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PubMed1995

Rearrangement of chromosome 1 is a frequent finding in endometrial carcinoma. An in situ hybridization study in nine endometrial carcinomas.

Nine endometrial carcinomas were examined for numerical aberrations of the chromosomes 1,7, and X by fluorescence in situ hybridization using highly repetitive chromosome-specific probes. In addition, a combination of a centromeric and a telomeric chromosome 1 probe was applied to detect structural chromosome 1 aberrations. Chromosome aberrations were found in six tumors. In four of these, an imbalance between 1q12 and 1p36 was detected, indicating the presence of an extra 1p- chromosome. In regard to the chromosomes 7 and X, monosomies and trisomies were found. Intratumoral genetic heterogeneity in endometrial carcinomas was detectable by FISH and flow cytometry. In conclusion, our findings confirm that chromosome 1 is frequently involved in structural chromosome changes, indicating chromosome 1 to be of importance in the evolution of endometrial carcinoma.

Adenocarcinoma↗
PubMed1996

Budding yeast SKP1 encodes an evolutionarily conserved kinetochore protein required for cell cycle progression.

The budding yeast SKP1 gene, identified as a dosage suppressor of a known kinetochore protein mutant, encodes an intrinsic 22.3 kDa subunit of CBF3, a multiprotein complex that binds centromere DNA in vitro. Temperature-sensitive mutations in SKP1 define two distinct phenotypic classes. skp1-4 mutants arrest predominantly as large budded cells with a G2 DNA content and short mitotic spindle, consistent with a role in kinetochore function. skp1-3 mutants, however, arrest predominantly as multiply budded cells with a G1 DNA content, suggesting an additional role during the G1/S phase. Identification of Skp1p homologs from C. elegans, A. thaliana, and H. sapiens indicates that SKP1 is evolutionarily highly conserved. Skp1p therefore represents an intrinsic kinetochore protein conserved throughout eukaryotic evolution and may be directly involved in linking kinetochore function with the cell cycle-regulatory machinery.

Alleles↗
PubMed2002

Tools for the study of genome rearrangements in laboratory and industrial yeast strains.

In order to investigate the extent of genome rearrangements in laboratory and industrial yeast strains, a set of plasmids, containing ca. 300 bp fragments from highly conserved genes from S. cerevisiae, has been constructed. We chose three unique PCR products, each from a single gene, per chromosome: one from close to the centromere, and one from each chromosome end. Using these plasmids as probes to hybridize a Southern blot from a pulsed-field gel electrophoresis separation of the 16 yeast chromosomes, it is possible to identify large chromosomal rearrangements such as reciprocal translocations.

Blotting, Southern↗
PubMed1997

Cytogenetics of the genus Leporinus (Pisces, Anostomidae). II. Molecular cytogenetics, organization and evolutionary conservation of a chromosome-specific satellite DNA from Leporinus obtusidens.

A chromosome-specific satellite DNA from the South American fish species Leporinus obtusidens has been isolated and characterized. Sequence analysis and Southern hybridization studies indicate that the cloned 483-bp fragment is 60% AT rich and appears to comprise two diverged monomers. A highly variable low-copy number polymorphism was detected and, thus, this satellite DNA may serve as a valuable genetic marker. Using a Southern blot approach, the cloned satellite DNA cross-hybridized strongly to the DNA of Leporinus elongatus but failed to detect homologous sequences in the genomes of other closely related Leporinus species and higher vertebrates. Using fluorescence in situ hybridization to mitotic metaphase spreads of L. obtusidens and L. elongatus, this satellite DNA was located to the (peri)centromeric region of one single chromosome pair in both species. As the cloned satellite DNA sequence clearly evolved along a chromosomal lineage and is highly variable, it may serve as a very useful marker in further genetic, molecular and cytogenetic studies of the genus Leporinus.

Animals↗
PubMed2004

A 1463 gene cattle-human comparative map with anchor points defined by human genome sequence coordinates.

A second-generation 5000 rad radiation hybrid (RH) map of the cattle genome was constructed primarily using cattle ESTs that were targeted to gaps in the existing cattle-human comparative map, as well as to sparsely populated map intervals. A total of 870 targeted markers were added, bringing the number of markers mapped on the RH(5000) panel to 1913. Of these, 1463 have significant BLASTN hits (E < e(-5)) against the human genome sequence. A cattle-human comparative map was created using human genome sequence coordinates of the paired orthologs. One-hundred and ninety-five conserved segments (defined by two or more genes) were identified between the cattle and human genomes, of which 31 are newly discovered and 34 were extended singletons on the first-generation map. The new map represents an improvement of 20% genome-wide comparative coverage compared with the first-generation map. Analysis of gene content within human genome regions where there are gaps in the comparative map revealed gaps with both significantly greater and significantly lower gene content. The new, more detailed cattle-human comparative map provides an improved resource for the analysis of mammalian chromosome evolution, the identification of candidate genes for economically important traits, and for proper alignment of sequence contigs on cattle chromosomes.

Animals↗
PubMed2006

[Genetic analysis of two extremely segregation distorted populations in rice (Oryza sativa L.)].

Segregation distortion is a quite common phenomenon in living species and thought to be a potent evolutional force. The main reasons of distorted segregation ratios are responsible for the selection of gametes or sporophytes. In this study, two extreme segregation distortions from the progenies of lmi x 02428 and d6 x 93-11 were identified. The segregation ratio of molecular markers tightly linked with LMI and D6 genes were analyzed and skew segregation were found in the markers tested which were indicated by significant deviation from the expected Mendelian segregation ratio(1:2:1). The segregation distorted regions were detected between molecular markers ST8 and ST8-2 near the centromere of chromosome 8, and ST7-1 and ST7-3 near telomere of chromosome 7, respectively. Meanwhile, the results indicated that segregation distortion had related with the different crossed combinations.

Chromosomes, Plant↗
PubMed2007

Comparison of the Z and W sex chromosomal architectures in elegant crested tinamou (Eudromia elegans) and ostrich (Struthio camelus) and the process of sex chromosome differentiation in palaeognathous birds.

To clarify the process of avian sex chromosome differentiation in palaeognathous birds, we performed molecular and cytogenetic characterization of W chromosome-specific repetitive DNA sequences for elegant crested tinamou (Eudromia elegans, Tinamiformes) and constructed comparative cytogenetic maps of the Z and W chromosomes with nine chicken Z-linked gene homologues for E. elegans and ostrich (Struthio camelus, Struthioniformes). A novel family of W-specific repetitive sequences isolated from E. elegans was found to be composed of guanine- and cytosine-rich 293-bp elements that were tandemly arrayed in the genome as satellite DNA. No nucleotide sequence homologies were found for the Struthioniformes and neognathous birds. The comparative cytogenetic maps of the Z and W chromosomes of E. elegans and S. camelus revealed that there are partial deletions in the proximal regions of the W chromosomes in the two species, and the W chromosome is more differentiated in E. elegans than in S. camelus. These results suggest that a deletion firstly occurred in the proximal region close to the centromere of the acrocentric proto-W chromosome and advanced toward the distal region. In E. elegans, the W-specific repeated sequence elements were amplified site-specifically after deletion of a large part of the W chromosome occurred.

Animals↗
PubMed1991

A proximal mouse chromosome 9 linkage map that further defines linkage groups homologous with segments of human chromosomes 11, 15, and 19.

A 42-cM map of proximal mouse chromosome 9, including eight loci defined by restriction fragment length variants, has been generated. Linkage was established by haplotype analyses of 114 interspecific backcross mice and indicated the following gene order: (centromere) Pvs-5.3 cM-Icam-1/Ldlr-18.4 cM-Thy-1-1.8 cM-Ncam-0.9 cM-Hexa-7.9 cM-Gsta-7.9 cM-Trf. Three of these loci, Pvs, Icam-1, and Hexa, have not been mapped previously. Together with previous mapping studies the current results suggested that chromosomal segments of mouse chromosomes 7 and 9 and chromosomal segments of human chromosomes 11, 15, and 19 derive from a single putative primordial chromosome. The studies support the postulate that detailed analysis of chromosome organization will be useful in defining events in mammalian evolution.

Animals↗
PubMed1987

Heterogeneity and balance of chromosomes in human cell line M-HeLa-76: analysis of 100 karyotypes.

The cell subline M-HeLa-76 with the modal chromosome number 49 was used to define the level of karyotypic variability. By means of a G-banding technique, 100 metaphase plates were analyzed. Among them, 11 different karyotypes were found to range from 2% to 34%. Most probable evolutionary pathways of cell karyotypes within the cell subline were demonstrated. Determination of the origin of all marker chromosomes (32 in all) and unique structural rearrangements (16) revealed a nonrandom distribution of chromosome breaks. These are primarily centromeric regions of chromosomes 3 and 5. Identification of the overall chromosome material in the cells of each karyotype via karyotype reconstruction showed their close similarity in spite of differences in the sets of normal and marker chromosomes. On the basis of reconstructed karyotypes (RK) of each cell group, a generalized reconstructed karyotype (GRK) of the cell line was obtained. This permitted the conclusion of a balanced chromosome set in a cell population as a whole and obligatory retention of diploidy in all chromosomes of a normal set. The role of variability and selection in the evolution of cell populations in vitro is discussed.

Chromosome Aberrations↗
PubMed1992

The affinity of DNA-microtubule protein complexes and their disruption by tubulin binding drugs.

Using the gel shift assay system, we have measured the apparent affinity constant for the interaction of two different DNAs with MAP proteins found in both total calf brain microtubules and heat stable brain preparations. Both DNAs studied contained centromere/kinetochore sequences- one was enriched in the calf satellite DNA; the other was a large restriction fragment containing the yeast CEN11 DNA sequence. Complexes formed using both DNAs had similar Kapp values in the range of 2.1 x 10(7) M-1 to 2.0 x 10(8) M-1. CEN11 DNA-MTP complexes had by far the highest Kapp value of 2.0 x 10(8) M-1. The CEN11 DNA sequence is where the yeast kinetochore of chromosome 11 is formed and where the single yeast microtubule is bound in vivo. The CEN11 conserved region II known binding sites-(dA/dT)n runs- for mammalian MAP2 protein, are in good agreement with this higher Kapp value. The effects of the classical tubulin binding drugs colchicine, podophyllotoxin and vinblastine on the DNA-MAP protein complex stability were investigated by determining the drug concentrations where the complexes were destabilized. Only the complexes formed from total microtubule protein (tubulin containing) were destabilized over a wide drug concentration range. Heat stable brain protein complexes (no tubulin) were largely unaffected. Furthermore, it took 10-100 fold higher drug concentrations to disrupt the CEN11 DNA complexes compared to the calf thymus satellite DNA enriched complexes. These data support our previous results suggesting that there is a DNA sequence dependent interaction with MAP proteins that appears to be conserved in evolution (Marx et. al., Biochim. Biophys. Acta. 783, 383-392, 1984; Marx and Denial, Molecular Basis of Cancer 172B, 65-75 1985). In addition, these results imply that the classical tubulin binding drugs may exert their biological effects in cells at least in part by disrupting DNA-Protein complexes of the type we have studied here.

Animals↗
PubMed1994

Structure of the human type-I interferon gene cluster determined from a YAC clone contig.

A map of the type-I interferon gene cluster located on the short arm of human chromosome 9 (9p) has been constructed using a contig of YAC clones. This map contains 26 interferon (IFN) genes and pseudogenes, and it accounts for all, except one, of the IFN sequences previously reported by other authors, plus a new IFNW pseudogene. The most distal gene on 9p is IFNB, and the most proximal one is IFNWP19. The direction of transcription for the 20 most distal IFN sequences is toward the telomere and for the 6 most proximal sequences, toward the centromere. Several regions of the cluster show evidence of ancestral duplication events. Some of these events may be explained by unequal crossing over between adjacent tandem genes. The location of several breakpoints within the cluster, from deletions associated with leukemias and gliomas, was also determined.

Base Sequence↗
PubMed2005

Equine FISH mapping of 36 genes known to locate on human chromosome ends.

The INRA and the CHORI-241 horse BAC libraries were screened by hybridization with DNA probes and/or directly by PCR with primers designed in consensus sequences of genes localized at the end of each human chromosome. BAC clones were retrieved and 36 could be FISH mapped after the expected gene was confirmed in each BAC by sequencing. Our results show that 16 BACs can be considered to be at telomeric or centromeric positions in the horse and 15 were found at the boundary of actually defined conserved segments even-though often located within conserved syntenic fragments between horse and human. There is no straightforward relation between the end position of a marker in human and its end position in the horse. A gene was first anchored to ECA27 by FISH mapping. The localization of these markers expands the cytogenetic map of the horse and will serve as anchors for the integrated and future physical maps. It should also help to better understand the different chromosomal rearrangements that occurred during evolution of genomes derived from a common ancestral karyotype.

Base Sequence↗
PubMed2005

Genomewide comparative analysis of the highly abundant transposable element DINE-1 suggests a recent transpositional burst in Drosophila yakuba.

DINE-1 (Drosophila interspersed element) is the most abundant repetitive sequence in the Drosophila genome derived from transposable elements. It comprises >1% of the Drosophila melanogaster genome (DMG) and is believed to be a relic from an ancient transpositional burst that occurred approximately 5-10 MYA. We performed a genomewide comparison of the abundance, sequence variation, and chromosomal distribution of DINE-1 in D. melanogaster and D. yakuba. Unlike the highly diverged copies in the DMG (pairwise distance approximately 15%), DINE-1's in the Drosophila yakuba genome (DYG) have diverged by only 3.4%. Moreover, the chromosomal distribution of DINE-1 in the two species is very different, with a significant number of euchromatic insertions found only in D. yakuba. We propose that these different patterns are caused by a second transpositional burst of DINE-1's in the D. yakuba genome approximately 1.5 MYA. On the basis of the sequence of these recently transposed copies, we conclude that DINE-1 is likely to be a family of nonautomomous DNA transposons. Analysis of the chromosomal distribution of two age groups of DINE-1's in D. yakuba indicates that (1) there is a negative correlation between recombination rates and the density of DINE-1's and (2) younger copies are more evenly distributed in the chromosome arms, while older copies are mostly located near the centromere regions. Our results fit the predictions of a selection-transposition balance model. Our data on whole-genome comparison of a highly abundant TE among Drosophila sibling species demonstrate the unexpectedly dynamic nature of TE activity in different host genomes.

Animals↗
PubMed1995

Visualization of INT2 and HST1 amplification in oral squamous cell carcinomas.

Oral squamous cell carcinoma (OSCC) develops along a multistep genetic pathway including loss of tumor suppressor genes and alteration of oncogenes. We characterized seven OSCC cell lines by classical and molecular cytogenetic analysis and fresh tumor and adjacent oral mucosa corresponding to three of the cell lines by molecular cytogenetics. We observed homogeneously staining regions (hsrs) in four of the seven cell lines, at 11q13 in three and at 11q23 and in an unidentified marker chromosome in the fourth. Amplification of band 11q13 occurs in 30-60% of head and neck squamous cell carcinomas. To determine whether INT2 and HST1, both located in band 11q13, are amplified in the tissues and cell lines and to confirm the chromosomal location(s) of the amplification, we used dual-color fluorescence in situ hybridization (FISH) with DNA probes for these genes and the chromosome 11 centromere. We report chromosomal localization of INT2/HST1 amplification in OSCC. Coamplification of INT2 and HST1 was detected in the hsrs in cultured tumor cells from the four hsr-containing tumors and in directly harvested tumor cells, which were available from only two of these tumors. Amplification was not present in tumors lacking hsrs or adjacent oral mucosa corresponding to any of the seven tumors. The observation of amplification in fresh tumor cells suggests that the amplification was present in the patients, may play a key role in the development and/or progression of OSCC, and is not due to karyotypic evolution in vitro. The absence of amplification in the adjacent mucosa suggests that 11q13 amplification is a relatively late event in OSCC tumorigenesis.

Biopsy↗
PubMed2002

B chromosomes of Korean field mouse Apodemus peninsulae (Rodentia, Murinae) analysed by microdissection and FISH.

Organization of B chromosomes in the Korean field mouse Apodemus peninsulae was analyzed. We painted its metaphase chromosomes with whole and partial chromosome paints generated by microdissection and DOP-PCR. The results of the painting indicated that all B chromosomes contained a large amount of repeated DNA sequences. The repeats could be classified in terms of their homology and predominant location. Pericentromeric repeats of B chromosomes were present in many copies in pericentromeric C-blocks of all autosomes and in non-centromeric C-blocks of the sex chromosomes. B arm specific type 1 repeats comprised the main body of the arms of almost all B chromosomes and were present in the arms of A chromosomes as interspersed sequences. B arm-specific type 2 repeats were found at the ends of some B chromosomes that did not undergo compaction at the interphase- metaphase transition and remained uncondensed. On the basis of comparative analysis of localization of B chromosome repeats in the chromosomes of two related species, A. peninsulae and A. agrarius, we suggest a hypothesis of B chromosome origin and evolution in the genus Apodemus.

Animals↗
PubMed1998

Identification and characterization of the gene encoding a second proteolipid subunit of human vacuolar H(+)-ATPase (ATP6F).

The proteolipid domain of vacuolar H(+)-ATPase (V-ATPase) plays a major role in H+ transport in microvesicles and other acidic organelles. We have cloned the second human proteolipid of the V-ATPase (designated hATP6F), a homologue of the Saccharomyces cerevisiae proteolipid VMA16, which is an essential subunit of yeast V-ATPase. hATP6F is a hydrophobic protein with five putative transmembrane segments, having 61% amino acid identity and 83% similarity to the yeast protein, except in the N-terminus, and contains a conserved glutamic acid residue (Glu98) that is essential for H(+)-transporting activity. The gene for hATP6F (gene symbol, ATP6F), which consists of eight exons and spans approximately 3.5 kb, was isolated and mapped to human chromosome band 1p32.3 and the region 10.81 cR centromeric of the STS marker SHGC36789 (LOD = 6.75) by fluorescence in situ hybridization and radiation hybrid mapping, respectively. This is the first evidence in human of the existence of a second gene encoding a distinct V-ATPase proteolipid.

Amino Acid Sequence↗
PubMed1999

A 450-kb contig of defensin genes on human chromosome 8p23.

Defensins are a large family of host defense peptides expressed in leukocytes and epithelia. Using P1 and BAC clones, we have determined the organization of the human alpha-defensin genes and the beta-defensin gene HDEFB1 on chromosome 8p23. From the telomere, the order of the genes (with encoded peptides in parentheses) is HDEFA5 (HD-5), HDEFA1/1A (HNP-1/3), HDEFA4 (HNP-4), HDEFA6 (HD-6), and HDEFB1 (HBD-1). These genes span a region of approximately 450kb. Genes encoding intestinal Paneth cell defensins (HDEFA5 and HDEFA6) flank the myeloid defensin gene cluster (HDEFA1, HDEFA1A, HDEFA4). Based on our previous studies, the remaining known defensin gene, HDEFB2 (HBD-2), is about 400kb centromeric to HDEFB1. This map supports the hypothesis, originally proposed because of sequence similarities, that myeloid alpha-defensin genes evolved by reduplication and divergence from Paneth cell defensin genes, and identifies regions and clones, which should be useful in the search for new defensin genes.

Base Sequence↗
PubMed2002

C-banded karyotypes of two Silene species with heteromorphic sex chromosomes.

Mitotic metaphase chromosomes of Silene latifolia (white campion) and Silene dioica (red campion) were studied and no substantial differences between the conventional karyotypes of these two species were detected. The classification of chromosomes into three distinct groups proposed for S. latifolia by Ciupercescu and colleagues was considered and discussed. Additionally, a new small satellite on the shorter arm of homobrachial chromosome 5 was found. Giemsa C-banded chromosomes of the two analysed species show many fixed and polymorphic heterochromatic bands, mainly distally and centromerically located. Our C-banding studies provided an opportunity to better characterize the sex chromosomes and some autosome types, and to detect differences between the two Silene karyotypes. It was shown that S. latifolia possesses a larger amount of polymorphic heterochromatin, especially of the centromeric type. The two Silene sex chromosomes are easily distinguishable not only by length or DNA amount differences but also by their Giemsa C-banding patterns. All Y chromosomes invariably show only one distally located band, and no other fixed or polymorphic bands on this chromosome were observed in either species. The X chromosomes possess two terminally located fixed bands, and some S. latifolia X chromosomes also have an extra-centric segment of variable length. The heterochromatin amount and distribution revealed by our Giemsa C-banding studies provide a clue to the problem of sex chromosome and karyotype evolution in these two closely related dioecious Silene species.

Chromosome Banding↗