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PubMed2004

Evolutionary genomics of chromoviruses in eukaryotes.

The diversity, origin, and evolution of chromoviruses in Eukaryota were examined using the massive amount of genome sequence data for different eukaryotic lineages. A surprisingly large number of novel full-length chromoviral elements were found, greatly exceeding the number of the known chromoviruses. These new elements are mostly structurally intact and highly conserved. Chromoviruses in the key Amniota lineage, the reptiles, have been analyzed by PCR to explain their evolutionary dynamics in amniotes. Phylogenetic analyses provide evidence for a novel centromere-specific chromoviral clade that is widespread and highly conserved in all seed plants. Chromoviral diversity in plants, fungi, and vertebrates, as shown by phylogenetic analyses, was found to be much greater than previously expected. The age of plant chromoviruses has been significantly extended by finding their representatives in the most basal plant lineages, the green and the red algae. The evolutionary origin of chromoviruses has been found to be no earlier than in Cercozoa. The evolutionary history and dynamics of chromoviruses can be explained simply by strict vertical transmission in plants, followed by more complex evolution in fungi and in Metazoa. The currently available data clearly show that chromoviruses indeed represent the oldest and the most widespread clade of Metaviridae.

Amino Acid Sequence↗
PubMed1993

Homoeologous relationships of rice, wheat and maize chromosomes.

A set of cDNA clones, which had previously been mapped onto wheat chromosomes, was genetically mapped onto the chromosomes of rice. The resulting comparative maps make it possible to estimate the degree of linkage conservation between these two species. A number of chromosomal rearrangements, some of which must have involved interchromosomal translocations, differentiate the rice and wheat genomes. However, synteny of a large proportion of the loci appears to be conserved between the two species. The results of this study, combined with those from a recently published comparative map of the rice and maize genomes, suggest that rice, wheat and maize share extensive homoeologies in a number of regions in their genomes. Some chromosomes (e.g. chromosome 4 in rice, chromosomes 2 and 2S in wheat and maize, respectively) may have escaped major rearrangement since the divergence of these species from their last common ancestor. Comparative maps for rice, wheat and maize should make it possible to begin uniting the genetics of these species and allow for transfer of mapping information (including centromere positions) and molecular marker resources (e.g. RFLP probes) between species. In addition, such maps should shed light on the nature of chromosome evolution that accompanied the radiation of grasses in the early stages of plant diversification.

Chromosome Mapping↗
PubMed1997

The chicken genome contains two functional nonallelic beta1,4-galactosyltransferase genes. Chromosomal assignment to syntenic regions tracks fate of the two gene lineages in the human genome.

Two distinct but related groups of cDNA clones, CKbeta4GT-I and CKbeta4GT-II, have been isolated by screening a chicken hepatoma cDNA library with a bovine beta1,4-galactosyltransferase (beta4GT) cDNA clone. CKbeta4GT-I is predicted to encode a type II transmembrane glycoprotein of 41 kDa with one consensus site for N-linked glycosylation. CKbeta4GT-II is predicted to encode a type II transmembrane glycoprotein of 43 kDa with five potential N-linked glycosylation sites. At the amino acid level, the coding regions of CKbeta4GT-I and CKbeta4GT-II are 52% identical to each other and 62 and 49% identical, respectively, to bovine beta4GT. Despite this divergence in amino acid sequence, high levels of expression of each cDNA in Trichoplusia ni insect cells demonstrate that both CKbeta4GT-I and CKbeta4GT-II encode an alpha-lactalbumin-responsive, UDP-galactose:N-acetylglucosamine beta4-galactosyltransferase. An analysis of CKbeta4GT-I and CKbeta4GT-II genomic clones established that the intron positions within the coding region are conserved when compared with each other, and these positions are identical to the mouse and human beta4GT genes. Thus CKbeta4GT-I and CKbeta4GT-II are the result of the duplication of an ancestral gene and subsequent divergence. CKbeta4GT-I maps to chicken chromosome Z in a region of conserved synteny with the centromeric region of mouse chromosome 4 and human chromosome 9p, where beta4-galactosyltransferase (EC 2.4.1.38) had previously been mapped. Consequently, during the evolution of mammals, it is the CKbeta4GT-I gene lineage that has been recruited for the biosynthesis of lactose. CKbeta4GT-II maps to a region of chicken chromosome 8 that exhibits conserved synteny with human chromosome 1p. An inspection of the current human gene map of expressed sequence tags reveals that there is a gene noted to be highly similar to beta4GT located in this syntenic region on human chromosome 1p. Because both the CKbeta4GT-I and CKbeta4GT-II gene lineages are detectable in mammals, duplication of the ancestral beta4-galactosyltransferase gene occurred over 250 million years ago in an ancestral species common to both mammals and birds.

Alleles↗
PubMed1998

Organization and distribution of a Sau3A tandem repeated DNA sequence in Picea (Pinaceae) species.

Repeated DNA families contribute to the large genomes of coniferous trees but are poorly characterized. We report the analysis of a 142 bp tandem repeated DNA sequence identified by the restriction enzyme Sau3A and found in approximately 20,000 copies in Picea glauca. Southern hybridization indicated that the repeated DNA family is specific to the genus, was amplified early in its evolution, and has undergone little structural alteration over evolutionary time. Fluorescence in situ hybridization localized arrays of the Sau3A repeating element to the centromeric regions of different subsets of the metaphase chromosomes of P. glauca and the closely related Picea sitchensis, suggesting that mechanisms leading to the intragenomic movement of arrays may be more active than those leading to mutation of the repeating elements themselves. Unambiguous identification of P. glauca and P. sitchensis chromosomes was made possible by co-localizing the Sau3A tandem repeats and the genes encoding the 5S and 18S-5.8S-26S ribosomal RNAs.

Base Sequence↗
PubMed1999

Polymorphisms and genomic organization of repetitive DNA from centromeric regions of Arabidopsis chromosomes.

A highly abundant repetitive DNA sequence family of Arabidopsis, AtCon, is composed of 178-bp tandemly repeated units and is located at the centromeres of all five chromosome pairs. Analysis of multiple copies of AtCon showed 95% conservation of nucleotides, with some alternative bases, and revealed two boxes, 30 and 24 bp long, that are 99% conserved. Sequences at the 3' end of these boxes showed similarity to yeast CDEI and human CENP-B DNA-protein binding motifs. When oligonucleotides from less conserved regions of AtCon were hybridized in situ and visualized by using primer extension, they were detected on specific chromosomes. When used for polymerase chain reaction with genomic DNA, single primers or primer pairs oriented in the same direction showed negligible amplification, indicating a head-to-tail repeat unit organization. Most primer pairs facing in opposite directions gave several strong bands corresponding to their positions within AtCon. However, consistent with the primer extension results, some primer pairs showed no amplification, indicating that there are chromosome-specific variants of AtCon. The results are significant because they elucidate the organization, mode of amplification, dispersion, and evolution of one of the major repeated sequence families of Arabidopsis. The evidence presented here suggests that AtCon, like human alpha satellites, plays a role in Arabidopsis centromere organization and function.

Arabidopsis↗
PubMed1996

Half tetrad analysis in alfalfa using multiple restriction fragment length polymorphism markers.

A maximum likelihood approach of half tetrad analysis (HTA) based on multiple restriction fragment length polymorphism (RFLP) markers was developed. This procedure estimates the relative frequencies of 2n gametes produced by mechanisms genetically equivalent to first division restitution (FDR) or second division restitution and simultaneously locates the centromere within a linkage group of RFLP marker loci. The method was applied to the diploid alfalfa clone PG-F9 (2n = 2x = 16) previously selected because of its high frequency of 2n egg production. HTA was based on four RFLP loci for which PG-F9 was heterozygous with codominant alleles that were absent in the tetraploid tester. Models including three linked and one unlinked RFLP loci were developed and tested. Results of the HTA showed that PG-F9 produced 6% FDR and 94% second division restitution 2n eggs. Information from a marker locus belonging to one linkage group was used to more precisely locate the centromere on a different linkage group. HTA, together with previous cytological analysis, indicated that in PG-F9, FDR 2n eggs are likely produced by diplospory, a mechanism common among apomictic species. The occurrence of FDR 2n eggs in plant species and their importance for crop evolution and breeding is discussed together with the potential applicability of multilocus HTA in the study of reproductive mutants.

Centromere↗
PubMed2003

Pericentromeric duplications in the laboratory mouse.

Duplications have long been postulated to be an important mechanism by which genomes evolve. Interspecies genomic comparisons are one method by which the origin and molecular mechanism of duplications can be inferred. By comparative mapping in human, mouse, and rat, we previously found evidence for a recent chromosome-fission event that occurred in the mouse lineage. Cytogenetic mapping revealed that the genomic segments flanking the fission site appeared to be duplicated, with copies residing near the centromere of multiple mouse chromosomes. Here we report the mapping and sequencing of the regions of mouse chromosomes 5 and 6 involved in this chromosome-fission event as well as the results of comparative sequence analysis with the orthologous human and rat genomic regions. Our data indicate that the duplications associated with mouse chromosomes 5 and 6 are recent and that the resulting duplicated segments share significant sequence similarity with a series of regions near the centromeres of the mouse chromosomes previously identified by cytogenetic mapping. We also identified pericentromeric duplicated segments shared between mouse chromosomes 5 and 1. Finally, novel mouse satellite sequences as well as putative chimeric transcripts were found to be associated with the duplicated segments. Together, these findings demonstrate that pericentromeric duplications are not restricted to primates and may be a common mechanism for genome evolution in mammals.

Animals↗
PubMed1990

Evolution of the pseudoautosomal boundary in Old World monkeys and great apes.

Mammalian sex chromosomes are divided into sex-specific and pseudoautosomal regions. Sequences in the pseudoautosomal region recombine between the sex chromosomes; the sex-specific sequences normally do not. The interface between sex-specific and pseudoautosomal sequences is the pseudoautosomal boundary. The boundary is the centromeric limit to recombination in the pseudoautosomal region. In man, an Alu repeat element is found inserted at the boundary on the Y chromosome. In the evolutionary comparison conducted here, the Alu repeat element is found at the Y boundary in great apes, but it is not found there in two Old World monkeys. During the evolution of the Old World monkey and great ape lineages, homology between the sex chromosomes was maintained by recombination in the sequences telomeric to the Alu insertion site. The Alu repeat element did not create the present-day boundary; instead, it inserted at the preexisting boundary after the Old World monkey and great ape lineages diverged.

Animals↗
PubMed1998

Localization of FCGR1 encoding Fcgamma receptor class I in primates: molecular evidence for two pericentric inversions during the evolution of human chromosome 1.

The human high-affinity receptor for immunoglobulin G, FcgammaRI (FCGR1), is encoded by a family of three genes that share over 95% sequence homology. Curiously, the three genes in this recently duplicated gene family flank the centromere of human chromosome 1, with FCGR1B located at 1p12 and both FCGR1A and FCGR1C located at 1q21. We have previously speculated that a pericentric inversion could account for the separation of the genes in the FCGR1 family and explain their current chromosomal location. Here we present evidence, obtained through fluorescence in situ hybridization analysis, that in the rhesus monkey (Macaca mulatta) and baboon (Papio papio) FCGR1 is located adjacent to the centromere on the chromosomal arm with greatest homology to human 1p, whereas in the chimpanzee (Pan troglodytes) it is located adjacent to the centromere on the chromosomal arm with greatest homology to human 1q. The separation of the FCGR1 gene family in humans suggests that the location of a second pericentric inversion, known to distinguish the human from the chimpanzee chromosome 1, is within the FCGR1 gene family. This finding refines the assignment of homology between the human and chimpanzee chromosomes 1.

Animals↗
PubMed1998

Gene-based anchoring of the rat genetic linkage and cytogenetic maps: new regional localizations, orientation of the linkage groups, and insights into mammalian chromosome evolution.

In order to generate anchor points connecting the rat cytogenetic and genetic maps, the cytogenetic position of 62 rat markers (including 55 genes) already localized genetically was determined by fluorescence in situ hybridization. Whenever possible, markers located near one end of the linkage groups were included. These new localizations allowed us to unambiguously orient the 20 autosomal and the X chromosome linkage groups. The position of the centromere in the linkage map could also be determined in the case of several metacentric chromosomes. In addition, the regional localization of 15 other rat genes was determined. These new data bring useful information with respect to comparative mapping with the mouse and the human and to mammalian evolution. They illustrate, for instance, that groups of genes can remain syntenic during mammalian evolution while being subjected to intrachromosomal rearrangements in some lineages (synteny is conserved while gene order is not). This analysis also disclosed cases of synteny conservation in one the two rodent species and the human, while the synteny is split in the other rodent species: such configurations are likely examples of lineage-specific interchromosomal rearrangements associated with speciation.

Animals↗
PubMed2001

Characterization of a widely expressed gene (LUC7-LIKE; LUC7L) defining the centromeric boundary of the human alpha-globin domain.

We have identified the first gene lying on the centromeric side of the alpha-globin gene cluster on human 16p13.3. The gene, called 16pHQG;16 (HGMW-approved symbol LUC7L), is widely transcribed and lies in the opposite orientation with respect to the alpha-globin genes. This gene may represent a mammalian heterochromatic gene, encoding a putative RNA-binding protein similar to the yeast Luc7p subunit of the U1 snRNP splicing complex that is normally required for 5' splice site selection. To examine the role of the 16pHQG;16 gene in delimiting the extent of the alpha-globin regulatory domain, we mapped its mouse orthologue, which we found to lie on mouse chromosome 17, separated from the mouse alpha-cluster on chromosome 11. Establishing the full extent of the human 16pHQG;16 gene has allowed us to define the centromeric limit of the region of conserved synteny around the human alpha-globin cluster to within an 8-kb segment of chromosome 16.

Alternative Splicing↗
PubMed1976

Satellite DNA in the kangaroo Macropus rufogriseus.

Two distinct satellite DNAs, amounting to 25% of the total DNA, were isolated from the nuclei of the red-necked wallaby, Macropus rufogriseus. The physical properties of native, single-stranded and reassociated molecules were studied in buoyant-density gradient centrifugation. The homogeneity of each satellite fraction was examined using melting characteristics of native and reassociated DNA, and renaturation kinetics. These data suggest that sequence heterogeneity exists in both fractions. Each satellite fraction was found by in situ hybridization to be localized in heterochromatin of interphase nuclei and in the centromeric regions of metaphase chromosomes. The chromosomal distributions of the two satellite DNAs differentiate the sex chromosomes, which have sequences of only one satellite, from the autosomes which have sequences of both satellites in the centromeric heterochromatin. Giemsa C-banding techniques also showed a differentiation of the centromeric regions of sex chromosomes from those of the autosomes.

Animals↗
PubMed2002

Cloning and characterization of a novel human gene RNF38 encoding a conserved putative protein with a RING finger domain.

RING finger (C3HC4-type zinc finger) is a variant zinc finger motif present in a large family of functionally distinct proteins. We describe the cloning and characterization of a novel human transcript RNF38 encoding a new member of the RING finger protein family. The complete mRNA consists of about 6.8 kb widely expressed in human tissues as a single transcript, most abundantly in testis. The predicted proline-rich protein consists of 432 amino acid residues with a coiled-coil motif and a RING-H2 motif (C3H2C2) at its carboxy-terminus. High degree homology was found between the human protein and hypothetical peptides from several other species including Rattus norvegicus, Mus musculus, and Drosophila melanogaster, indicating a significant conservation throughout evolution. The RNF38 genomic structure was determined and comprises at least 13 exons extending over more than 65 kb in the genome, 78 kb centromeric to the GNE gene on human chromosome 9p12-p13. The involvement of this chromosomal segment in a large number of human diseases and in particular in various types of malignancies urges the assessment of the potential functional role of RNF38 in these disorders.

Amino Acid Sequence↗
PubMed2003

The 200-kb segmental duplication on human chromosome 21 originates from a pericentromeric dissemination involving human chromosomes 2, 18 and 13.

Regions close to human centromeres contain DNA fragments spanning hundreds of kilobases that exhibit a high degree of sequence identity (>95%). Here we report the genomic structure and evolution of a family of four paralogous regions related to a 220-kb genomic fragment present on the long arm of human chromosome 21 (21q22.1). Phylogenetic classification of the paralogous sequences obtained from the draft of the Human Genome Project are in agreement with results from comparative fluorescence in situ hybridization on metaphase chromosomes from human and great apes. The original copy present in 21q22.1 in human was duplicated in great apes after the divergence of the orang-utan and inserted in a pericentromeric region, most likely the ancestor of HSA2q, then disseminated by transposition of a larger fragment to other pericentromeric locations: HSA18p11, HSA13q11 and HSA21q11.1. The degree of dissemination varies among species.

Animals↗
PubMed1989

[Study on karyotypes C-banding and Ag-NORs of Rana minimus and Hyla chinensis from Fuzhou].

Using bone marrow preparing chromosome method, BSG technique and a quick Ag-stained NORs method, the conventional, C-banded and Ag-stained karyotypes of Rana minimus Ting et Ts'ai and Hyla chinensis Guenther were studied. The diploid number of R. minimus is 2n = 26, consisting of 5 pairs of large and 8 pairs of small chromosomes. A secondary constriction is observed at a position near the centromere on the short arm of chromosome No. 6 and it is also the position of the "standard NORs" Chromosome C-banding shows that the heterochromations of R. minimus are located in the centromeric and pericentromeric regions, with comparatively few lightly-stained interstitial C-bands and no telomeric ones. And the secondary constriction is C-banding positively stained. H. chinensis has 24 chromosomes which divide into a group of 6 large pairs and a group of 6 small pairs. A secondary constriction appears at a position on the long arm of chromosome No. 10. It is also the position of the "standard NORs" and C-banding positively stained. The C-banding pattern is mainly composed of centromeric C-bands with few interstitial ones and no telomeric ones. The karyotypic characters of Ranidae and Hylidae and the relationship to the evolution are also discussed.

Animals↗
PubMed2003

Genomic sequence and transcriptional profile of the boundary between pericentromeric satellites and genes on human chromosome arm 10p.

Contiguous finished sequence from highly duplicated pericentromeric regions of human chromosomes is needed if we are to understand the role of pericentromeric instability in disease, and in gene and karyotype evolution. Here, we have constructed a BAC contig spanning the transition from pericentromeric satellites to genes on the short arm of human chromosome 10, and used this to generate 1.4 Mb of finished genomic sequence. Combining RT-PCR, in silico gene prediction, and paralogy analysis, we can identify two domains within the sequence. The proximal 600 kb consists of satellite-rich pericentromerically duplicated DNA which is transcript poor, containing only three unspliced transcripts. In contrast, the distal 850 kb contains four known genes (ZNF248, ZNF25, ZNF33A, and ZNF37A) and up to 32 additional transcripts of unknown function. This distal region also contains seven out of the eight intrachromosomal duplications within the sequence, including the p arm copy of the approximately 250-kb duplication which gave rise to ZNF33A and ZNF33B. By sequencing orthologs of the duplicated ZNF33 genes we have established that ZNF33A has diverged significantly at residues critical for DNA binding but ZNF33B has not, indicating that ZNF33B has remained constrained by selection for ancestral gene function. These results provide further evidence of gene formation within intrachromosomal duplications, but indicate that recent interchromosomal duplications at this centromere have involved transcriptionally inert, satellite rich DNA, which is likely to be heterochromatic. This suggests that any novel gene structures formed by these interchromosomal events would require relocation to a more open chromatin environment to be expressed.

Amino Acid Sequence↗
PubMed2006

Multidirectional chromosome painting reveals a remarkable syntenic homology between the greater galagos and the slow loris.

We report on the first reciprocal chromosome painting of lorisoids and humans. The chromosome painting showed a remarkable syntenic homology between Otolemur and Nycticebus. Eight derived syntenic associations of human segments are common to both Otolemur and Nycticebus, indicative of a considerable period of common evolution between the greater galago and the slow loris. Five additional Robertsonian translocations form the slow loris karyotype, while the remaining chromosomes are syntenically equivalent, although some differ in terms of centromere position and heterochromatin additions. Strikingly, the breakpoints of the human chromosomes found fragmented in these two species are apparently identical. Only fissions of homologs to human chromosomes 1 and 15 provide significant evidence of a cytogenetic link between Lemuriformes and Lorisiformes. The association of human chromosomes 7/16 in both lorisoids strongly suggests that this chromosome was present in the ancestral primate genome.

Animals↗
PubMed2004

GTF2IRD2 is located in the Williams-Beuren syndrome critical region 7q11.23 and encodes a protein with two TFII-I-like helix-loop-helix repeats.

Williams-Beuren syndrome (also known as Williams syndrome) is caused by a deletion of a 1.55- to 1.84-megabase region from chromosome band 7q11.23. GTF2IRD1 and GTF2I, located within this critical region, encode proteins of the TFII-I family with multiple helix-loop-helix domains known as I repeats. In the present work, we characterize a third member, GTF2IRD2, which has sequence and structural similarity to the GTF2I and GTF2IRD1 paralogs. The ORF encodes a protein with several features characteristic of regulatory factors, including two I repeats, two leucine zippers, and a single Cys-2/His-2 zinc finger. The genomic organization of human, baboon, rat, and mouse genes is well conserved. Our exon-by-exon comparison has revealed that GTF2IRD2 is more closely related to GTF2I than to GTF2IRD1 and apparently is derived from the GTF2I sequence. The comparison of GTF2I and GTF2IRD2 genes revealed two distinct regions of homology, indicating that the helix-loop-helix domain structure of the GTF2IRD2 gene has been generated by two independent genomic duplications. We speculate that GTF2I is derived from GTF2IRD1 as a result of local duplication and the further evolution of its structure was associated with its functional specialization. Comparison of genomic sequences surrounding GTF2IRD2 genes in mice and humans allows refinement of the centromeric breakpoint position of the primate-specific inversion within the Williams-Beuren syndrome critical region.

Amino Acid Sequence↗