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PubMed2004

Centric fission--simple and complex mechanisms.

Centric fission describes a rather poorly molecularly defined process of the transverse division of a functional centromere to result in two new centric chromosomes. While centric fission occurs rarely in humans, this process has been attributed an important role in eukaryotic karyotype evolution. Recent studies have given insight into the complex molecular mechanisms that lead to apparent centric fission events, including evidence in support of a mechanism driven by centric preduplication. These studies suggest that the traditional definition of centric fission, based on gross cytogenetic and molecular cytogenetic observations, needs to be broadened. It is necessary to distinguish between simple centric fissions, that involve the direct transverse breakage of a functional centromere, and other more complex fission events at or around a centromere that may be preceded by chromosomal rearrangements.

Animals↗
PubMed2004

Genome sequence of the Brown Norway rat yields insights into mammalian evolution.

The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.

Animals↗
PubMed2006

High rate of chimeric gene origination by retroposition in plant genomes.

Retroposition is widely found to play essential roles in origination of new mammalian and other animal genes. However, the scarcity of retrogenes in plants has led to the assumption that plant genomes rarely evolve new gene duplicates by retroposition, despite abundant retrotransposons in plants and a reported long terminal repeat (LTR) retrotransposon-mediated mechanism of retroposing cellular genes in maize (Zea mays). We show extensive retropositions in the rice (Oryza sativa) genome, with 1235 identified primary retrogenes. We identified 27 of these primary retrogenes within LTR retrotransposons, confirming a previously observed role of retroelements in generating plant retrogenes. Substitution analyses revealed that the vast majority are subject to negative selection, suggesting, along with expression data and evidence of age, that they are likely functional retrogenes. In addition, 42% of these retrosequences have recruited new exons from flanking regions, generating a large number of chimerical genes. We also identified young chimerical genes, suggesting that gene origination through retroposition is ongoing, with a rate an order of magnitude higher than the rate in primates. Finally, we observed that retropositions have followed an unexpected spatial pattern in which functional retrogenes avoid centromeric regions, while retropseudogenes are randomly distributed. These observations suggest that retroposition is an important mechanism that governs gene evolution in rice and other grass species.

Evolution, Molecular↗
PubMed1978

Cytogenetic aspects of phylogeny in the Bovidae. II. C-banding.

Constitutive heterochromatin in the Bovidae, as revealed by C-banding, was mostly located in the centromeric regions. Considerable variation was, however, evident in the size of the C-bands both within and between subfamilies. Some evidence was found for a reduction in the amount of centromeric heterochromatin in bi-armed relative to acrocentric autosomes, and these findings are discussed in relation to karyotype evolution in the group.

Animals↗
PubMed1987

A highly repetitive DNA component common to all Cervidae: its organization and chromosomal distribution during evolution.

In recent work we have isolated and characterized a highly repetitive DNA (MMV satellite IA) from Muntiacus muntjak vaginalis, the species with the most reduced karyotype in the Cervidae family. We have now analysed the genomes of nine related species for the presence of MMV satellite IA components, and have determined their organization and chromosomal distribution. Repetitive satellite IA type DNA is present in all species of the Cervidae, and also in the bovine, but not in a species of the Tragulidae suggesting that these sequences were generated after the phylogenetic separation of Bovidae and Tragulidae. Studies on the organization of the satellite IA DNA in the various species revealed three main repeat lengths: 1400, 1000 and 807 bp. The relative proportion of satellite IA sequences present in any one of the three registers is strikingly different within the various species and can be correlated with the phylogeny of the Cervidae. The chromosomal locations of the satellite IA sequences were determined in seven species by in situ hybridization. It turned out that the chromosomal rearrangements leading to the reduction in the number of chromosomes during karyotype evolution have led to the elimination of satellite I DNA at most locations. In all tandem fusions, the satellite IA sequences located at the centromeres of the ancestral acrocentric chromosomes are lost. In contrast, during the centric fusion that generates the M. m. vaginalis X chromosome satellite IA sequences are amplified. Sequence motifs, which are known to be involved in recombinational events are present in the satellite IA and might have contributed to the unique karyotype variation in the Cervidae.

Animals↗
PubMed2005

A genetic and molecular profile of third chromosome centric heterochromatin in Drosophila melanogaster.

In this review, we combine the results of our published and unpublished work with the published results of other laboratories to provide an updated map of the centromeric heterochromatin of chromosome 3 in Drosophila melanogaster. To date, we can identify more than 20 genes (defined DNA sequences with well-characterized functions and (or) defined genetic complementation groups), including at least 16 essential loci. With the ongoing emergence of data from genetic, cytological, and genome sequencing studies, we anticipate continued, substantial progress towards understanding the function, structure, and evolution of centric heterochromatin.

Animals↗
PubMed2005

Heterochromatin differentiation shows the pathways of karyotypic evolution in Israeli mole rats (Spalax, Spalacidae, Rodentia).

C-banding, base-specific fluorochrome staining (CMA3/DA/DAPI), and comparative genomic hybridization (CGH) were used to analyze the constitutive heterochromatin in two Israeli Spalax species, S. galili (2n = 52) and S. judai (2n = 60). It was shown that C-positive centromeric heterochromatin and some telomeric sites comprise GC-rich DNA sequences in both species. Comparative genomic in situ hybridization revealed slight qualitative differences in highly repetitive sequences in the two Spalax species. Eight acrocentric pairs in S. judai that are involved in Robertsonian rearrangements, possessed composite heterochromatin with a preference of S. judai highly repetitive sequences in the proximal region. Heterochromatin of the sex chromosomes, two biarmed homologous pairs (4 and 5) in both species, and acrocentric chromosomes from the group with a variable centromere position in S. judai was entirely species-specific. The high level of homology in the composition of heterochromatin may relate to the recent divergence of Israeli Spalax. Interspecies heterochromatin differences are discussed in the context of possible mechanisms in the Spalax chromosome evolution.

Animals↗
PubMed1971

Heterochromatin, satellite DNA, and cell function. Structural DNA of eucaryotes may support and protect genes and aid in speciation.

With the assumption that a portion that comprises some 10 percent of the genomes in higher organisms cannot be without a raison d'être, an extensive review led us to conclude that a certain amount of constitutive heterochromatin is essential in multicellular organisms at two levels of organization, chromosomal and nuclear. At the chromosomal level, constitutive heterochromatin is present around vital areas within the chromosomes. Around the centromeres, for example, heterochromatin is believed to confer protection and strength to the centromeric chromatin. Around secondary constrictions, heterochromatic blocks may ensure against evolutionary change of ribosomal cistrons by decreasing the frequency of crossing-over in these cistrons in meiosis and absorbing the effects of mutagenic agents. During meiosis heterochromatin may aid in the initial alignment of chromosomes prior to synapsis and may facilitate speciation by allowing chromosomal rearrangement and providing, through the species specificity of its DNA, barriers against cross-fertilization. At the nuclear level of organization, constitutive heterochromatin may help maintain the proper spatial relationships necessary for the efficient operation of the cell through the stages of mitosis and meiosis. In the unicellular procaryotes, the presence of a small amount of genetic information in one chromosome obviates the need for constitutive heterochromatin and a nuclear membrane. At higher levels of organization, with an increase in the size of the genome and with evolution of cellular and sexual differentiation, the need for compartmentalization and structural components in the nucleus became imminent. The portion of the genome that was concerned with synthesis of ribosomal RNA was enlarged and localized in specific chromosomes, and the centromere became part of each chromosome when the mitotic spindle was developed in evolution. Concomitant with these changes in the genome, repetitive sequences in the form of constitutive heterochromatin appeared, probably as a result of large-scale duplication. The repetitive DNA's were kept through natural selection because of their importance in preserving these vital regions and in maintaining the structural and functional integrity of the nucleus. The association of satellite (or highly repetitive) DNA with constitutive heterochromatin is understandable, since it stresses the importance of the structural rather than transcriptional roles of these entities. Nuclear satellite DNA's have one property in common despite their species specificity, namely heterochromatization. In this sense the apparent species specificity of satellite DNA may be the result of natural selection for duplicated short polynucleotide segments that are nontranscriptional and can be utilized in specific structural roles.

Animals↗
PubMed1993

Structure and evolution of a highly repetitive DNA sequence from Brassica napus.

A Hind III family of highly repetitive DNA sequences, canrep (canola repeat), was cloned from the nuclear DNA of canola (Brassica napus cv. Westar). The basic units of this family of repeats consists of 176 bp and are arranged in clusters of tandem direct repeats. Each canrep repeat is composed of three related subrepeats of ca. 60 bp. Each subrepeat contains two inverted repeats of about 23 bp and another unrelated sequence of about 12 bp. Based on the internal structure, a possible scheme for the evolution of canrep is proposed. At least two subfamilies of the canrep sequences are present in the genome, as revealed by sequence analyses. In situ hybridization showed that canrep sequences are mainly clustered at centromeric regions of chromosomes. Northern hybridizations indicate that there are no transcripts related to canrep in the total RNAs extracted from plant seedlings.

Base Sequence↗
PubMed2002

Ty1 /copia- and Ty3 /gypsy-like DNA sequences in Helianthus species.

Two repeated DNA sequences isolated from a partial genomic DNA library of Helianthus annuus, p HaS13 and p HaS211, were shown to represent portions of the int gene of a Ty3 /gypsy retroelement and of the RNase-Hgene of a Ty1 /copia retroelement, respectively. Southern blotting patterns obtained by hybridizing the two probes to BglII- or DraI-digested genomic DNA from different Helianthus species showed p HaS13 and p HaS211 were parts of dispersed repeats at least 8 and 7 kb in length, respectively, that were conserved in all species studied. Comparable hybridization patterns were obtained in all species with p HaS13. By contrast, the patterns obtained by hybridizing p HaS211 clearly differentiated annual species from perennials. The frequencies of p HaS13- and p HaS211-related sequences in different species were 4.3x10(4)-1.3x10(5) copies and 9.9x10(2)-8.1x10(3) copies per picogram of DNA, respectively. The frequency of p HaS13-related sequences varied widely within annual species, while no significant difference was observed among perennial species. Conversely, the frequency variation of p HaS211-related sequences was as large within annual species as within perennials. Sequences of both families were found to be dispersed along the length of all chromosomes in all species studied. However, Ty3 /gypsy-like sequences were localized preferentially at the centromeric regions, whereas Ty1/ copia-like sequences were less represented or absent around the centromeres and plentiful at the chromosome ends. These findings suggest that the two sequence families played a role in Helianthusgenome evolution and species divergence, evolved independently in the same genomic backgrounds and in annual or perennial species, and acquired different possible functions in the host genomes.

Amino Acid Sequence↗
PubMed2005

Centromeric chromatin: what makes it unique?

Centromeres represent the final frontier of eukaryotic genomes. Although they are defining features of chromosomes--the points at which spindle microtubules attach--the fundamental features that distinguish them from other parts of the chromosome remain mysterious. The function of centromeres is conserved throughout eukaryotic biology, but their DNA sequences are not. Rather, accumulating evidence favors chromatin-based centromeric identification. To understand how centromeric identity is maintained, researchers have studied DNA-protein interactions at native centromeres and ectopic "neocentromeres". Other studies have taken a comparative approach focusing on centromere-specific proteins, of which mammalian CENP-A and CENP-C are the prototypes. Elucidating the assembly and structure of chromatin at centromeres remain key challenges.

Animals↗
PubMed2003

The human gene CXorf17 encodes a member of a novel family of putative transmembrane proteins: cDNA cloning and characterization of CXorf17 and its mouse ortholog orf34.

We report the identification and cloning of a novel human gene, CXorf17, together with its mouse ortholog, orf34. The human and mouse transcripts were cloned from brain cDNA and encode deduced proteins of 1096 and 1091 amino acids, respectively. These proteins are 92% identical and 95% similar at the protein level. CXorf17 appears to be expressed at low levels and could be detected by RT-PCR in several adult and fetal human tissues. Analysis of the deduced amino acid sequence identified five putative transmembrane domains but no significant homology to previously described protein domains or sequence motifs. The CXorf17 protein has homology to two other non-annotated human proteins, C9orf10 and BC012177, the sequence similarity between them being strongest across two discrete domains of 250-270 amino acids in the N- and C-terminal parts of their sequences. We propose that these proteins belong to a previously undescribed family of putative transmembrane proteins. The identification of ESTs coding for similar proteins in other chordates but not lower eukaryotes suggests that these proteins may have first evolved during early chordate evolution. CXorf17 consists of 16 coding exons and maps to Xp11.22, approximately 14 kb telomeric to PRKWNK3 and 27 kb centromeric to KIAA1111. Its identification contributes to the annotation of expressed genes in the proximal part of the X chromosome.

Adult↗
PubMed1998

INCENP centromere and spindle targeting: identification of essential conserved motifs and involvement of heterochromatin protein HP1.

The inner centromere protein (INCENP) has a modular organization, with domains required for chromosomal and cytoskeletal functions concentrated near the amino and carboxyl termini, respectively. In this study we have identified an autonomous centromere- and midbody-targeting module in the amino-terminal 68 amino acids of INCENP. Within this module, we have identified two evolutionarily conserved amino acid sequence motifs: a 13-amino acid motif that is required for targeting to centromeres and transfer to the spindle, and an 11-amino acid motif that is required for transfer to the spindle by molecules that have targeted previously to the centromere. To begin to understand the mechanisms of INCENP function in mitosis, we have performed a yeast two-hybrid screen for interacting proteins. These and subsequent in vitro binding experiments identify a physical interaction between INCENP and heterochromatin protein HP1(Hsalpha). Surprisingly, this interaction does not appear to be involved in targeting INCENP to the centromeric heterochromatin, but may instead have a role in its transfer from the chromosomes to the anaphase spindle.

Anaphase↗
PubMed2001

The domain structure of centromeres is conserved from fission yeast to humans.

The centromeric DNA of fission yeast is arranged with a central core flanked by repeated sequences. The centromere-associated proteins, Mis6p and Cnp1p (SpCENP-A), associate exclusively with central core DNA, whereas the Swi6 protein binds the surrounding repeats. Here, electron microscopy and immunofluorescence light microscopy reveal that the central core and flanking regions occupy distinct positions within a heterochromatic domain. An "anchor" structure containing the Ndc80 protein resides between this heterochromatic domain and the spindle pole body. The organization of centromere-associated proteins in fission yeast is reminiscent of the multilayered structures of human kinetochores, indicating that such domain structure is conserved in eukaryotes.

Cell Cycle Proteins↗
PubMed2003

Evolutionary dynamics of a satellite DNA in the tiger beetle species pair Cicindela campestris and C. maroccana.

Satellite repeat elements are an abundant component of eukaryotic genomes, but not enough is known about their evolutionary dynamics and their involvement in karyotype and species differentiation. We report the nucleotide sequence, chromosomal localization, and evolutionary dynamics of a repetitive DNA element of the tiger beetle species pair Cicindela maroccana and Cicindela campestris. The element was detected after restriction digest of C. maroccana total genomic DNA with EcoRI as a single band and its multimers on agarose gels. Cloning and sequencing of several isolates revealed a consensus sequence of 383 bp with no internal repeat structure and no detectable similarity to any entry in GenBank. Hybridization of the satellite unit to C. maroccana mitotic and meiotic chromosomes revealed the presence of this repetitive DNA in the centromeres of all chromosomes except the Y chromosome, which exhibited only a very weak signal in its short arm. PCR-based tests for this satellite in related species revealed its presence in the sister species C. campestris, but not in other closely related species. Phylogenetic analysis of PCR products revealed well-supported clades that generally separate copies from each species. Because both species exhibit the multiple X chromosome karyotypic system common to Cicindela, but differ in their X chromosome numbers (four in C. maroccana vs. three in C. campestris), structural differences could also be investigated with regard to the position of satellites in a newly arisen X chromosome. We find the satellite in a centromeric position in all X chromosomes of C. maroccana, suggesting that the origin of the additional X chromosome involves multiple karyotypic rearrangements.

Animals↗
PubMed2004

Isolation and chromosomal localization of ZFX homologue in genome of rice field eel (Monopterus albus Zuiew).

When used as a probe in rice field eel (Monopterus albus Zuiew) genomic Southern blotting hybridization, the giant panda Zfx gene hybridized strongly to a fragment of about 9.5 kb. A 512 bp long DNA fragment has been isolated by polymerase chain reaction from rice field eel genomic DNA using the primers for amplifying zinc finger repeats 7 to 13 of mammalian and reptilian ZFX-related genes. Cloned in pBS, four recombinant plasmids were selected randomly from male and female specimens and sequenced. The nucleotide sequences in these clones were identical and showed 88% and 87% identity to human ZFX and ZFY respectively. But its extent of homology was greater with American alligator Zfc (90%). And the amino acid sequences of the putative protein showed 95.9%, 95.9% and 93.5% identity to human ZFX and ZFY and American alligator Zfc respectively. Thus, the cloned sequence encodes a homologue of mammalian ZFX/ZFY and was named Zfa for rice field eel zinc finger domain gene. It appears that the mammalian and reptilian ZFX-related genes evolved from fish ancestors with a considerable degree of conservation. By fluorescence in situ hybridization, the Zfa has been mapped to rice field eel chromosome 1 and at the position of 60.1 +/- 0.38 from the centromere. Chromosomal mapping of fish genes related to mammalian X-linked genes might lead to further understanding of the evolution of vertebrate sex chromosomes.

Amino Acid Sequence↗
PubMed1998

An alphoid-like satellite DNA sequence is present in the genome of a lacertid lizard.

A PstI DNA family was isolated from the genome of a lacertid, Lacerta graeca. The 185-bp monomeric unit (pGPS) was cloned and hybridized to DNAs and chromosomes of several lacertid species. The data showed that pGPS hybridizes to the (1) centromeric or pericentromeric heterochromatin of almost all the chromosomes of L. graeca and (2) genomic DNA of species phylogenetically related and unrelated to L. graeca. The presence of pGPS even in species immunologically apart more than 30 million years suggests that this repeated family might be either very ancient or have been conserved during evolution due to its functional role. The latter hypothesis might be supported by the results of sequence analysis which showed some homology with both several alphoid sequences of primates and the CDEIII centromeric sequence of yeast. Segments of the satellite sequence are similar to the mammalian CENP-B box. These observations suggest that pGPS might have a role in determining the centromeric function in lacertid lizards.

Animals↗
PubMed2000

Stable methylation patterns in interspecific antelope hybrids and the characterization and localization of a satellite fraction in the Alcelaphini and Hippotragini.

Conflicting data has recently appeared concerning altered methylation patterns in interspecific mammalian hybrids and the potential this may hold for driving karyotypic evolution. We report no detectable methylation difference in the genomic DNA of different interspecific F1 antelope hybrids (family Bovidae) and their parent species using the methylation-sensitive enzyme HpaII and its methylation insensitive isoschizomer MspI. However, both enzymes released a tandemly repeated satellite array. Characterization of the repeat using Southern blotting and a combination of sequencing, fluorescence in-situ hybridization (FISH) and C-banding, shows some similarity in the family of repeats between the hybridizing antelope species groups, and that the satellite is localized in the centromeric C-band positive regions of the chromosomes. Moreover, although there is little meaningful sequence homology with the well characterized bovine 1.715 satellite DNA, there is 86% sequence similarity with the sheep/goat satellite I, suggesting that they are related and are likely to have originated and evolved separately from the bovine unit.

Animals↗