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PubMed1991

On the mode of evolution of alpha satellite DNA in human populations.

The hypothesis that highly reiterated satellite DNAs in present-day populations evolve by molecular mechanisms that create, by saltatory amplification steps, new long arrays of satellite DNA, and that such long arrays are used for homogenization purposes, has been tested both in mouse and in humans. In mouse, the data obtained are consistent with this hypothesis. This was tested in more detail on chromosomes 13 and 21 of the human genome. A Centre d'Etudes du Polymorphisme Humain family, which in some individuals exhibits strong supplementary DNA bands following TaqI restriction endonuclease digestion and conventional gel electrophoresis, was analyzed by pulse field gel electrophoresis following restriction by BamHI. The supplementary bands on chromosome 13 (18 times the basic alpha satellite DNA repeat) and on chromosome 21 (a 9.5-mer) segregated with centromeric alpha satellite DNA blocks of 5 and 5.3 megabases, respectively. These are by far the largest alpha satellite block lengths seen in all chromosome 13 and chromosome 21 centromeric sequences so far analyzed in this manner. The possibility that these supplementary alpha satellite sequences were created in single individuals by saltatory amplification steps is discussed in light of our own data and that published by others. It is proposed that deletion events and unequal cross-overs, which both occur in large satellite DNA arrays, contribute to the homogenization of size and sequence of the alpha satellite DNA on most chromosomes of humans.

Animals↗
PubMed1996

FLO11, a yeast gene related to the STA genes, encodes a novel cell surface flocculin.

We report the characterization of a gene encoding a novel flocculin related to the STA genes of yeast, which encode secreted glucoamylase. The STA genes comprise sequences that are homologous to the sporulation-specific glucoamylase SGA and to two other sequences, S2 and S1. We find that S2 and S1 are part of a single gene which we have named FLO11. The sequence of FLO11 reveals a 4,104-bp open reading frame on chromosome IX whose predicted product is similar in overall structure to the class of yeast serine/threonine-rich GPI-anchored cell wall proteins. An amino-terminal domain containing a signal sequence and a carboxy-terminal domain with homology to GPI (glycosyl-phosphatidyl-inositol) anchor-containing proteins are separated by a central domain containing a highly repeated threonine- and serine-rich sequence. Yeast cells that express FLO11 aggregate in the calcium-dependent process of flocculation. Flocculation is abolished when FLO11 is disrupted. The product of STA1 also is shown to have flocculating activity. When a green fluorescent protein fusion of FLO11 was expressed from the FLO11 promoter on a single-copy plasmid, fluorescence was observed in vivo at the periphery of cells. We propose that FLO11 encodes a flocculin because of its demonstrated role in flocculation, its structural similarity to other members of the FLO gene family, and the cell surface location of its product. FLO11 gene sequences are present in all yeast strains tested, including all standard laboratory strains, unlike the STA genes which are present only in the variant strain Saccharomyces cerevisiae var. diastaticus. FLO11 differs from all other yeast flocculins in that it is located near a centromere rather than a telomere, and its expression is regulated by mating type. Repression of FLO11-dependent flocculation in diploids is conferred by the mating-type repressor al/alpha2.

Cloning, Molecular↗
PubMed2002

Chromosomal studies on ten species of notothenioid fishes (Notothenioidei: Bathydraconidae, Channichthyidae, Nototheniidae).

The results of a cytogenetic study conducted with banding and in situ hybridization techniques using ribosomal and telomeric probes on various species belonging to three families (Bathydraconidae, Channichthyidae and Nototheniidae) of the perciform suborder, Notothenioidei, are reported. The heterochromatin distribution and composition, nucleolar organiser and localisation of telomeric sequences seem to indicate that both in karyologically conservative families such as channichthyids and in families exhibiting greater karyological variability, certain DNA fractions like ribosomal genes and centromeric and telomeric DNAs are prone to some variability. This could play an important role in favouring or hampering chromosome rearrangements.

Animals↗
PubMed1999

Isolated tetrasomy 8 in minimally differentiated acute myeloid leukemia (AML-M0).

Tetrasomy 8 as a sole anomaly in hematological disorders is relatively rare. To the best of our knowledge, only 19 such cases have been described in the literature to date. Of them, acute myeloid leukemia (AML) in 13 (M1, one; M2, three; M4, one; M5, eight), acute lymphoblastic leukemia(ALL) in one, myelodysplastic syndrome(MDS) in 3, polycythemia vera(PV) and myelofibrosis(MF), one case each. Their median survival was 20 weeks. Here, we report the first case of a 29-year-old man with minimally differentiated AML (AML-M0) displaying a tetrasomy 8 clone. Immunophenotyping showed positivity with CD33, CD34 and intracellular MPO, but all lymphoid markers tested were negative. Conventional cytogenetics of bone marrow cells showed 84.9% of metaphases with tetrasomy 8 in addition to 15.1% with normal diploidy. However, Fluorescence in situ hybridization(FISH) using a centromeric probe specific for chromosome 8 revealed trisomy 8 in 14.2% of interphase nuclei besides tetrasomy 8 in 82.4%. The patient died four weeks after diagnosis without therapy. In conclusion, these findings suggest that tetrasomy 8 is associated with a heterogeneous group of myeloid disorders and heralds a bad prognosis. It may be a consequence of clonal evolution of trisomy 8.

Acute Disease↗
PubMed2000

Molecular cytogenetic dissection of human chromosomes 3 and 21 evolution.

Chromosome painting in placental mammalians illustrates that genome evolution is marked by chromosomal synteny conservation and that the association of chromosomes 3 and 21 may be the largest widely conserved syntenic block known for mammals. We studied intrachromosomal rearrangements of the syntenic block 3/21 by using probes derived from chromosomal subregions with a resolution of up to 10-15 Mbp. We demonstrate that the rearrangements visualized by chromosome painting, mostly translocations, are only a fraction of the actual chromosomal changes that have occurred during evolution. The ancestral segment order for both primates and carnivores is still found in some species in both orders. From the ancestral primate/carnivore condition an inversion is needed to derive the pig homolog, and a fission of chromosome 21 and a pericentric inversion is needed to derive the Bornean orangutan condition. Two overlapping inversions in the chromosome 3 homolog then would lead to the chromosome form found in humans and African apes. This reconstruction of the origin of human chromosome 3 contrasts with the generally accepted scenario derived from chromosome banding in which it was proposed that only one pericentric inversion was needed. From the ancestral form for Old World primates (now found in the Bornean orangutan) a pericentric inversion and centromere shift leads to the chromosome ancestral for all Old World monkeys. Intrachromosomal rearrangements, as shown here, make up a set of potentially plentiful and informative markers that can be used for phylogenetic reconstruction and a more refined comparative mapping of the genome.

Animals↗
PubMed1990

Molecular mapping of deletion sites in the short arm of chromosome 3 in human lung cancer.

We used 10 restriction fragment length polymorphism (RFLP) probes spanning the length of the short arm of chromosome 3 (3p) to map deletion sites in human lung cancer. Two approaches were used. 1) When a patient's tumor and normal tissue were available, loci with allelic heterozygosity in the normal tissue were tested for loss of alleles at 3p. 2) When the corresponding normal tissue was not available, the frequency of heterozygosity at each locus in a panel of tumors was compared to the corresponding published frequencies in nontumor tissue of healthy individuals or patients with lung cancer. In 14 small cell lung carcinomas (SCLC) with normal DNA for comparison, allele loss was found at all heterozygous loci, with one exception at a locus near the 3p centromere (D3S4). In the total of 53 SCLCs, which included tumors without paired normal tissue, frequency of heterozygosity was significantly reduced in all 10 3p loci. Three loci, DNF 15S2, RAF1, and D3S18, were homozygous in all tumors in the SCLC panel. These loci, which are in regions 3p21 and 3p25, may thus be involved in the origin or evolution of SCLC. We also investigated 24 non-SCLC tumors. In this panel, frequency of heterozygosity was significantly reduced at seven of the 10 loci tested. Comparison of the results shows that the pattern of allele loss on 3p is different in SCLC and non-SCLC, suggesting a difference in pathogenesis at the genetic level.

Alleles↗
PubMed1992

A primate transfer RNA gene cluster and the evolution of human chromosome 1.

The localisation of tRNA(Asn) gene clusters in the karyotypes of primates has been studied by means of in situ hybridisation. In the human and orangutan (Pongo pygmaeus) karyotypes there are two such gene clusters, one each on the long and short arms of chromosome 1. Old World monkeys, however, contain both gene clusters on their equivalent of the human chromosome 1 short arm, which can be explained by a pericentric inversion which (amongst other chromosome changes) distinguishes the human and Old World monkey chromosomes 1. The capuchin (Cebus appella), however, a New World monkey, has only one tRNA(Asn) gene cluster, at least on the elements equivalent to human chromosome 1. This cluster is located proximal to the centromere on a chromosome that has been tentatively identified (by others) as the equivalent of the long arm of human chromosome 1. Should this prove to be correct, it would indicate that the large primate metacentric came into being in the form found today in the great apes, rather than in the form currently found in Old World monkeys. These data further show that the tRNA(Asn) gene cluster has been split in two since before the Old World monkeys and hominids diverged, i.e., over 30 million years ago, and also that the original transfer of these genes from one arm of chromosome 1 to the other was unlikely to have involved a pericentric inversion but, rather, some form of replicative transposition.

Animals↗
PubMed1991

Comparative mapping of a gorilla-derived alpha satellite DNA clone on great ape and human chromosomes.

We have isolated an alpha satellite DNA clone, pG3.9, from gorilla DNA. Fluorescence in situ hybridization on banded chromosomes under high stringency conditions revealed that pG3.9 identifies homologous sequences at the centromeric region of ten gorilla chromosomes, and, with few exceptions, also recognizes the homologous chromosomes in human. A pG3.9-like alphoid DNA is present on a larger number of orangutan chromosomes, but, in contrast, is present on only two chromosomes in the chimpanzee. These results show that the chromosomal subsets of related alpha satellite DNA sequences may undergo different patterns of evolution.

Animals↗
PubMed1990

Mapping of class alpha glutathione S-transferase 2 (GST-2) genes to the vicinity of the d locus on mouse chromosome 9.

Recombinant inbred strains of mice were used to localize the genes coding for the class alpha glutathione S-transferase 2 (Gst-2). The genes showed three distinct strain distribution patterns, indicating that they occur in at least three clusters separable by recombination. All three clusters are located in the vicinity of the d locus on mouse chromosome 9, but two of them are closer to d than the third. Linked to Gst-2 on mouse chromosome 9 are two enzyme-encoding loci, Pgm-3 and Mod-1. The human counterparts of Gst-2, Pgm-3, and Mod-1 map to 6p12, 6q12, and 6q12, respectively. Thus, the pericentric region of human chromosome 6 has its homolog in the segment spanning Gst-2, Pgm-3, and Mod-1 on mouse chromosome 9. The fact that the syntenic group extends across the centromere of human chromosome 6 can best be explained by a pericentric inversion postulated to have taken place in the primate lineage leading to Catarhini.

Animals↗
PubMed2001

Molecular and cytogenetic characterization of highly repeated DNA sequences in the vole Microtus cabrerae.

The genus Microtus presents several species with extremely large sex chromosomes that contain large blocks of constitutive heterochromatin. Several cytogenetic and molecular studies of the repetitive sequences in species of the genus Microtus have demonstrated that the heterochromatin is highly heterogeneous. We have cloned and characterized a family of repetitive DNA sequences from M. cabrerae, a species with large heterochromatic blocks on the giant sex chromosomes. These repetitive sequences are 65.84% A-T rich, organized in tandem, with a 161-bp unit and are located on the centromeric region of autosomes and the X chromosome. In addition, this repetitive DNA is located throughout the entire heterochromatic block of the X chromosome and on three interstitial bands in the heterochromatic block of the Y chromosome. Comparative analysis of this family of repetitive sequences from three Microtus species revealed that the development of these sequences has occurred by concerted evolution. Our results support the hypothesis that the heterochromatic blocks from the sex chromosomes of different species are evolving independently and they probably have the genetic capacity to amplify and retain different satellite DNAs. For a topic related to the location of these repetitive DNA sequences on the Y chromosome of M. cabrerae, we propose a model to explain the origin of a length polymorphism previously described for this chromosome.

Animals↗
PubMed1995

The human SB1.8 gene (DXS423E) encodes a putative chromosome segregation protein conserved in lower eukaryotes and prokaryotes.

We report that the human gene SB1.8 (DXS423E) encodes a protein of 1233 amino acids that is highly homologous (30% identity) to the essential yeast protein SMC1 which is required for the segregation of chromosomes at mitosis. Both SB1.8 and SMC1 contain an N-terminal NTP binding site, a central coiled-coil region and a C-terminal helix-loop-helix domain, and have structural features in common with the force generating proteins myosin and kinesin. SB1.8 also exhibits regions of homology and overall structural similarity to the prokaryote (Mycoplasma hyorhinis) protein 115p. Thus SB1.8 and SMC1 are members of a highly conserved and ubiquitous family of proteins that appear to have a fundamental role in cell division. In addition we show that SB1.8 (DXS423E) maps to a cosmid contig that lies centromeric to the OATL2 locus at chromosome Xp11.2.

Amino Acid Sequence↗
PubMed1991

The Oxford Grid.

The 'Oxford Grid' is a term used to denote a method of displaying homologous loci from two species. It may also be used as a basis for historical inferences relating to co-ancestry. These uses are discussed with special reference to man and mouse. It is inferred that as few as 30 reciprocal translocations are sufficient to explain the differences defined by the present grid and that the telocentric karyotype, through which the mouse differs from both man and many closely related rodents, including the rat, must have evolved mainly through the formation and suppression of centromeres rather than through pericentric inversions. Mouse and man share the widest distribution of any mammal and their success appears to be related to being omnivorous with behavioural modifications allowing a wide range of habitat.

Animals↗
PubMed2006

Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice.

In Arabidopsis, tandemly arrayed genes (TAGs) comprise >10% of the genes in the genome. These duplicated genes represent a rich template for genetic innovation, but little is known of the evolutionary forces governing their generation and maintenance. Here we compare the organization and evolution of TAGs between Arabidopsis and rice, two plant genomes that diverged ~150 million years ago. TAGs from the two genomes are similar in a number of respects, including the proportion of genes that are tandemly arrayed, the number of genes within an array, the number of tandem arrays, and the dearth of TAGs relative to single copy genes in centromeric regions. Analysis of recombination rates along rice chromosomes confirms a positive correlation between the occurrence of TAGs and recombination rate, as found in Arabidopsis. TAGs are also biased functionally relative to duplicated, nontandemly arrayed genes. In both genomes, TAGs are enriched for genes that encode membrane proteins and function in "abiotic and biotic stress" but underrepresented for genes involved in transcription and DNA or RNA binding functions. We speculate that these observations reflect an evolutionary trend in which successful tandem duplication involves genes either at the end of biochemical pathways or in flexible steps in a pathway, for which fluctuation in copy number is unlikely to affect downstream genes. Despite differences in the age distribution of tandem arrays, the striking similarities between rice and Arabidopsis indicate similar mechanisms of TAG generation and maintenance.

Arabidopsis↗
PubMed1990

Pyruvate dehydrogenase E1 alpha subunit genes in the mouse: mapping and comparison with human homologs.

Two gene loci for the E1 alpha subunit of the pyruvate dehydrogenase (PDH) complex have been mapped in the mouse by in situ hybridization. One locus maps to the X chromosome in the region F3-F4, the other to chromosome 19, in band B close to the centromere. This arrangement is exactly comparable to the situation in man where there is an X-linked PDH E1 alpha locus and an autosomal locus on chromosome 4. Comparison of the regional localization of the human and mouse X-linked PDH E1 alpha genes provides further information concerning sites of rearrangement of segments of the X chromosome during mammalian evolution. The human autosomal PDH E1 alpha gene is a "processed" gene, which lacks the introns that are present in the X-linked gene. It codes for a testis-specific E1 alpha subunit that is only expressed after the onset of spermatogenesis. The comparative mapping results in the mouse suggest that the genetic organization and pattern of expression of the two PDH E1 alpha genes is the same in the two species.

Animals↗
PubMed1998

Undermethylation associated with retroelement activation and chromosome remodelling in an interspecific mammalian hybrid.

Genetic models predict that genomic rearrangement in hybrids can facilitate reproductive isolation and the formation of new species by preventing gene flow between the parent species and hybrid (sunflowers are an example). The mechanism underlying hybridization-induced chromosome remodelling is as yet unknown, although mobile element activity has been shown to be involved in DNA rearrangement in some dysgenic Drosophila hybrids. It has been proposed that DNA methylation evolved as a means of repressing the movement of mobile elements (the host defence model). If such a protective mechanism were to fail, mobile elements could be activated, and could cause major and rapid genome alterations. Here we demonstrate the occurrence of genome-wide undermethylation, retroviral element amplification and chromosome remodelling in an interspecific mammalian hybrid (Macropus eugenii x Wallabia bicolor). Atypically extended centromeres of Macropus eugenii derived autosomes in the hybrid were composed primarily of an unmethylated, amplified retroviral element not detectable in either parent species. These results, taken with the observation of deficient methylation and de novo chromosome change in other mammalian hybrids, indicate that the failure of DNA methylation and subsequent mobile-element activity in hybrids could facilitate rapid karyotypic evolution.

Animals↗
PubMed2003

Genome-wide search and identification of a novel gel-forming mucin MUC19/Muc19 in glandular tissues.

Gel-forming mucins are major contributors to the viscoelastic properties of mucus secretion. Currently, four gel-forming mucin genes have been identified: MUC2, MUC5AC, MUC5B, and MUC6. All these genes have five major cysteine-rich domains (four von Willebrand factor [vWF] C or D domains and one Cystine-knot [CT] domain) as their distinctive features, in contrast to other non-gel-forming type of mucins. The CT domain is believed to be involved in the initial mucin dimer formation and have very succinct relationship between different gel-forming mucins across different species. Because of gene duplication and evolutional modification, it is very likely that other gel-forming mucin genes exist. To search for new gel-forming mucin candidate genes, a "Hidden Markov Model"(HMM) was built from the common features of the CT domains of those gel-forming mucins. By using this model to screen all protein databases as well as the six-frame translated expression sequence tag and translated human genomic databases, we identified a locus located at the peri-centromere region of human chromosome 12 and the corresponding homologous region of mouse chromosome 15. We cloned the 3' end of this gene and its mouse homolog. We found one vWF C domain, one CT domain, and various mucin-like threonine/serine-rich repeats. Phylogenetic analysis indicated the close relationship between this gene and the submaxillary mucin from porcine and bovine. A polydispersed signal was observed on the Northern blot, which indicates very large mRNA size. Further analysis of the upstream genomic sequences generated from human and mouse genome projects revealed three additional vWF D domains and many mucin-like threonine/serine-rich repeats. The expression of this gene is restricted to the mucous cells of various glandular tissues, including sublingual gland, submandibular gland, and submucosal gland of the trachea. Based on the chronological convention, we have given the name MUC19 to the human ortholog and Muc19 to the mouse.

Amino Acid Sequence↗
PubMed1993

Re-localization of Actsk-1 to mouse chromosome 8, a new region of homology with human chromosome 1.

We present here the genetic mapping of the alpha-skeletal actin locus (Actsk-1) on mouse Chromosome (Chr) 8, on the basis of the PCR analysis of a microsatellite in an interspecific backcross. Linkage and genetic distances were established for four loci by analysis of 192 (or 222) meiotic events and indicated the following gene order: (centromere)-Es-1-11.7 cM-Tat-8.3 cM-Actsk-1-0.5 cM-Aprt. Mapping of ACTSK to human Chr 1 and of TAT and APRT to human Chr 16 demonstrates the existence of a new short region of homology between mouse Chr 8 and human Chr 1. Intermingling on this scale between human and mouse chromosomal homologies that occurred during evolution creates disorders in comparative linkage studies.

Actins↗
PubMed1993

Chromosome aberrations in mesoblastic nephroma.

Mesoblastic nephroma (MN) is the most common renal tumor diagnosed in infancy. Histologically, MNs are designated as classic, cellular, or mixed type based upon variations in cellularity. Recent karyotypic reports have suggested that extra copies of chromosome 11 are a nonrandom occurrence in MNs. We analyzed nuclear suspensions prepared from a group of 17 formalin-fixed, paraffin-embedded tumors to determine the possible role of chromosome 11 copy number in the genesis of MN. Extra copies of D11Z1 (a probe for the centromeric region of chromosome 11) were detected in seven out of 10 MNs with cellular or mixed histology, whereas each of six classic histology MNs were disomic for D11Z1 (P < 0.05). Additional fluorescence in situ hybridization studies utilizing the probes for the alpha satellite, centromeric regions of chromosomes 7, 8, 9, 12, 17, and 20 were then carried out on all cases with cellular or mixed histology. Five out of 10 cellular or mixed MNs had extra copies of D8Z1, and four out of 10 had extra copies of D17Z1, suggesting that gains of chromosomes 8 and 17 may be additional nonrandom cytogenetic events associated with the evolution of MNs. DNA aneuploidy, as determined by image analysis, was detected in three tumors: all had greater than four chromosomal aberrations documented by fluorescence in situ hybridization.

Chromosome Aberrations↗