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PubMed1997

Evolution of the black muntjac (Muntiacus crinifrons) karyotype revealed by comparative chromosome painting.

The black muntjac (Muntiacus crinifrons) has an unusual karyotype of 2n = 8 in females and 2n = 9 in males. We have studied the evolution of this karyotype by hybridising chromosome-specific paints derived from flow-sorted chromosomes of the Chinese muntjac (M. reevesi, 2n = 46) to chromosomes of the black muntjac. The hybridisation pattern allowed us to infer chromosomal homologies between these two species. Tandem and centromeric fusions, reciprocal translocations, and insertions are involved in the reduction of the diploid number from 2n = 46 to 2n = 8, 9. The painting patterns further show complex chromosomal rearrangements in the male black muntjac which involve more than half the karyotype, including both sex chromosomes. Since early meiosis is reported to be normal without any visible inversion loops of the synaptonemal complex, the observed chromosomal rearrangements would lead to heterosynapsis and, therefore, leave a large fraction of the male black muntjac karyotype balanced between the two sexes.

Animals↗
PubMed1996

Recent fusion events during evolution of pig chromosomes 3 and 6 identified by comparison with the babirusa karyotype.

The chromosomes of the babirusa, a species considered to have diverged from an ancestor of the pig during the Miocene epoch, about 12-26 million years ago, were studied to determine the sites of recent rearrangements during evolution of the domestic pig. It is shown that there is a pericentric inversion of the entire short arm on pig chromosome 1, compared to its counterpart in the babirusa (chromosome 15). We also present evidence suggesting that pig chromosome 3 was derived by a telomere-centromere fusion of two ancestral chromosomes homoelogous to babirusa chromosomes 12 and 17. Likewise, we conclude that pig chromosome 6 was most likely derived by a telomere-telomere fusion of ancestral chromosomes homoelogous to babirusa chromosomes 6 and 14. The detection of interstitial hybridization signals from presumptive subteloemeric repeats in the same chromosome region as the evolutionary fusion points on pig chromosomes 3 and 6 indicates that the fusion sites may still contain elements that are otherwise restricted to the telomere regions of pig chromosomes.

Animals↗
PubMed2001

Between rat and mouse zoo-FISH reveals 49 chromosomal segments that have been conserved in evolution.

Mouse single chromosome paints were applied to rat prophase/prometaphase chromosomes to detect homologous chromosome regions. The analysis revealed 49 rat chromosomal regions ranging in size from whole chromosomes down to small bands near the limit of detection with this method, which was estimated to be 2-3 Mb. When all the painted regions were taken into account, the whole rat genome was covered with mouse-homologous regions, with the exception of small segments near the centromeres and the short arms of Chromosomes (Chrs) 3, 11, 12, and 13. These regions were shown to contain high levels of rat-specific repetitive DNA. The number of conserved segments between rat and mouse detected by our high-resolution zoo-FISH method was significantly higher than that reported in previous studies.

Animals↗
PubMed2001

Comparative structure, proximal promoter elements, and chromosome location of the human eosinophil major basic protein genes.

Human eosinophil major basic protein (MBP) is strongly implicated as a mediator of disease, especially bronchial asthma. We recently isolated a highly divergent human homologue of MBP (MBPH). Given human MBP's importance in disease and the restricted expression of it and human MBPH, we isolated the 4.6-kb human MBPH gene (HGMW-approved symbol PRG3). Comparisons among the human MBP (PRG2), human MBPH, and murine MBP-1 (mMBP-1; Prg2) genes suggest that the human MBP and mMBP-1 genes are more closely related than either is to the human MBPH gene. Proximal promoters of these three genes show conservation of potential binding sites for IK2 and STAT and of a known GATA site. However, a known C/EBP site is altered in the human MBPH gene's proximal promoter. The human MBP and MBPH genes localized to chromosome 11 in the centromere to 11q12 region. Thus, the human MBP and MBPH genes have diverged considerably, probably following a gene duplication event. Furthermore, the identified conserved and distinct proximal promoter elements likely contribute to the eosinophil-restricted and relatively reduced transcription of the human MBPH gene.

Animals↗
PubMed1978

Conservation and chromosomal localization of DNA satellites in balenopterid whales.

DNA satellites were isolated from three balenopterid species, viz. the minke, sei, and fine whales. In each of them at least two DNA satellites were recognizable with buoyant densities in neutral CsCl of rho = 1.702/1.703 and rho = 1.710/1;711, respectively. cRNAs from each satellite group were used for filter and in situ hybridisations. Homo-and heterologous DNA-cRNA hybrids within each satellite group yielded virtually identical melting curve profiles showing conservation of at least a considerable part of the DNA satellite sequences. There was no evident sequence homology between the rho = 1.702/1.703 and the rho = 1.710/1;711 satellites by filter hybridisation.--The in situ hybridisation showed that in each species the rho = 1.702/1.703 satellite was located in centromeric-paracentromeric C-bands in a few pairs, whereas the rho = 1.710/1.711 satellite was located in terminal C-bands throughout the karyotypes.--The data on the whale DNA satellites indicate that the quantitative evolution of the sateliite DNA sequences preceded species divergence of the balenopterids and that the satellite sequences have remained relatively unaltered since the divergence took place. The function of satellite DNA is considered to imply the introduction of both chromosomal and genic polymorphisms and thus being of great importance in speciation, Based upon these concepts a model is postulated for the function of satellite DNA. According to this model at meiotic pairing euchromatinheterochromatin overlapping between homologous chromosomes is considered to be of a general occurrence. This overlapping is presumed to be accentuated by the size heteromorphism frequently observed between homologous heterochromatic segments (C-bands). In the region of such euchromatinheterochromatin overlapping, cross-over would be excluded. The overlapping is suggested to be rectified progresssively in the chromosome arms, leaving unaffected crossing-over distant to the euchromatin-heterochromatin junctions. The consequence of this will be that genes in the proximity of the junctions are collectively inherited and selected, whereas genes distant to the the heterochromatin will be independently assorted and selected.

Animals↗
PubMed1998

Mapping the distribution of the telomeric sequence (T2AG3)n in the Macropodoidea (Marsupialia), by fluorescence in situ hybridization. I. The swamp wallaby, Wallabia bicolor.

Thylogale spp. (pademelons) retain the plesiomorphic (ancestral) 2n = 22 karyotype for the marsupial family Macropodidae (kangaroos and wallabies). The swamp wallaby, Wallabia bicolor, has the most derived macropodid karyotype with the lowest chromosome number (2n = 10 female, 11 male), and a multiple sex chromosome system (XX female, XY1Y2 male). All but one of the W. bicolor chromosomes are fusion chromosomes. Two of these chromosomes, the X chromosome and chromosome 1, are composed of three plesiomorphic Thylogale-like chromosomes. The distribution of the vertebrate telomeric sequence (T2AG3)n was examined by fluorescence in situ hybridization (FISH) in both species and a 'map' of non-telomeric (T2AG3)n sites on W. bicolor chromosomes relative to Thylogale chromosomes was constructed. (T2AG3)n signals were observed at six fusion sites in the four fusions chromosomes examined, indicating that the (T2AG3)n sequence is consistently retained during fusions. The distribution of the interstitial signals on the long arm of chromosome 1 of W. bicolor and the X chromosome suggests how a combination of inversions, fusions and centromeric transpositions have resulted in interstitial telomeric sequence.

Animals↗
PubMed1987

Evolution of P transposable elements: sequences of Drosophila nebulosa P elements.

P elements have been cloned and sequenced from Drosophila nebulosa. Their sequences have diverged less than 6% from P elements of Drosophila melanogaster. However D. nebulosa P elements have nucleotide changes that close all four open reading frames found in the D. melanogaster P element. Microinjection experiments show that D. nebulosa P elements cannot provide transposase function for D. melanogaster P elements, nor are D. nebulosa P elements mobilized by the transposase provided by a D. melanogaster P factor. Three D. nebulosa P elements appear to have integrated into the same position of a complex, centromeric repeated sequence. Comparison of nucleotide sequences suggests that D. nebulosa P elements have diverged upon different pathways from a common ancestor that was 99% homologous to the P elements of D. melanogaster.

Base Sequence↗
PubMed2002

Contribution of cytogenetics and in situ hybridization to the study of monoclonal gammopathies of undetermined significance.

Monoclonal gammopathies of undetermined significance (MGUS) are characterized by the presence of a monoclonal protein in serum in quite asymptomatic patients. Ten to 33% of MGUS patients eventually will develop overt multiple myeloma, but no single laboratory test exists that can predict changes toward a malignant evolution. The aim of the present study was to apply conventional cytogenetics, the MAC (morphology, antibody, chromosome) method and fluorescence in situ hybridization (FISH) techniques in a series of 50 MGUS patients and 4 "smoldering" multiple myeloma patients to test the usefulness of their approaches as predictive methodologies. All patients studied by conventional cytogenetics presented a normal karyotype independent of the culture conditions used. The MAC method revealed that all mitotic cells showing a normal karyotype were positive for anti-MOP7 or anti-CD3 in 12 patients studied. In addition, two of them presented a numerical abnormality detected by FISH. Using a FISH technique with direct labeled centromeric probes for chromosomes 3, 7, 11, and 18 we showed a numerical abnormality in eight of 35 patients (23%) with a normal karyotype. The common occurrence of MGUS and the fact that they may evolve toward lymphoproliferative disorders displays the importance of being able to identify laboratory results that are capable of predicting the evolution of these patients. In the literature, patients who presented an IgA peak of immunoglobulin type have been associated with a higher risk of evolving to a malignant condition. Our study shows the correlation of MGUS patients who presented monosomy 18 with the presence of an immunoglobulin peak of the IgA type. Prospective follow-up is needed to evaluate the clinical value of monosomy 18 as a predictive factor for defining a high risk of malignant transformation in MGUS patients.

Adult↗
PubMed2026

The genetic control of rapid genome content divergence in Arabidopsis thaliana.

Genome evolution in eukaryotes is predominantly driven by the dynamics of repetitive sequences, which vary widely in both copy number and sequence composition. Rates of repeat evolution differ between and within species and are likely modulated by both genetics and environment. To uncover factors shaping the rate of genome content evolution, we analyzed 1,142 resequenced Arabidopsis thaliana genomes using a novel K-mer based approach to characterize genome content variation and identify hypervariable regions underlying differences in repeat abundance. We next treated repeat abundance as a quantitative trait and performed genome-wide association analyses across more than 400 repeat families to identify the genetic basis of copy number variation. Integrating these results through a meta-GWAS approach revealed both cis-acting variants and more than 50 trans-acting loci that regulate repeat abundance genome-wide. Cis-acting variation was predominantly localized to pericentromeric and centromeric regions, whereas trans-acting loci were enriched for candidate genes involved in DNA replication, DNA repair, DNA methylation regulation. Finally, we found evidence that purifying selection acts against mutations that accelerate genome content divergence, favoring alleles that constrain repeat expansion. Together, these findings provide new insights into the genetic architecture and evolutionary forces shaping genome evolution in A. thaliana and establish a framework for investigating these processes in other plant species.

Journal Article↗
PubMed1981

Karyotype evolution and sex chromosome differentiation in Schistosomes (Trematoda, Schistosomatidae).

The morphology of C-banded metaphase chromosomes has been studied in two hermaphroditic and ten gonochoristic digenetic trematodes (schistosomes). Comparison of numbers and morphology of chromosomes indicates that the karyotype of primitive trematodes probably was composed of 10 (or 11) pairs of telocentric or subtelocentric chromosomes, and reduction of chromosome numbers in advanced species resulted from centromeric fusion rather than elimination of chromosomes. Observation of heteromorphic chromosomes in a hermaphroditic trematode (Spirorchis) suggested a differentiation of "pre-sex" chromosomes in species ancestral to dioecious trematodes which possess distinctly differentiated sex chromosomes. Our results indicate that differentiation of Z and W chromosomes in the gonochoristic trematodes resulted from: (a) partial constitutive heterochromatinization of the W chromosome (Schistosoma mansoni and S. haematobium complexes, African schistosomes), (b) deletion of part of the W (S. japonicum and S. mekongi, Asian schistosomes), and (c) translocation of part of one sex chromosome onto another (Schistosomatium douthitti and Heterobilharzia americana, American schistosomes) with subsequent heterochromatinization of the W in H. americana.

Animals↗
PubMed2005

Gonadoblastoma in Turner syndrome and Y-chromosome-derived material.

The identification of Y-chromosome material is important in females with Ullrich-Turner syndrome (UTS) due to the risk of developing gonadoblastoma or other gonadal tumors. There is controversy regarding the frequency of the Y-chromosome-derived material and the occurrence of gonadoblastoma in these patients. The aim of our study was to evaluate a large number of patients with UTS, followed before and during the pubertal age for the prevalence of Y-chromosome derived material, the occurrence of gonadoblastoma, and the incidence of possible neoplastic degeneration. An unselected series of 171 patients with UTS (1-34 years old), diagnosed cytogenetically, was studied for Y-chromosome markers (SRY and Y-centromeric DYZ3 repeats). The follow-up was of 2-22 years; 101 of these patients were followed during pubertal age. Y-chromosome material was found in 14 patients (8%): 12 of these were gonadectomized (2.8-25.9 years). A gonadoblastoma was detected in four patients under 16 years of age: in two, Y-material was detected only at molecular analysis (at conventional cytogenetic analysis, one was included in the 45,X group and one in the X + mar group) and one had also an immature teratoma and an endodermal sinus carcinoma. The prevalence of gonadoblastoma in our series of gonadectomized UTS patients with Y-positive material was of 33.3% (4/12). Our data suggest that the age of appearance and the possibility of malignant degeneration of gonadoblastoma can occur early in life. These patients, in particular those with 45,X or a marker chromosome may benefit from molecular screening to detect the presence of Y-chromosome material; PCR is a rapid and inexpensive technique. At the moment, laparoscopy and preventive gonadectomy performed as soon as possible remain the procedures of choice for patients with UTS, when Y-chromosome has been identified, as we are still unable to predict a future malignant evolution of gonadoblastoma.

Adolescent↗
PubMed2026

The genetic control of rapid genome content divergence in Arabidopsis thaliana.

Genome evolution in eukaryotes is predominantly driven by the dynamics of repetitive sequences, which vary widely in both copy number and sequence composition. Rates of repeat evolution differ between and within species and are likely modulated by both genetics and environment. To uncover factors shaping the rate of genome content evolution, we analyzed 1043 resequenced Arabidopsis thaliana genomes using a novel K-mer-based approach to characterize genome content variation and identify hypervariable regions underlying differences in repeat abundance. We next treated repeat abundance as a quantitative trait and performed genome-wide association analyses across more than 400 repeat families to identify the genetic basis of copy number variation. Integrating these results through a meta-GWAS approach revealed both cis-acting variants and more than 50 candidate trans-acting loci associated with repeat abundance genome-wide. Cis-acting variation was predominantly localized to pericentromeric and centromeric regions, whereas trans-acting loci were enriched for candidate genes involved in DNA replication, DNA repair, and DNA methylation regulation. The results are consistent with purifying selection acting against mutations that accelerate genome content divergence, favoring alleles that constrain repeat expansion. Together, these findings provide new insights into the genetic architecture and evolutionary forces shaping genome evolution in A. thaliana and establish a framework for investigating these processes in other plant species.

Arabidopsis↗
PubMed2006

Positive selection in the evolution of cancer.

We hypothesize that forms of antagonistic coevolution have forged strong links between positive selection at the molecular level and increased cancer risk. By this hypothesis, evolutionary conflict between males and females, mothers and foetuses, hosts and parasites, and other parties with divergent fitness interests has led to rapid evolution of genetic systems involved in control over fertilization and cellular resources. The genes involved in such systems promote cancer risk as a secondary effect of their roles in antagonistic coevolution, which generates evolutionary disequilibrium and maladaptation. Evidence from two sources: (1) studies on specific genes, including SPANX cancer/testis antigen genes, several Y-linked genes, the pem homebox gene, centromeric histone genes, the breast cancer gene BRCA1, the angiogenesis gene ANG, cadherin genes, cytochrome P450 genes, and viral oncogenes; and (2) large-scale database studies of selection on different functional categories of genes, supports our hypothesis. These results have important implications for understanding the evolutionary underpinnings of cancer and the dynamics of antagonistically-coevolving molecular systems.

Animals↗
PubMed1991

Chromosome banding in Amphibia. XVI. High-resolution replication banding patterns in Xenopus laevis.

High-resolution replication banding patterns were induced in prometaphase and prophase chromosomes of Xenopus laevis by treating kidney cell lines with 5-bromodeoxyuridine (BrdU) and deoxythymidine (dT) in succession. Up to 650 early and late replicating bands per haploid karyotype were demonstrated in the very long prophase chromosomes. This permits an exact identification of all chromosome pairs of X. laevis. Late replicating heterochromatin was located by analysing the time sequence of replication throughout the second half of S-phase. Neither heteromorphic sex chromosomes nor sex chromosome-specific replication bands were demonstrated in the heterogametic ZW females of X. laevis. A detailed examination of the BrdU/dT-labelled prometaphases and prophases revealed that the X. laevis chromosomes can be arranged in groups of four (quartets), most of which show conspicuous similarities in length, centromere position, and replication pattern. This is interpreted as further evidence for an ancient allotetraploid origin of X. laevis.

Animals↗
PubMed1995

Aneuploidy in breast cancer: a fluorescence in situ hybridization study.

Although ploidy is associated with the development and progression of most breast cancers, the value of flow cytometric ploidy as a clinical prognostic factor remains controversial. The technique of fluorescence in situ hybridization (FISH) can be used not only to determine overall ploidy, but also to assess the over-representation or under-representation of specific chromosomes in interphase cells. This information may be of prognostic value. We studied 84 primary breast cancers and 20 metastatic tumors by FISH, using chromosome-specific fluorescent centromeric probes. Of these, 100 cases were also studied by DNA flow cytometry. The FISH studies were concordant with DNA flow cytometry with regard to distinguishing aneuploid from diploid tumors in 78% of cases. The FISH data suggested that aneuploidy arises by a process of chromosome complement doubling with subsequent chromosome loss. In tumors that exhibited evidence of more than one round of chromosome complement doubling, the selective accumulation of multiple copies of specific chromosomes or chromosome segments was common. Multiple copies of chromosomes centromeres 1, 3, and 17 were accumulated selectively in the cells of individual tumors more frequently than chromosomes centromeres 7, 11, and 16. Multiple copies of chromosomes centromeres 10 and 20 were selectively accumulated only rarely, if at all. Aneuploidy in breast cancer can be divided into distinct stages using fluorescence in situ hybridization techniques. The stages of aneuploidy provide potential landmarks in the genetic evolution of this disease with possible links to chromosome-specific evolutionary changes.

Aged↗
PubMed2002

Distribution of telomeric (TTAGGG)(n) sequences in avian chromosomes.

The physical ends of mammalian and other vertebrate chromosomes consist of tandemly repeated (TTAGGG)(n) hexamers, nucleating a specialized telomeric structure. However, (TTAGGG)(n) sequences can also occur at non-telomeric sites, providing important insights into karyotypic evolution. By fluorescence in situ hybridization (FISH) we studied the chromosomal distribution of (TTAGGG)(n) sequences in 16 bird species, representing seven different orders. Many species, in particular the ratites, display (TTAGGG)(n) hybridization signals in interstitial and centromeric regions of their macrochromosomes in addition to the typical telomeric signals. In some but not all species these non-telomeric sites coincide with C-band-positive heterochromatin. The retention and/or amplification of telomeric (TTAGGG)(n) repeats at interstitial and centromeric sites may indicate the fusion of ancestral chromosomes. Compared with the macrochromosomes, the microchromosomes of most species are enriched with (TTAGGG)(n) sequences, displaying heterogeneous hybridization patterns. We propose that this high density of (TTAGGG)(n) repeats contributes to the exceptionally high meiotic recombination rate of avian microchromosomes.

Animals↗
PubMed2004

Multicolor chromosome painting in diagnostic and research applications.

For many years whole chromosome painting probes have been the work-horses in a large variety of clinical and research molecular cytogenetic applications. In recent years painting probes have been complemented by an increasing number of further region-specific probes, which allow the specific staining of centromeres, subtelomeres or other regions within the genome. This development of new probe sets was greatly facilitated by the Human Genome Project from which well-characterized probes for any region within the genome have emerged. Furthermore, the evolution of different multicolor fluorescence in situ hybridization (FISH) technologies now allows the cohybridization of multiple DNA-probes of different colors. These developments have paved the way for FISH-based automated karyotyping or the simultaneous analysis of multiple defined regions within the genome. Using appropriate instrumentation and image processing, the analysis can be performed two-dimensionally on metaphase spreads or three-dimensionally in intact interphase nuclei. Here we summarize some of the most recent developments and discuss the application of painting probes in different scenarios.

Animals↗
PubMed2000

Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.

The genome of the model plant Arabidopsis thaliana has been sequenced by an international collaboration, The Arabidopsis Genome Initiative. Here we report the complete sequence of chromosome 5. This chromosome is 26 megabases long; it is the second largest Arabidopsis chromosome and represents 21% of the sequenced regions of the genome. The sequence of chromosomes 2 and 4 have been reported previously and that of chromosomes 1 and 3, together with an analysis of the complete genome sequence, are reported in this issue. Analysis of the sequence of chromosome 5 yields further insights into centromere structure and the sequence determinants of heterochromatin condensation. The 5,874 genes encoded on chromosome 5 reveal several new functions in plants, and the patterns of gene organization provide insights into the mechanisms and extent of genome evolution in plants.

Animals↗