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PubMed2004

Centromeric DNA sequences in the pathogenic yeast Candida albicans are all different and unique.

In an approach to clone and characterize centromeric DNA sequences of Candida albicans by chromatin immunoprecipitation, we have used antibodies directed against an evolutionarily conserved histone H3-like protein, CaCse4p (CENP-A homolog). Sequence analysis of clones obtained by this procedure reveals that only eight relatively small regions (approximately 3 kb each) of the Can. albicans genome are selectively enriched. These CaCse4-bound sequences are located within 4- to 18-kb regions lacking ORFs and occur once in each of the eight chromosomes of Can. albicans. Binding of another evolutionarily conserved kinetochore protein, CaMif2p (CENP-C homolog), colocalizes with CaCse4p. Deletion of the CaCse4p-binding region of chromosome 7 results in a high rate of loss of the altered chromosome, confirming that CaCse4p, a centromeric histone in the CENP-A family, indeed identifies the functional centromeric DNA of Can. albicans. The CaCse4p-rich regions not only lack conserved DNA motifs of point (<400 bp) centromeres and repeated elements of regional (>40 kb) centromeres, but also each chromosome of Can. albicans contains a different and unique CaCse4p-rich centromeric DNA sequence, a centromeric property previously unobserved in other organisms.

Amino Acid Sequence↗
PubMed2002

An evolutionarily conserved putative insulator element near the 3' boundary of the imprinted Igf2/H19 domain.

Igf2 and H19 are closely linked imprinted genes lying at the centromeric end of a 1 Mb imprinted domain on mouse chromosome 7. L23mrp and other genes located 3' (more centromeric) to H19 are not imprinted and do not interact with the enhancers shared by Igf2 and H19. It is therefore suggested that the intergenic region between H19 and L23mrp contains a boundary or an insulator element. We have identified a binding site for CTCF, a nuclear factor that mediates insulator activity in vertebrates, in the intergenic region. This site is conserved between human and mouse, associated with a major DNase I-hypersensitive site, and bound by CTCF in vivo. Functional assays using reporter constructs demonstrated that this element functions as an insulator in transfected cells. The findings suggest that this CTCF site contributes to the 3' boundary of this imprinted domain. Together with the findings on the differentially methylated CTCF sites 5' to H19, CTCF-dependent insulators may not only regulate but also delimit the imprinted domain.

3' Flanking Region↗
PubMedDate not supplied

NOR activity, heterochromatin differentiation, and the Robertsonian polymorphism in Sus scrofa L.

The karyotype of the European wild pig (Sus scrofa scrofa L.) was analysed by means of silver-staining and the chromomycin A3/distamycin A/DAPI fluorescent banding technique to locate active NORs and to differentiate types of C-bands. The ribosomal RNA genes are localized at the secondary constrictions of chromosomes 8 and 10. All biarmed chromosomes, with the exception of chromosome 15/17 and the Y, had a chromomycin bright centromeric region that was moderately fluorescent with distamycin A/DAPI (DA/DAPI). Conversely, all acrocentric chromosomes and the Robertsonian fusion product (15/17) exhibited DA/DAPI bright centromeric heterochromatin. The results are compared with the chromosomal staining behavior of the domestic pig (Sus scrofa domestica L.) and discussed with respect to presumptive mechanisms of karyotypic evolution.

Animals↗
PubMed1994

Transposition of minisatellite-like DNA in Chironomus midges.

Cla elements are a family of tandem repetitive DNA sequences present in the genome of several Chironomus species. Interspersed clusters of Cla elements are widely distributed all over the chromosomes in C. thummi thummi, while they seem to be limited to the centromeric regions in the closely related subspecies C. t. piger. Here we present molecular evidence that this differential distribution is due to a transposition of Cla elements during evolution of the C. t. thummi genome. We have cloned a "filled" integration site (containing a Cla element cluster) from C. t. thummi and the corresponding "empty"genomic site from C. t. piger and other related species. The comparison shows that tandem repetitive elements may be mobilized together with flanking DNA.

Animals↗
PubMed2004

Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids.

Polyploidization is an abrupt speciation mechanism for eukaryotes and is especially common in plants. However, little is known about patterns and mechanisms of gene regulation during early stages of polyploid formation. Here we analyzed differential expression patterns of the progenitors' genes among successive selfing generations and independent lineages. The synthetic Arabidopsis allotetraploid lines were produced by a genetic cross between A. thaliana and A. arenosa autotetraploids. We found that some progenitors' genes are differentially expressed in early generations, whereas other genes are silenced in late generations or among different siblings within a selfing generation, suggesting that the silencing of progenitors' genes is rapidly and/or stochastically established. Moreover, a subset of genes is affected in autotetraploid and multiple independent allotetraploid lines and in A. suecica, a natural allotetraploid derived from A. thaliana and A. arenosa, indicating locus-specific susceptibility to ploidy-dependent gene regulation. The role of DNA methylation in silencing progenitors' genes is tested in DNA-hypomethylation transgenic lines of A. suecica using RNA interference (RNAi). Two silenced genes are reactivated in both ddm1- and met1-RNAi lines, consistent with the demethylation of centromeric repeats and gene-specific regions in the genome. A rapid and stochastic process of differential gene expression is reinforced by epigenetic regulation during polyploid formation and evolution.

Arabidopsis↗
PubMed1984

The synaptonemal complex, recombination nodules and chiasmata in human spermatocytes.

Reconstruction from serial sections of 120 human spermatocyte nuclei, ranging in stage from leptotene to anaphase I, has led to the following conclusions. The reconstructed nuclei form a continuous sequence of developmental stages. With few exceptions, all of the bivalents are identifiable by length, centromere index and morphological markers. Crossing over is accompanied by a transformation of the recombination nodule (RN) into a fusiform bar lying across the synaptonemal complex (SC). The evolution of the crossover distribution at late pachytene is regulated at two levels both involving the SC. Each bivalent displays a pattern of SC regions - domains - with high affinity for RNs in the middle and low affinity at the ends. The occurrence of crossing over in a domain reduces the probability of attachment of new RNs and causes RNs not yet involved in crossing over to be released from that domain. Positive interference between crossovers is a consequence of these phenomena. At diplotene the degradation of the SC is initiated in regions with low affinity for RNs and small segments of the SC are retained at the crossover sites until late diakinesis. The site of crossing over is only identifiable by an RN for a certain period of time during pachytene. The distribution of total crossovers in a nucleus is similar but not identical to the distribution of chiasmata as seen in the light microscope. The number of crossovers has been estimated to be 70 and exceeds the number of chiasmata determined by light microscopy by a factor of 1.4.

Animals↗
PubMed2005

The two-domain hypothesis in Beckwith-Wiedemann syndrome: autonomous imprinting of the telomeric domain of the distal chromosome 7 cluster.

A large cluster of imprinted genes is located on the mouse distal chromosome 7. This cluster is well conserved in humans and its dysregulation results in the overgrowth- and tumour-associated Beckwith-Wiedemann syndrome. Two imprinting centres (IC1 and IC2) controlling different sets of genes have been identified in the cluster, raising the hypothesis that the cluster is divided into two functionally independent domains. However, the mechanisms by which imprinting of genes in the IC2 domain (e.g. Cdkn1c and Kcnq1) is regulated have not been well defined, and recent evidence indicates that distantly located cis-acting elements are required for IC2 imprinting. We show that the maternal germ-line methylation at IC2 and the imprinted expression of five genes of the IC2 domain are correctly reproduced on an 800 kb YAC transgene when transferred outside of their normal chromosomal context. These results, together with previous transgenic studies, locate key imprinting control elements within a 400 kb region centromeric of IC2 and demonstrate that each of the two domains of the cluster contains the cis-acting elements required for the imprinting control of its own genes. Finally, maternal, but not paternal, transmission of the transgene results in fetal growth restriction, suggesting that during evolution the acquisition of imprinting may have been facilitated by the opposite effects of the two domains on embryo growth.

Animals↗
PubMed2000

Genomic exploration of the hemiascomycetous yeasts: 5. Saccharomyces bayanus var. uvarum.

Saccharomyces bayanus var. uvarum investigated here is the species closest to Saccharomyces cerevisiae. Random sequence tags (RSTs) allowed us to identify homologues to 2789 open reading frames (ORFs) in S. cerevisiae, ORFs duplicated in S. uvarum but not in S. cerevisiae, centromeres, tRNAs, homologues of Ty1/2 and Ty4 retrotransposons, and a complete rDNA repeat. Only 13 RSTs seem to be homologous to sequences in other organisms but not in S. cerevisiae. As the synteny between the two species is very high, cases in which synteny is lost suggest special mechanisms of genome evolution. The corresponding RSTs revealed that S. uvarum can exist without any S. cerevisiae DNA introgression. Accession numbers are from AL397139 to AL402278 in the EMBL databank.

Ascomycota↗
PubMed2023

Neotelomeres and Telomere-Spanning Chromosomal Arm Fusions in Cancer Genomes Revealed by Long-Read Sequencing.

Alterations in the structure and location of telomeres are key events in cancer genome evolution. However, previous genomic approaches, unable to span long telomeric repeat arrays, could not characterize the nature of these alterations. Here, we applied both long-read and short-read genome sequencing to assess telomere repeat-containing structures in cancers and cancer cell lines. Using long-read genome sequences that span telomeric repeat arrays, we defined four types of telomere repeat variations in cancer cells: neotelomeres where telomere addition heals chromosome breaks, chromosomal arm fusions spanning telomere repeats, fusions of neotelomeres, and peri-centromeric fusions with adjoined telomere and centromere repeats. Analysis of lung adenocarcinoma genome sequences identified somatic neotelomere and telomere-spanning fusion alterations. These results provide a framework for systematic study of telomeric repeat arrays in cancer genomes, that could serve as a model for understanding the somatic evolution of other repetitive genomic elements.

Telomere↗
PubMed2000

The genomic organization and evolution of the natural killer immunoglobulin-like receptor (KIR) gene cluster.

Natural killer (NK) immunoglobulin-like receptors (KIRs) are a family of polymorphic receptors which interact with specific motifs on HLA class I molecules and modulate NK cytolytic activity. In this study, we analyzed a recently sequenced subgenomic region on chromosome 19q13.4 containing eight members of the KIR receptor repertoire. Six members are clustered within a 100-kb continuous sequence. These genes include a previously unpublished member of the KIR gene family 2DS6, as well as 2DL1, 2DL4, 3DL1, 2DS4, 3DL2, from centromere to telomere. Two additional KIR genes, KIRCI and 2DL3, which may be located centromeric of this cluster were also analyzed. We show that the KIR genes have undergone repeated gene duplications. Diversification between the genes has occurred postduplication primarily as a result of retroelement indels and gene truncation. Using pre- and postduplication Alu sequences identified within these genes as evolutionary molecular clocks, the evolution and duplication of this gene cluster is estimated to have occurred 30-45 million years ago, during primate evolution. A proposed model of the duplication history of the KIR gene family leading to their present organization is presented.

Alleles↗
PubMed1997

Cytoplasmic antiproteinase 2 (PI8) and bomapin (PI10) map to the serpin cluster at 18q21.3.

High-molecular-weight serine proteinase inhibitors (serpins) regulate a diverse set of intracellular and extracellular processes such as complement activation, fibrinolysis, coagulation, cellular differentiation, tumor suppression, apoptosis, and cell migration. The ov-serpins are a subset of the serpin superfamily and are characterized by their high degree of homology to chicken ovalbumin, the lack of N- and C-terminal extensions, the absence of a signal peptide, and a Ser rather than an Asn residue at the penultimate position. Recently, we mapped four members of the family [SCCA1, SCCA2, PAI2, and PI5 (maspin)] to a 300-kb region within 18q21.3. Using a panel of 18q21.3 YAC clones, PCR, and DNA blotting, we mapped two additional ov-serpins, cytoplasmic antiproteinase 2 [CAP2 (PI8)] and bone marrow-associated serpin [bomapin (PI10)], to the same region. Three of the serpins, PI8, PI10, and PAI2 mapped to the same YACs, yA27D8 and yA24E4. We estimated that the size of the 18q21.3 serpin cluster spanned approximately 500 kb and contained at least six serpin genes. The order was cen-PI5, SCCA2, SCCA1, PAI2, PI10, PI8-tel. The clustering of serpins at 18q21 provides new opportunities to study coordinate gene regulation and the evolution of gene families.

Amino Acid Sequence↗
PubMed2002

Evolutionary history of chromosome 10 in primates.

We have tracked the evolutionary history of chromosomes homologous to HSA10 (PHYL-10) in primates using appropriate panels of PCP, YAC, and BAC probes. This approach allowed us to delineate more precisely the PHYL-10 constitution in the ancestor of catarrhine, platyrrhine, and prosimians. The results suggest that (i) in the ancestor of prosimians PHYL-10 was organized in two separate PHYL-10p and PHYL-10q chromosomes; (ii) in the progenitor of New World monkeys PHYL-10p was a separate chromosome, while PHYL-10q was associated with a chromosome homologous to HSA16; (iii) in the ancestor of Old World monkeys PHYL-10 was a unique chromosome with a marker order corresponding to the orang form. We have also analyzed the cat, chosen as an outgroup for its very conserved karyotype. In agreement with published data our experiments show that the PHYL-10 in cat is structured in two blocks, PHYL-10p and PHYL-10q, both as part of larger chromosomes. The overall data indicate that, contrary to common opinion, PHYL-10p and PHYL-10q were distinct chromosomes in the primate ancestor. Analysis of the Saimiri sciureus (SSC) PHYL-10q marker order showed that it was isosequential with the Callithrix jacchus PHYL-10q, as well as with the PHYL-10q platyrrhine ancestral form. The SSC centromere, nevertheless, was located in a different chromosomal region, therefore suggesting that a centromeric repositioning event occurred in this species.

Animals↗
PubMed1999

Structure, functionality, and evolution of the BARE-1 retrotransposon of barley.

The BARE-1 retrotransposon is a major, active component of the genome of barley (Hordeum vulgare L.) and other Hordeum species. Copia-like in its organization, it consists of 1.8-kb long terminal repeats bounding an internal domain of 5275 bp which encodes a predicted polyprotein of 1301 residues. The polyprotein contains the key residues, structural motifs, and conserved regions associated with retroviral and retrotransposon GAG, aspartic proteinase, integrase, reverse transcriptase, and RNaseH polypeptides. BARE-1 is actively transcribed and translated. As part of our effort to understand the evolution and function of BARE-1, we have examined its copy number and localization. Full-length members of the BARE-1 family constitute 2.8% of the barley genome. Globally, they are dispersed throughout the genome, excepting the centromeric, telomeric, and NOR regions. Locally, BARE-1 occurs more commonly in repetitive DNA than in coding regions, forming clusters of nested insertions. Both barley and other Hordeum genomes contain a high proportion of BARE-1 solo LTRs. New techniques have been developed which exploit the insertion site polymorphism generated by BARE-1 integration to produce molecular markers for breeding, biodiversity, and mapping applications.

Evolution, Molecular↗
PubMed2005

The DNA sequence of the human X chromosome.

The human X chromosome has a unique biology that was shaped by its evolution as the sex chromosome shared by males and females. We have determined 99.3% of the euchromatic sequence of the X chromosome. Our analysis illustrates the autosomal origin of the mammalian sex chromosomes, the stepwise process that led to the progressive loss of recombination between X and Y, and the extent of subsequent degradation of the Y chromosome. LINE1 repeat elements cover one-third of the X chromosome, with a distribution that is consistent with their proposed role as way stations in the process of X-chromosome inactivation. We found 1,098 genes in the sequence, of which 99 encode proteins expressed in testis and in various tumour types. A disproportionately high number of mendelian diseases are documented for the X chromosome. Of this number, 168 have been explained by mutations in 113 X-linked genes, which in many cases were characterized with the aid of the DNA sequence.

Animals↗
PubMed2002

Cytological study of Tibetia (Fabaceae) in the Hengduan Mountains region, China.

The Hengduan Mountains comprise one of the world's most important hot spots of biodiversity. Tibetia (Ali) H.P. Tsui (Fabaceae), which has four or five species in two sections, is one of the genera endemic to the region. This paper describes for the first time the karyotype of three of those species. The chromosome counts of all three are 2 n = 16. The karyotypes of the species examined contain chromosomes of variable karyotypic symmetry with centromeres at median and submedian positions that correlate with the morphological characteristics of the species. Karyotypic variation at the diploid level appears to be the predominant feature of chromosome evolution in the genus and may provide a clue to the study of evolutionary patterns of plants in this region.

Journal Article↗
PubMed2001

Gene mapping in fishes: a means to an end.

Genetic research in fishes is poised to contribute a vast amount of information on the structural organization and function of vertebrate genomes. Recent advances in molecular biology have made possible the widescale characterization of genomes in all living organisms. This includes defining chromosomes at the cytological level down to their linear composition at individual nucleotide base pairs. Pioneering gene mapping studies into the genomes of fishes will only serve as the starting point for more detailed studies into the function of these genomes. Future research directed at understanding the mechanisms of gene actions and interactions will benefit all areas of biology, including ecology, ethology, evolution, and physiology. Gene mapping data from brown trout and rainbow trout are used to exemplify how basic information on gene transmission in a species may help to localize centromeres onto a genetic map and identify chromosomal regions possessing a high degree of segregation distortion. Genetic maps may also be used to identify differences in recombination levels among individuals and between the sexes when multiple mapping families are utilized in studies. Observations of this type are the antecedents to more complex biological investigations on the genetic architecture underlying these phenomena.

Animals↗
PubMed1981

Abnormalities of chromosome no. 1 related to blood dyscrasias: study of 10 cases.

Partial excess of chromosome 1 (q25-q32) was noted in malignant cells from all of 10 patients who had disorders such as non-African Burkitt's lymphoma, adult T-cell leukemia, myelofibrosis, malignant lymphoma, chronic lymphocytic leukemia or chronic myelocytic leukemia in blast crisis. The break points on chromosome 1 were at centromere, q12, q21, q23, q25 and q32. Variations in the specific region of the long arm of chromosome 1, q25-q32, were thought to be important in the evolution of malignant cell proliferation.

Adult↗
PubMed1986

The heterochromatin of grasshoppers from the Caledia captiva species complex. I. Sequence evolution and conservation in a highly repeated DNA family.

The restriction enzyme TaqI digests 0.2% of the genomic DNA from the grasshopper Caledia captiva to a family of sequences 168 bp in length (length of consensus sequence). The sequence variation of this "Taq family" of repeat units was examined among four races from C. captiva to assay the pattern of evolution within this highly repeated DNA. The Taq-family repeats are located in C-banded heterochromatin on at least one member of each homologous pair of chromosomes; the locations range from centromeric to telomeric. Thirty-nine cloned repeats isolated from two population 1A individuals along with 11 clones from seven populations taken from three of the races demonstrated sequence variation at 72 positions. Pairwise comparisons of the cloned repeats, both within an individual and between different races, indicate that levels of intraspecific divergence, as measured by reproductive incompatibility, do not correlate with sequence divergence among the 168-bp repeats. A number of subsequences within the repeat remain unchanged among all 50 clones; the longest of these is 18 bp. That the same 18-bp subsequence is present in all clones examined is a finding that departs significantly (P less than 0.01) from what would be expected to occur at random. Two other cloned repeats, from a reproductively isolated race of C. captiva, have sequences that show 56% identity with this 18-bp conserved region. An analysis showed that the frequency of occurrence of an RsaI recognition site within the 168-bp repeat in the entire Taq family agreed with that found in the cloned sequences. These data, along with a partial sequence for the entire Taq family obtained by sequencing uncloned repeats, suggest that the consensus sequence from the cloned copies is representative of this highly repeated family and is not a biased sample resulting from the cloning procedure. The 18-bp conserved sequence is part of a 42-bp sequence that possesses dyad symmetry typical of protein-binding sites. We speculate that this may be significant in the evolution of the Taq family of sequences.

Animals↗