which escaped earlier metaphase examinations. Consistent tiny deletions have been detected in some well established malformation syndromes: an interstitial deletion in 15q11/12 in the majority of patients with the Prader-Willi syndrome and in a minority of patients with the Angelman (happy puppet) syndrome; a terminal deletion of 17p13.3 in most patients examined with the Miller-Dieker syndrome; an interstitial deletion of 8q23.3/24.1 in a large majority of patients with the Giedion-Langer syndrome; an interstitial deletion of 11p13 in virtually all patients with the WAGR (Wilms' tumour-aniridia-gonadoblastoma-retardation) syndrome; and an interstitial deletion in 22q11 in about one third of patients with the DiGeorge sequence. In addition, a combination of chromosome prometaphase banding and DNA marker studies has allowed the localisation of the genes for retinoblastoma and for Wilms' tumour and the clarification of both the autosomal recessive nature of the mutation and the possible somatic mutations by which the normal allele can be lost in retina and kidney cells. After a number of X linked genes had been mapped, discrete deletions in the X chromosome were detected by prometaphase banding with specific attention paid to the sites of the gene(s) in males who had from one to up to four different X linked disorders plus mental retardation. Furthermore, the detection of balanced translocations in probands with disorders caused by autosomal dominant or X linked genes has allowed a better insight into the localisation of these genes. In some females with X linked disorders, balanced X; autosomal translocations have allowed the localisation of X linked genes at the breakpoint on the X chromosome. Balanced autosome; autosome translocations segregating with autosomal dominant conditions have provided some clues to the gene location of these conditions. In two conditions, Greig cephalopolysyndactyly and dominant aniridia, two translocation families with one common breakpoint have allowed quite a confident location of the genes at the common breakpoint at 7p13 and 11p13, respectively.
Topics: Chromosome Aberrations; Chromosome Banding; Chromosome Deletion; Chromosome Disorders; Chromosome Mapping; Genetic Markers; Humans; Karyotyping; Sex Chromosome Aberrations; Syndrome; Translocation, Genetic
PubMed: 3050093
DOI: 10.1136/jmg.25.7.454