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Results for “genomic tandem array”

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PubMed1997

A family of highly repetitive DNAs from "ginbuna" (Carassius auratus langsdorfi) genome common to Carassius auratus populations.

A family of highly repetitive DNAs (Hi-a) in the genome from a population of the crucian carp, tentatively identified as the ginbuna (Carassius auratus langsdorfi), was isolated from the HindIII digests and characterized. The Hi-a monomer (268 or 269 bp) was AT-rich (64.9%) with internal repetitive oligomers. The nucleotide similarity among monomers within the same individual was 88-98%, whose sequence alterations occurred mostly at restricted sites. Hybridization analyses revealed that the Hi-a family was organized into tandem array(s) representing satellite DNAs, and that its variants that share certain restriction sites of the repeat unit were dispersed into the tandem array(s) of Hi-a DNAs at varying periodicities. The lack of sequences homologous to the ginbuna Hi-a in the genomes from cyprinid fishes other than gengorobuna and goldfish suggests that Hi-a DNAs are specifically present in the species C. auratus. The genome of goldfish differed somewhat in the quantity or the genomic organization of Hi-a DNAs from that of the ginbuna.

Animals↗

PubMed1995

Characterization of human telomeric repeat sequences from human herpesvirus 6 and relationship to replication.

Here we examine by polymerase chain reaction amplification followed by cloning and sequence analyses selected regions of the human herpesvirus 6 (HHV-6) genome which contain human telomeric repeats (TTA-GGG). We determine the relative number, arrangement and orientation of the repeats in the unit length genome, in concatemeric replicative intermediates and in heterogeneous (het) regions. We also examine distribution of the repeats in the entire genome (159 kb) and their orientation relative to DNA packaging motifs and the origin of lytic replication. In the prototype orientation the HHV-6 repeat is the related complement, TAACCC. We show that tandem arrays of this repeat are present in the right and left long direct repeats (DRL and DRR, 8 kb each) which bound the long unique sequence (UL, 143 kb). Within each DR there is a left terminal imperfect tandem array and a right terminal perfect tandem array (58 copies). In DR they are each adjacent to DNA packaging motifs, pac1 and pac2, described for herpes simplex virus and human cytomegalovirus, in the arrangement pac1-imperfect repeat-7.2 kb-perfect repeat-pac2. Five independent clones were isolated and sequence determined from junctions of concatemeric replicative intermediates which showed adjacent pac2 and pac1 motifs surrounded by telomeric repeats. Favoured cleavage sites for unit length genomes were indicated which avoided cleavage within the repeats. Analyses of the complete genome showed no tandem repeats within UL but did show a polar distribution of monomeric copies and related sequences around the origin of replication, with an effect on the overall base composition. The implications for virus replication are discussed.

Amino Acid Sequence↗

PubMed1997

Adeno-associated virus Rep proteins target DNA sequences to a unique locus in the human genome.

We have developed a system for site-specific DNA integration in human cells, mediated by the adeno-associated virus (AAV) Rep proteins. In its normal lysogenic cycle, AAV integrates at a site on human chromosome 19 termed AAVS1. We describe a rapid PCR assay for the detection of integration events at AAVS1 in whole populations of cells. Using this assay, we determined that the AAV Rep proteins, delivered in cis or trans, are required for integration at AAVS1. Only the large forms of the Rep protein, Rep78 and Rep68, promoted site-specific integration. The AAV inverted terminal repeats, present in cis, were not essential for integration at AAVS1, but in cells containing Rep, they increased the efficiency of integration. In the presence of the Rep proteins, the integration of a plasmid containing AAV inverted terminal repeats occurred at high frequency, such that clones containing the plasmid could be isolated without selection. In two of the five clones analyzed by fluorescence in situ hybridization, the plasmid DNA was integrated at AAVS1. In most of the clones, at least one copy of the entire plasmid was integrated in a tandem array. Detailed analysis of the integrated plasmid structure in one clone suggested a complex mechanism producing rearrangements of the flanking genomic DNA, similar to those observed with wild-type AAV.

Adenoviruses, Human↗

PubMed2003

Telomeres in the chicken: genome stability and chromosome ends.

Telomeres are the complex nucleoprotein structures at the termini of linear chromosomes. Telomeric DNA consists of a highly conserved hexanucleotide arranged in tandem repeats. Telomerase, a ribonucleoprotein of the reverse transcriptase family, specifies the sequence of telomeric DNA and maintains telomere array length. Numerous studies in model organisms established the significance of telomere structure and function in regulating genome stability, cellular aging, and oncogenesis. Our overall research objectives are to understand the organization of the telomere arrays in chicken in the context of the unusual organization and specialized features of this higher vertebrate genome (which include a compact genome, numerous microchromosomes, and high recombination rate) and to elucidate the role telomeres play in genome stability impacting cell function and life span. Recent studies found that the chicken genome contains three overlapping size classes of telomere arrays that differ in location and age-related stability: Class I 0.5 to 10 kb, Class II 10 to 40 kb, and Class III 40 kb to 2 Mb. Some notable features of chicken telomere biology are that the chicken genome contains ten times more telomeric DNA than the human genome and the Class III telomere arrays are the largest described for any vertebrate species. In vivo, chicken telomeres (Class II) shorten in an age-related fashion and telomerase activity is high in early stage embryos and developing organs but down-regulates during late embryogenesis or postnatally in most somatic tissues. In vitro, chicken cells down-regulate telomerase activity unless transformed. Knowledge of chicken telomere biology contributes information relevant to present and future biotechnology applications of chickens in vivo and chicken cells in vitro.

Aging↗

PubMed2001

Two 5S rDNA arrays in neotropical fish species: is it a general rule for fishes?

In this paper we describe Southern blot hybridization results probed with 5S rRNA genes for several Neotropical fish species representing different taxonomic groups. All the studied species showed a general trend with the 5S rDNA tandem repeats organized in two distinct size-classes. At the same time, data on 5S rDNA organization in fish genome were summarized. Previous information on the organization and evolution of 5S rRNA gene arrays in the genome of this vertebrate group are in agreement with the Southern results here presented. Sequences obtained for several fish species have revealed the occurrence of two distinct 5S rDNA classes characterized by distinct nontranscribed spacer sequences, which are clustered in different chromosomes in some species. Moreover, the 5S rDNA loci are generally distributed in an interstitial position in the chromosomes and they are usually not syntenic to the 45S rDNA. The presence of two classes of 5S rDNA in several non-related fish species suggests that this could be a common condition for the 5S rRNA gene organization in the fish genome.

Animals↗

PubMed1998

Analysis of homologous XRCC1-linked zinc-finger gene families in human and mouse: evidence for orthologous genes.

Genetic and physical mapping studies indicate that hundreds of zinc-finger (ZNF)-containing genes populate the human genome and that many of these genes are arranged in familial clusters. However, the extent to which these tandemly arrayed families are conserved among mammalian species is largely unknown. In a previous study, we identified a conserved cluster of Kruppel-associated box (KRAB)-containing ZNF genes located near the XRCC1 gene in human chromosome 19q13.2 and mouse chromosome 7 and analyzed two members of the murine gene family, Zfp93 and Zfp94, in detail. Here we report the identification and characterization of putative human orthologs of these murine genes. The human genes ZFP93 and ZNF45 are substantially similar to their murine counterparts in overall structure, but two notable differences exist between the sets of genes. First, the human genes encode more ZNF repeats than their murine counterparts. Second, the ZNF repeats that are common to orthologs exhibit varying degrees of conservation. Expression studies indicate that the human genes, like their mouse equivalents, are expressed widely and are coexpressed at similar levels in most adult tissues. These comparative gene sequence and expression studies therefore suggest that at least two members of the mammalian XRCC1-linked KRAB-ZNF gene family were elaborated prior to the divergence of primate and rodent lineages and were well conserved in human and mouse.

Adult↗

PubMed1987

Tandemly arranged gene clusters of malarial parasites that are highly conserved and transcribed.

A molecular clone containing a 5.8 kb Eco RI fragment was isolated from a genomic library of the rodent malarial parasite Plasmodium yoelii. The P. yoelii genome contains about 150 copies of this sequence, making up almost 3% of the DNA. These sequences are tandemly arrayed in head-to-tail configurations with the unit length of the repeat being 5.8 kb. Several poly(A+) RNAs of P. yoelii ranging from 1.6 to 0.3 kb are recognized by the 5.8 kb clone. Five additional species of malarial parasites (P. chabaudi, P. berghei, P. falciparum, P. knowlesi, and P. cynomolgi) contain tandemly repeated arrays of sequences having the same unit length of 5.8 kb, which readily hybridize to the sequence cloned from P. yoelii.

Animals↗

PubMed2005

Trypanosoma cruzi 5S rRNA arrays define five groups and indicate the geographic origins of an ancestor of the heterozygous hybrids.

Isolates of the etiological agent of Chagas disease, Trypanosoma cruzi, have been subdivided into six subgroups referred to as discrete typing units. The subgroups are related through two distinct hybridisation events: representatives of homozygous discrete typing units I and IIb fused to form discrete typing units IIa and IIc, whose homozygous genotypes have features of both ancestral types; a second fusion between strains of homozygous discrete typing units IIb and IIc created the heterozygous hybrid strains discrete typing units IId and IIe. The intergenic region of the tandemly repeated 5S rRNA array displays four variant sequence classes, allowing the discrimination of five discrete typing units. The genome project reference strain, CL Brener, is a hybrid discrete typing unit IIe strain that contains both discrete typing unit IIb and IIc classes of 5S rRNA repeats in distinct arrays present on different chromosomes. The CL Brener discrete typing unit IIb-type array contains approximately 193 repeated units, of which about one-third contain a 129 bp sequence that replaces a majority of the 5S rRNA sequence. The 129 bp 'invader' sequence was detected within the arrays of all hybrid discrete typing unit IId and IIe strains and in a subset of discrete typing unit IIb strains. This array invader replaces the internal promoter elements conserved in 5S rRNA. The discrete typing unit IIb Esmeraldo strain contains approximately 135 repeats and shows a region of homology to the array invader in the 5' flank of the array, but no evidence of the invading sequence element within the array. A survey of additional discrete typing unit IIb strains revealed a split within the subgroup, in which some strains contained invaded arrays and others were homogeneous for the 5S rRNA. The putative discrete typing unit IIb ancestor of the hybrid discrete typing units IId and IIe more closely resembles the extant Bolivian/Chilean IIb isolates than the Brazilian IIb isolates based on the correlation with the array invader.

Animals↗

PubMed1989

Trichome Development in Arabidopsis thaliana. I. T-DNA Tagging of the GLABROUS1 Gene.

Progeny from a transformed Arabidopsis plant (produced by the Agrobacterium-mediated seed transformation procedure) were found to be segregating for an altered trichome phenotype. The mutant plants have normal leaf trichomes but completely lack trichomes usually found on the stem. The mutation is tightly linked to a T-DNA insert. Complementation analysis with genetically characterized trichome mutants revealed that the new mutation is an allele of the GL1 locus. The new trichome mutant has been designated gl1-43. DNA gel blot analysis indicated that the insert site contains a complex array of at least four tandemly linked T-DNA units oriented as both direct and inverted repeats. A genomic library, constructed using DNA from gl1-43 plants, was used to clone DNA that flanks the left end of the T-DNA insert. The availability of DNA from the region interrupted by the insert has allowed initial characterization of the wild-type GL1 gene and will permit the eventual cloning and sequencing of this developmentally interesting gene.

Journal Article↗

PubMed2007

Fast skeletal muscle myosin heavy chain gene cluster of medaka Oryzias latipes enrolled in temperature adaptation.

To disclose mechanisms involved in temperature acclimation of fish muscle, we subjected eurythermal fish of medaka Oryzias latipes to cloning of myosin heavy chain genes (MYHs). We cloned cDNAs encoding fast skeletal muscle myosin heavy chain (MYH) isoforms from cDNA libraries of medaka acclimated to 10 and 30 degrees C and observed that different MYH cDNA clones are expressed in the two temperature-acclimated fish. Subsequently, we isolated several overlapping MYH contigs by shotgun cloning strategy from a medaka genomic library. Contig assembly of the complete medaka MYH (mMYH) locus of 219 kbp revealed a cluster of tandemly arrayed 11 mMYHs, in which eight genes are actually transcribed, with the remaining three being pseudogenes. Expression analysis of the transcribed genes revealed that two genes were each highly expressed in medaka acclimated to 10 and 30 degrees C, whereas comparatively lower expression levels of the three genes were exclusively observed in medaka acclimated to 30 degrees C. cDNAs of the remaining genes were too underrepresented in the libraries to determine the expression levels, and the transcripts could only be obtained by reverse transcription-polymerase chain reaction. Deduced amino acid sequences in the loop 1 and loop 2 regions of mMYHs were highly variable, suggesting that these isoforms were functionally different. The present findings consolidate our knowledge on teleost MYH multigene family and would provide further insight into the mechanisms by which expressions of individual MYH molecules are fine-tuned with environmental temperature fluctuations with further functional analysis of the genes concerned.

Adaptation, Physiological↗

PubMed1997

Hybridization capture of microsatellites directly from genomic DNA.

A rapid approach for isolation of microsatellites and other tandem repeated sequences in described. The method is based on hybridization capture of repetitive elements from digested genomic DNA using biotinylated oligonucleotide probes in solution and subsequent attachment to magnetic beads coated with streptavidin. Captured fragments are amplified by adapter polymerase chain reaction (PCR) and the PCR products enriched for microsatellites cloned directly into a T-vector for sequencing. The results presented here show that this approach is highly effective, allowing di- and trinucleotide repeats to be isolated and sequenced directly from fish and mammalian genomic DNA within four to five days. Assuming a density and relative abundance of repeats with AC/GT motifs corresponding to that found in the human genome, the protocol presented gives at least a 35-fold enrichment of AC/GT microsatellites using an (AC)10 oligo probe. In addition, four out of five sequences captured by a (CAG)9 oligo probe contained one or several CAG repeat arrays. The efficiency of this direct approach suggests that it can be used for extracting other types of tandem and interspersed repeated sequences (including transposons, rRNA and tRNA genes and proviruses) from vertebrate genomes.

Animals↗

PubMed2003

Evolution of olfactory receptor genes in the human genome.

Olfactory receptor (OR) genes form the largest known multigene family in the human genome. To obtain some insight into their evolutionary history, we have identified the complete set of OR genes and their chromosomal locations from the latest human genome sequences. We detected 388 potentially functional genes that have intact ORFs and 414 apparent pseudogenes. The number and the fraction (48%) of functional genes are considerably larger than the ones previously reported. The human OR genes can clearly be divided into class I and class II genes, as was previously noted. Our phylogenetic analysis has shown that the class II OR genes can further be classified into 19 phylogenetic clades supported by high bootstrap values. We have also found that there are many tandem arrays of OR genes that are phylogenetically closely related. These genes appear to have been generated by tandem gene duplication. However, the relationships between genomic clusters and phylogenetic clades are very complicated. There are a substantial number of cases in which the genes in the same phylogenetic clade are located on different chromosomal regions. In addition, OR genes belonging to distantly related phylogenetic clades are sometimes located very closely in a chromosomal region and form a tight genomic cluster. These observations can be explained by the assumption that several chromosomal rearrangements have occurred at the regions of OR gene clusters and the OR genes contained in different genomic clusters are shuffled.

Biological Evolution↗

PubMed1993

Expression of the lacZ gene targeted to the HPRT locus in embryonic stem cells and their derivatives.

Transgenes in mice often exhibit different expression patterns in different transgenic lines. While the basis for this phenomenon is not understood, it is widely believed that the site at which the transgene becomes integrated into the mouse genome is a major factor in determining the pattern of expression. Most transgenic mice have been produced by microinjection of DNA into the male pronucleus, which results in integration of tandem arrays of the transgene at random chromosomal sites. In the experiments described in this report, electroporation of embryonic stem (ES) cells was used to place single copies of a lacZ transgene into either random sites or into the HPRT (hypoxanthine phosphoribosyl transferase) locus of the mouse genome. Expression of lacZ was assayed by histochemical staining for Escherichia coli beta-galactosidase activity in ES cells and in differentiated derivatives obtained by teratocarcinoma formation. Several of the randomly integrated cell lines expressed lacZ at high levels in a variety of cell types present in the tumours, but most notably in epithelial cells. Targeted cell lines with lacZ in opposite orientation to the direction of HPRT gene transcription also expressed well in epithelial cells, but the targeted cell lines did not express in a wider variety of cell types than some of the nontargeted cell lines. Targeted cell lines transcribing lacZ in the same orientation as HPRT transcription did not express high levels of lacZ in any differentiated cell type. Analysis of transcripts suggested that this orientation effect may have been the result of transcriptional interference perpetrated by the HPRT gene promoter.

Animals↗

PubMed1992

The polymorphic integumentary mucin B.1 from Xenopus laevis contains the short consensus repeat.

The frog integumentary mucin B.1 (FIM-B.1), discovered by molecular cloning, contains a cysteine-rich C-terminal domain which is homologous with von Willebrand factor. With the help of the polymerase chain reaction, we now characterize a contiguous region 5' to the von Willebrand factor domain containing the short consensus repeat typical of many proteins from the complement system. Multiple transcripts have been cloned, which originate from a single animal and differ by a variable number of tandem repeats (rep-33 sequences). These different transcripts probably originate solely from two genes and are generated presumably by alternative splicing of an huge array of functional cassettes. This model is supported by analysis of genomic FIM-B.1 sequences from Xenopus laevis. Here, rep-33 sequences are arranged in an interrupted array of individual units. Additionally, results of Southern analysis revealed genetic polymorphism between different animals which is predicted to be within the tandem repeats. A first investigation of the predicted mucins with the help of a specific antibody against a synthetic peptide determined the molecular mass of FIM-B.1 to greater than 200 kDa. Here again, genetic polymorphism between different animals is detected.

Amino Acid Sequence↗

PubMed2006

The complete mitochondrial genome of a basal teleost, the Asian arowana (Scleropages formosus, Osteoglossidae).

BACKGROUND: Mitochondrial DNA-derived sequences have become popular markers for evolutionary studies, as their comparison may yield significant insights into the evolution of both the organisms and their genomes. From the more than 24,000 teleost species, only 254 complete mtDNA sequences are available (GenBank status on 06 Sep 2006). In this paper, we report the complete mitochondrial genome sequence of Asian arowana, a basal bonytongue fish species, which belongs to the order of Osteoglossiformes. RESULTS: The complete mitochondrial genomic sequence (mtDNA) of Asian arowana (Scleropages formosus) was determined by using shotgun sequencing method. The length of Asian arowana mtDNA is ca. 16,650 bp (its variation is due to polymorphic repeats in the control region), containing 13 protein-coding genes, 22 tRNA and 2 rRNA genes. Twelve of the thirteen protein coding genes were found to be encoded by the heavy strand in the order typically observed for vertebrate mitochondrial genomes, whereas only nad6 was located on the light strand. An interesting feature of Asian arowana mitogenome is that two different repeat arrays were identified in the control region: a 37 bp tandem repeat at the 5' end and an AT-type dinucleotide microsatellite at the 3' end. Both repeats show polymorphism among the six individuals tested; moreover the former one is present in the mitochondrial genomes of several other teleost groups. The TACAT motif described earlier only from mammals and lungfish was found in the tandem repeat of several osteoglossid and eel species. Phylogenetic analysis of fish species representing Actinopterygii and Sarcopterygii taxa has shown that the Asian arowana is located near the baseline of the teleost tree, confirming its status among the ancestral teleost lineages. CONCLUSION: The mitogenome of Asian arowana is very similar to the typical vertebrate mitochondrial genome in terms of gene arrangements, codon usage and base composition. However its control region contains two different types of repeat units at both ends, an interesting feature that to our knowledge has never been reported before for other vertebrate mitochondrial control regions. Phylogenetic analysis using the complete mtDNA sequence of Asian arowana confirmed that it belongs to an ancestral teleost lineage.

Animals↗

PubMed2005

Copy number polymorphism and expression level variation of the human alpha-defensin genes DEFA1 and DEFA3.

We have defined unexpectedly extensive copy number variation at the human anti-microbial alpha-defensin genes DEFA1 and DEFA3, encoding human neutrophil peptides HNP-1, HNP-2 and HNP-3. There was variation in both number and position of DEFA1/DEFA3 genes in arrays of 19 kb tandem repeats on 8p23.1, so that the DEFA1 and DEFA3 genes appear to be interchangeable variant cassettes within tandem gene arrays. For this reason, the official symbol for this locus has been revised to DEFA1A3. The total number of gene copies per diploid genome varied between four and 11 in a sample of 111 control individuals from the UK, with approximately 10% (11/111) of people lacking DEFA3 completely. DEFA1 appeared to be at high copy number in all great apes studied; at one variable site in the repeat unit, both variants have persisted in humans, chimpanzees and gorillas since their divergence. Analysis of expression levels in human white blood cells showed a clear correlation between the relative proportions of DEFA1:DEFA3 mRNA and corresponding gene numbers. However, there was no relationship between total (DEFA1+DEFA3) mRNA levels and total gene copy number, suggesting the superimposed influence of trans-acting factors. The persistence of DEFA1 at high copy number in other apes suggests an alternative model for the early stages of the evolution of novel genes by duplication and divergence. Duplicated genes present in variant tandem arrays may have greater potential than simple duplications for the combinatorial creation of new functions by recombination and gene conversion, while still preserving pre-existing functions on the same haplotype.

Blotting, Southern↗

PubMed2006

Cancer-linked DNA hypomethylation and its relationship to hypermethylation.

It is not surprising that cancer, a kind of derangement of development, hijacks DNA methylation, which is necessary for normal mammalian embryogenesis. Both decreases and increases in DNA methylation are a frequent characteristic of a wide variety of cancers. There is often more hypomethylation than hypermethylation of DNA during carcinogenesis, leading to a net decrease in the genomic 5-methylcytosine content. Although the exact methylation changes between different cancers of the same type are not the same, there are cancer type-specific differences in the frequency of hypermethylation or hypomethylation of certain genomic sequences. These opposite types of DNA methylation changes appear to be mostly independent of one another, although they may arise because of a similar abnormality leading to long-lasting epigenetic instability in cancers. Both tandem and interspersed DNA repeats often exhibit cancer-associated hypomethylation. However, one of these repeated sequences (NBL2) displayed predominant increases in methylation in some ovarian carcinomas and Wilms tumors and decreases in others. Furthermore, decreases and increases in CpG methylation can be interspersed within a small subregion of the 1.4-kb repeat unit of these tandem arrays. While the transcription-silencing role of DNA hypermethylation at promoters of many tumor-suppressor genes is clear, the biological effects of cancer-linked hypomethylation of genomic DNA are less well understood. Evidence suggests that DNA hypomethylation functions in direct or indirect control of transcription and in destabilizing chromosomal integrity. Recent studies of cancer-linked DNA hypomethylation indicate that changes to DNA methylation during tumorigenesis and tumor progression have a previously underestimated plasticity and dynamic nature.

Chromosome Aberrations↗

PubMed1995

Concerted evolution of the tandemly repeated genes encoding primate U2 small nuclear RNA (the RNU2 locus) does not prevent rapid diversification of the (CT)n.(GA)n microsatellite embedded within the U2 repeat unit.

The RNU2 locus encoding human U2 small nuclear RNA (snRNA) is organized as a nearly perfect tandem array containing 5 to 22 copies of a 5.8-kb repeat unit. Just downstream of the U2 snRNA gene in each 5.8-kb repeat unit lies a large (CT)n.(GA)n dinucleotide repeat (n approximately equal to 70). This form of genomic organization, in which one repeat is embedded within another, provides an unusual opportunity to study the balance of forces maintaining the homogeneity of both kinds of repeats. Using a combination of field inversion gel electrophoresis and polymerase chain reaction, we have been able to study the CT microsatellites within individual U2 tandem arrays. We find that the CT microsatellites within an RNU2 allele exhibit significant length polymorphism, despite the remarkable homogeneity of the surrounding U2 repeat units. Length polymorphism is due primarily to loss or gain of CT dinucleotide repeats, but other types of deletions, insertions, and substitutions are also frequent. Polymorphism is greatly reduced in regions where pure (CT)n tracts are interrupted by occasional G residues, suggesting that irregularities stabilize both the length and the sequence of the dinucleotide repeat. We further show that the RNU2 loci of other catarrhine primates (gorilla, chimpanzee, orangutan, and baboon) contain orthologous CT microsatellites; these also exhibit length polymorphism, but are highly divergent from each other. Thus, although the CT microsatellite is evolving far more rapidly than the rest of the U2 repeat unit, it has persisted through multiple speciation events spanning > 35 Myr. The persistence of the CT microsatellite, despite polymorphism and rapid evolution, suggests that it might play a functional role in concerted evolution of the RNU2 loci, perhaps as an initiation site for recombination and/or gene conversion.

Animals↗