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Results for “genomic tandem array”

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PubMed1999

Simultaneous genetic typing from multiple short tandem repeat loci using a 96-capillary array electrophoresis system.

Short tandem repeat (STR) markers are highly polymorphic and widely used in human identification and genetic mapping. We demonstrate fast and reliable genotyping based on the four STR loci vWF, THO1, TPOX, CSF1PO by multiple-capillary array electrophoresis. Extracted human genomic DNA was amplified by polymerase chain reaction (PCR). The PCR products were mixed with pooled allelic ladder as an absolute standard and coinjected from a 96-vial tray. Separations were performed in polyvinylpyrrolidone (PVP) sieving matrix with a one-hour turnaround time, with no degradation over 27 runs. Simultaneous one-color laser-induced fluorescence detection was achieved by using a charge-coupled device (CCD) camera. The allele peaks for the unknown sample were identified by comparing the normalized peak intensities of the mixtures to those of the pooled ladder by using a straightforward algorithm. An extremely high level of confidence in matching the bands was indicated with negligible crosstalk (< 0.89%) between adjacent capillaries. This scheme is applicable for STR genotyping with high resolution, high speed and high throughput.

Algorithms↗

PubMed1983

Complex organization of a cryptic satellite DNA in the genome of the marine invertebrate Rapana thomasiana Grosse (Gastropoda).

Isopicnic centrifugation in Cs2SO4-Ag+ gradients at pH 7.0 reveals that the genome of the marine snail Rapana thomasiana Grosse (Gastropoda) contains an AT-rich satellite fraction comprising 5% of the DNA. Restriction enzyme analysis shows that the satellite DNA is composed of a number of related subsets arranged in tandem arrays. They have evolved from the segmental amplification of an 1460 bp long monomer unit with a complex inner organization. Most probably, the present basic repeat originates from an ancestral 400-500 bp long sequence in which some insertions and/or deletions have occurred.

Animals↗

PubMed1997

Polyploid-specific repetitive DNA sequences from triploid ginbuna (Japanese silver crucian carp, Carassius auratus langsdorfi).

Repetitive DNA sequences (Cal3nDr) in the genome of a triploid ginbuna (Carassius auratus langsdorfi) were isolated from the DraI digests of the genomic DNA. This AT-rich (61%) Cal3nDr monomer was 137 bp in length. The nucleotide similarity among the monomers from the same individual was considerably high (above 97%). Hybridization analyses revealed that the Cal3nDr sequences were organized into tandem arrays. These DNA sequences were present only in triploid and tetraploid ginbunas and were absent from diploid ginbuna, gengorobuna, goldfish, and other cyprinid fishes, and therefore appeared to be specific to polyploid ginbunas. In situ hybridization data showed their localization on one to four out of a total of 150 to 156 chromosomes, depending on the individuals or clonal lines, of the triploid ginbuna. The origin of the Cal3nDr sequences is also discussed on the basis of observation of the artificial triploid ginbuna produced by crossing a diploid female with a tetraploid male.

Animals↗

PubMed1994

Human satellites 2 and 3.

The most abundant human satellites are alphoid sequences and simple sequence satellites (satellite 2 and 3). Alphoid sequences are now regarded as the DNA component of the centromere and have therefore attracted most attention, leaving satellite 2 and 3 in outer darkness. The classical satellite definition stems from the characterisation of the most abundant repeat family of density gradient fractions. This definition has been reviewed in the light of recent publications. Satellite 2 and 3 sequences and organisation are clearly distinct. Satellite 3 shows a strict periodicity of 5 bp, and satellite 2 is built from two related units of 23 and 26 bp. The distinctive behaviour of satellite-2-containing regions in genetic alterations of cytosine methylation suggests that these two tandemly repeated families participate in distinct heterochromatin organisations, and that variations in satellite sequences at many separate position in the genome may be caused by alterations of heterochromatin-associated proteins. Restriction enzyme analysis indicates that satellite 2 and 3 arrays contain regularly spaced sequence alterations creating a restriction site. This homogeneity contrasts with the scattering of numerous variant sequences all over the length of the higher-order unit, and suggests that two distinct molecular processes are the cause of local variant scattering and higher-order regular homogeneity. Higher-order homogeneity reflects paradoxically a local alterations of homogeneity. Since fixation of mutations by unequal crossovers is very efficient only in small arrays, sequence replacement by biased gene conversion must explain homogeneity in the larger arrays.

Base Sequence↗

PubMed1993

Genomic organization and expression of two independent gene arrays coding for two antigenic acidic ribosomal proteins of Leishmania.

In the present paper we describe the isolation and characterization of four novel genes of the parasitic protozoan Leishmania infantum. These genes are organized as two independent gene clusters, and they are related by nucleotide sequence to eukaryotic genes encoding acidic ribosomal proteins. Each gene cluster contains two tandemly linked genes coding for identical proteins. Each of the proteins coded by the gene clusters (called LiP and LiP') are highly divergent in sequence, showing the characteristic features of eukaryotic P-proteins from the P2 group. In spite of the sequence conservation of the coding regions of each of the genes in the cluster, the 5'- and 3'-untranslated regions are heterogeneous in sequence. The analysis of the expression of these genes indicates that logarithmic phase promastigotes show increased levels of LiP- and LiP'-specific transcripts compared with stationary phase promastigotes. The steady state RNA levels of the LiP and LiP' genes show a similar dependence of the growth phase of the parasite. Using specific probes for the divergent 3'-untranslated regions of each of the genes, it was found that the abundance of the mature transcripts is different even when the transcripts are derived from the same gene cluster. These findings probably indicate that the 3'-untranslated regions may influence the stability or turnover of the transcripts derived from both LiP and LiP' gene clusters.

Amino Acid Sequence↗

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↗

PubMed2001

Human rDNA: evolutionary patterns within the genes and tandem arrays derived from multiple chromosomes.

Human rDNA forms arrays on five chromosome pairs and is homogenized by concerted evolution through recombination and gene conversion (loci RNR1, RNR2, RNR3, RNR4, RNR5, OMIM: 180450). Homogenization is not perfect, however, so that it becomes possible to study its efficiency within genes, within arrays, and between arrays by measuring and comparing DNA sequence variation. Previous studies with randomly cloned genomic DNA fragments showed that different parts of the gene evolve at different rates but did not allow comparison of rDNA sequences derived from specific chromosomes. We have now cloned and sequenced rDNA fragments from specific acrocentric chromosomes to (1) study homogenization along the rDNA and (2) compare homogenization within chromosomes and between homologous and nonhomologous chromosomes. Our results show high homogeneity among regulatory and coding regions of rDNA on all chromosomes, a surprising homogeneity among adjacent distal non-rDNA sequences, and the existence of one to three very divergent intergenic spacer classes within each array.

Animals↗

PubMed1991

Molecular and histological characterizations of the Om(2D) mutants in Drosophila ananassae.

A series of transposon-induced optic morphology (Om) mutants found in a hypermutable marker stock of Drosophila ananassae provides a useful system for analyzing the molecular mechanism of eye morphogenesis. In the present study, one of the 25 Om loci so far reported, Om(2D), has been subjected to histological and molecular analyses as a first step toward understanding the role of Om genes in eye morphogenesis. Histological abnormalities observed during eye morphogenesis of the mutant, i.e. cell death within the eye-antennal discs of third instar larvae, and loss of the lamina, disorganized ommatidia and atrophied optic lobes in adults, were all comparable to those reported with various eye morphology mutants of D. melanogaster. Approximately 25 kb of genomic DNA including the Om (2D) locus was cloned by tom tagging. Southern blot and cloning analyses of two alleles of the Om (2D) locus revealed that insertions of the tom element occurred at three sites within 359 bp; two tandemly arrayed toms sharing one long terminal repeat at the junction and an internally deleted tom were present 359 bp apart from each other in Om (2D) 63, while a single tom in reverse orientation was present within the 359 bp in Om (2D) 10a. Host DNA sequences at the three insertion sites were TATAT or AATAT, and ATAT was duplicated upon the tom insertion.(ABSTRACT TRUNCATED AT 250 WORDS)

Alleles↗

PubMed2004

A comparison of the nature and abundance of microsatellites in 14 fungal genomes.

An overview of the character of microsatellites in 14 fungal genomes was obtained by analyzing databases containing complete or nearly complete genome sequences. Low GC content, rather than genome size, was the best predictor of high microsatellite density, although very long iterations of tandem repeats were less common in small genomes. Motif type correlated with %GC in that low-GC genomes were more likely to be dominated by A/T-rich motifs, and vice versa, although some exceptions were noted. The experimentally useful dinucleotide and trinucleotide arrays were analyzed in greater detail. Although these varied in sequence and length among fungal species, some that are likely to be universally useful were identified. This information will be useful for researchers wanting to identify the most useful microsatellites to analyze for the fungi included in this survey and provides a platform for choosing microsatellites to target in fungi that are not yet sequenced.

Base Sequence↗

PubMed1999

A striking organization of a large family of human neural cadherin-like cell adhesion genes.

We have identified 52 novel human cadherin-like genes organized into three closely linked clusters. Comparison of the genomic DNA sequences with those of representative cDNAs reveals a striking genomic organization similar to that of immunoglobulin and T cell receptor gene clusters. The N-terminal extracellular and transmembrane domains of each cadherin protein are encoded by a distinct and unusually large exon. These exons are organized in a tandem array. By contrast, the C-terminal cytoplasmic domain of each protein is identical and is encoded by three small exons located downstream from the cluster of N-terminal exons. This unusual organization has interesting implications regarding the molecular code required to establish complex networks of neuronal connections in the brain and the mechanisms of cell-specific cadherin-like gene expression.

Amino Acid Sequence↗

PubMed1988

A related moderately repetitive DNA family in the nematodes Ascaris lumbricoides and Panagrellus silusiae.

Digestion of genomic DNA from the nematodes Panagrellus silusiae and Ascaris lumbricoides with restriction endonuclease BamH1 releases a 0.7 kilobase (kb) fragment. The 0.7 kb fragment from both nematodes was cloned onto E. coli plasmid pUC19. Using representative clones as DNA hybridization probes, it was found that (i) the BamH1 fragments cross-hybridize; (ii) a ladder-effect with multiples of 0.7 kb was evident in both species after hybridization to genomic DNA and (iii) the genomic copy number of BamH1 elements is 150 and 195 for P. silusiae and A. lumbricoides respectively. DNA sequence analysis of the inserts, AL700-1 and PS700-1, revealed nucleotide blocks with over 85% similarity. No open reading frames are present in either DNA fragment. Neither fragment hybridizes to genomic DNA from Caenorhabditis elegans. Northern blot hybridization indicated that the 0.7 kb element is transcribed into poly(A)(-)-RNA in P. silusiae; but, is not transcribed in adult Ascaris muscle. Thus, P. silusiae and A. lumbricoides share a homologous, tandemly arrayed, moderately repetitive DNA family.

Animals↗

PubMed1996

Molecular characterization of the complex sex-chromosome heterochromatin in the rodent Microtus chrotorrhinus.

The sex chromosomes of Microtus chrotorrhinus are unusually large compared to those of other mammals, comprising about 20% of the karyotype and containing substantial amounts of constitutive heterochromatin. Previous studies have described two highly repeated DNA families (MSAT-160 and MSAT-2570) that localize to this heterochromatin (Modi, 1992, 1993c). The present report describes a third satellite DNA family (termed MSAT-21) in M. chrotorrhinus that is also located in the sex heterochromatin. This repeat consists of diverged copies (average similarity = 75%) of a tandemly repeated 21-mer. Southern blotting of MSAT-21 revealed that although some higher order (5-20 kb) repeats do exist, none has spread throughout an appreciable portion of the genome. Pulsed field gel experiments indicated that most of the larger arrays (50-700 kb) of all three satellite families are distributed across numerous size classes, suggesting that the three repeats are interspersed with one another in this heterochromatin. Analysis of a boundary between MSAT-21 and MSAT-160 showed that the junction monomers of each satellite are intact and that a pentanucleotide has apparently been transferred from MSAT-21 to MSAT-160 via recombination. Sequence comparisons of MSAT-160 with another rodent satellite and with the U3 region of the Rous sarcoma virus (RSV) long terminal repeat identified inverted repeats and similarities with viral enhancer domains in the rodent sequences. Additionally, the MSAT-21 consensus was found to be similar to the R region of RSV, suggesting a retroviral ancestor for these rodent repeated DNA families.

Animals↗

PubMed1987

Genomic organization of human centromeric alpha satellite DNA: characterization of a chromosome 17 alpha satellite sequence.

We characterized a recombinant clone E7 containing a 1.6-kb Eco RI insert of human alpha satellite DNA (alpha DNA) which hybridized in situ predominantly to the centromere of chromosome 17. Three thousand copies of this sequence were detected on chromosome 17, although a lesser number of copies were also found on the centromeres of chromosomes 11, X, and the other human chromosomes, except Y. In the human genome, sequences homologous to E7 were organized principally as five major polymorphic (Pst I) forms of tandem alpha DNA repeats with molecular weights between 2.0 and 2.7 kb. We We studied the higher-order organization of these major forms using a series of 12 cosmid clones. Close linkage of the different polymorphic forms was demonstrated, with no two cosmids showing an identical linkage pattern. Six of the cosmid clones carried a considerable amount (20-25%) of nonhomologous (non-alpha) DNA, indicating that the repeat arrays are relatively frequently interrupted by other genomic DNA. In none of the cosmid inserts were the repeat arrays bound on both sides by non-alpha DNA, suggesting that short arrays are not common. However, some of the intervening non-alpha DNA sequences were relatively short, and vary in size from 6 to 24 kb. Our results suggest an irregular and complex pattern of organization of alpha DNA in the human genome.

Chromosome Mapping↗

PubMed2001

Comparative sequence analysis of the imprinted Dlk1-Gtl2 locus in three mammalian species reveals highly conserved genomic elements and refines comparison with the Igf2-H19 region.

The Dlk1-Gtl2 domain on mouse chromosome 12 contains reciprocally imprinted genes with the potential to contribute to our understanding of common features involved in imprinting control. We have sequenced this conserved region in the mouse and sheep and included the human sequence in a three species comparison. This analysis resulted in a precise conservation map and identification of highly conserved sequence elements, some of which we have shown previously to be differentially methylated in the mouse. Additionally, this analysis facilitated identification of a CpG-rich tandem repeat array located approximately 13-15 kb upstream of Gtl2. Furthermore, we have identified a third imprinted transcript that overlaps with the last Dlk1 exon in the mouse. This transcript lacks a conserved open reading frame and is probably generated by cleavage of extended Dlk1 transcripts. Because Dlk1 and Gtl2 share many of the imprinting properties of the well-characterized Igf2-H19 domain, it has been proposed that the two regions may be regulated in the same way. Comparative genomic examination of the two domains indicates that although there are similarities, other features are very different, including the location of conserved CTCF-binding sites, and the level of conservation at regulatory regions.

Animals↗

PubMed1994

Structure and heterogeneity of the a sequences of human herpesvirus 6 strain variants U1102 and Z29 and identification of human telomeric repeat sequences at the genomic termini.

The unit-length genome of human herpesvirus 6 (HHV-6) consists of a single unique component (U) bounded by direct repeats DRL and DRR and forms head-to-tail concatemers during productive infection. cis-elements which mediate cleavage and packaging of progeny virions (a sequences) are found at the termini of all herpesvirus genomes. In HHV-6, DRL and DRR are identical and a sequences may therefore also occur at the U-DR junctions to give the arrangement aDRLa-U-aDRRa. We have sequenced the genomic termini, the U-DRR junction, and the DRR.DRL junction of HHV-6 strain variants U1102 and Z29. A (GGGTTA)n motif identical to the human telomeric repeat sequence (TRS) was found adjacent to, but did not form, the termini of both strain variants. The DRL terminus and U-DRR junction contained sequences closely related to that of the well-conserved herpesvirus packaging signal Cn-Gn-Nn-Gn (pac-1), followed by tandem arrays of TRSs separated by single copies of a hexanucleotide repeat. HHV-6 strain U1102 contained repeat sequences not found in HHV-6 Z29. In contrast, the DRR terminus of both variants contained a simple tandem array of TRSs and a close homolog of a herpesvirus pac-2 signal (GCn-Tn-GCn). The DRR.DRL junction was formed by simple head-to-tail linkage of the termini, yielding an intact cleavage signal, pac-2.x.pac-1, where x is the putative cleavage site. The left end of DR was the site of intrastrain size heterogeneity which mapped to the putative a sequences. These findings suggest that TRSs form part of the a sequence of HHV-6 and that the arrangement of a sequences in the genome can be represented as aDRLa-U-a-DRRa.

Base Sequence↗

PubMed1989

Mouse major (gamma) satellite DNA is highly conserved and organized into extremely long tandem arrays: implications for recombination between nonhomologous chromosomes.

We have isolated and sequenced 30 independent clones derived from MnlI digestion of purified mouse major (gamma) satellite DNA. These clones contained between 0.9 and 1.1 gamma monomeric units derived presumably from random chromosomal sources. Individual clones showed a mean deviation from the mouse consensus satellite sequence of 3.9%, with a range of 0.9-9.1%. Cleavage of total mouse LTK cell genomic DNA with three different restriction enzymes (HindIII, BglII, BamHI) that do not cut within satellite monomers, followed by Southern and pulsed-field gel electrophoretic analyses, showed that the majority of monomers were organized into largely uninterrupted arrays that varied from a minimum of 240 kb to greater than 2000 kb in length. We suggest that the high degree of conservation of the mouse gamma-satellite sequences throughout the mouse genome results from frequent recombinational exchange between nonhomologous chromosomes. Further, this same process, facilitated by the all-acrocentric constitution of the typical mouse karyotype, and the extremely long and homologous gamma-satellite arrays, may be related to the common occurrence of Robertsonian translocation in mouse.

Animals↗

PubMed1985

Repeat arrays in cellular DNA related to the Epstein-Barr virus IR3 repeat.

We isolated clones and determined the sequence of portions of mouse and human cellular DNA which cross-hybridize strongly with the IR3 repetitive region of Epstein-Barr virus. The sequences were found to be tandem arrays of a simple sequence based on the triplet GGA, very similar to the IR3 repeat. The cellular repeats have distinct differences from the viral repeat region, however, and their sequences do not appear capable of being translated into a purely glycine-plus-alanine protein domain like the portion of the Epstein-Barr nuclear antigen coded by IR3. Although the relationship between IR3 and the cellular repeats is left unclear, the cellular repeats have many interesting features. The tandem arrays are about 1 to several kilobases long, much shorter than satellite tandem repeats and larger than other interspersed, tandem repeats. Each of the repeats is a distinct variation, perhaps diverged from a common sequence, (GGA)n. This family is present in the genomes of all species tested and appears to be a ubiquitous feature of all higher eucaryotic genomes.

Animals↗

PubMed2005

Characterization of the pufferfish Takifugu rubripes apolipoprotein multigene family.

We have characterized the apolipoprotein multigene family of the pufferfish Takifugu rubripes. The pufferfish mainly contains 28-kDa, 27-kDa, and 14-kDa apolipoproteins in its plasma and was designated apo-28 kDa, apo-27 kDa, and apo-14 kDa, respectively. N-terminal amino acid sequencing revealed that pufferfish apo-28 kDa and apo-27 kDa have an identical amino acid sequence except an additional propeptide in the former; and both are homologues of apoA-I from other animals. The sequence of pufferfish apo-14 kDa is homologous to that of eel apo-14 kDa previously reported, both being apparently specific to fish. In silico screening, using the publicly available Fugu genome database confirmed the pufferfish apoA-I and apo-14 kDa genes. The database further contained the genes encoding four types of apoA-IV, one apoC-II and two types of apoE. Thus, pufferfish contains nine genes encoding apolipoprotein multigene family. Two apoA-IV and one apoE genes were tandemly arrayed and located on one scaffold. Thus two sets of these genes formed two gene clusters. The apoC-II and apo-14 kDa genes are also located on a single scaffold. apoA-I and apo-14 kDa gene transcripts were mainly expressed in liver and less abundantly in brain. The transcripts of the former gene were also observed in intestine. In contrast, the transcripts encoding four apoA-IVs, one apoC-II, and two apoEs were mainly expressed in intestine. These structural details of pufferfish apolipoproteins and tissue distribution of their gene transcripts provide a novel evidence for better understanding of evolutionary relationships of apolipoprotein multigene family.

Amino Acid Sequence↗