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Results for “Interspersed Repetitive Sequences”

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PubMed1977

DNA sequence organization in the water mold Achlya.

Experiments are described that characterize the organization of DNA sequences in the water mold Achlya bisexualis. These experiments demonstrate that repetitive and single copy sequences in the Achlya genome are arranged in a long-period interspersion pattern. Estimates of the spacing intervals between repetitive and single copy DNA indicate, however, that the interspersion pattern in Achlya is longer than has been previously reported in other eukaryotes. These data and measurements of structural gene expression in Achlya [Timberlake, W.E., Shumard, D. S. & Goldberg, R. B. (1977) Cell 10, 623-632] make it difficult to propose a regulatory function for repeated DNA in this eukaryote.

Journal Article↗

PubMed1978

Sequence organization of the rat genome by electron microscopy.

The size and arrangement of repetitive and inverted repeat (foldback) sequences in rat DNA were studied by visualization of hybrid and heteroduplex structures in the electron microscope. The self-reassociation of repetitive sequence-bearing DNA strands often results in the formation of four-ended "H" structures, whose duplex regions equal the repetitive sequence length and can be measured in the electron microscope. In this way, it was determined that the average size of the class of numerous short repetitive sequences is 0.40 +/- 0.15 kbp. Heteroduplex structures were prepared between long whole DNA single strands and short repeat-sequence-bearing strands. The analysis of these structures confirms that the size of the repetitive sequences in 0.4 kbp on average. Length measurements between adjacent duplexes show that the average spacing between two interspersed repeats is at least 1.5-1.8 kbp. By examining 29.4-kbp single strands after brief renaturation, the size and distribution of foldback sequences were determined. There are 1.9 X 10(5) foldback apirs per rat genome, spaced an average of 9.7 kbp apart according to our measurement. Repetitive, inverted repeat and unique sequences are interspersed with each other in at least half the genome.

Animals↗

PubMed1994

Transcribed repetitive DNA sequences in telomeric regions of rice (Oryza sativa).

We have isolated and characterized from rice three repetitive DNA sequences, Os48, Osc-567, and OsG3-430. Our results indicate that these repetitive sequences are highly transcribed, and transcripts complementary to both strands of the Os48 family of sequences account for up to 3% of the total cellular RNA. Pulsed-field gel electrophoresis, restriction mapping, and DNA sequence analyses have revealed a complex pattern of structural organization of the three families of repetitive sequences. Os48 and Osc-567 are organized in long tandem arrays, whereas copies of the OsG3-340 sequence are interspersed with other sequences including arrays of the Os48 and Osc567 families. Interestingly, the three families of repetitive sequences are closely linked not only to each other, but also to telomeric sequences of rice, suggesting that transcription of these repetitive sequences may occur in regions very close to telomeres in rice.

Base Sequence↗

PubMed1990

Differential distribution of long and short interspersed element sequences in the mouse genome: chromosome karyotyping by fluorescence in situ hybridization.

Fluorescence in situ hybridization has been used to demonstrate the differential distribution of interspersed repetitive elements in the genome of Mus musculus domesticus. Hybridization with a mouse long interspersed element sequence results in a sharp, highly reproducible banding pattern on metaphase chromosomes, which is quite similar to Giemsa banding for all chromosomes except 7 and X. The families of short interspersed elements, B1 and B2, preferentially cluster in the R, or reverse, bands. There is no evidence of any interspersed repeat present in the centromeric heterochromatic regions. Both the long interspersed element and B2 probes give banding patterns suitable for karyotype analysis. Simultaneous hybridization of the biotinylated long interspersed element probe and a digoxigenin-labeled cosmid to metaphase spreads allows rapid localization of a probe of interest to a particular cytogenetic band on a chromosome.

Animals↗

PubMed1994

Transposition of minisatellite-like DNA in Chironomus midges.

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

Animals↗

PubMedDate not supplied

[Repetitive sequences of the tree shrew genome (Mammalia, Scandentia)].

Copies of two repetitive elements of the genome of common tree shrew (Tupaia glis) were cloned and sequenced. The first element, Tu III, is a approximately 260 bp long short interspersed element (SINE) with the 5'-end derived from glycine RNA. Tu III carries long polypurine- and polypyrimidine-rich tracts, which may contribute to the specific secondary structure of Tu III RNA. This SINE was also found in the genome of smooth-tailed tree shrew of another genus (Dendrogale). Tu III seems to be confined to the order Scandentia (tree shrews) since it was not found in DNA of other tested mammals. The second element Tu-SAT1 is a tandem repeat with a monomer length of 365 bp. Some properties of its nucleotide sequence suggest that Tu-SAT1 is a centromeric satellite.

Animals↗

PubMed1981

Genome organization and ploidy number in Trypanosoma cruzi.

Trypanosoma cruzi total DNA was analyzed by DNA:DNA reassociation kinetics. The nonlinear least-squares computer solution could reasonably be fitted to three second-order kinetic components. The highly repetitive, middle repetitive, and single copy components comprised 9, 35 and 49% of the genome, respectively. The single copy sequences showed a kinetic complexity of approximately 4 times that of Escherichia coli and of some 11,000 average-sized structural genes. The repetitive sequences (about 6900) presented the long-period pattern of interspersion with a modal length of 7800 bases. The kinetic complexity of total DNA was compatible with a value of at least a diploid genome per cell.

Animals↗

PubMed1989

Identification of a conserved sequence in the non-coding regions of many human genes.

We have analyzed a sequence of approximately 70 base pairs (bp) that shows a high degree of similarity to sequences present in the non-coding regions of a number of human and other mammalian genes. The sequence was discovered in a fragment of human genomic DNA adjacent to an integrated hepatitis B virus genome in cells derived from human hepatocellular carcinoma tissue. When one of the viral flanking sequences was compared to nucleotide sequences in GenBank, more than thirty human genes were identified that contained a similar sequence in their non-coding regions. The sequence element was usually found once or twice in a gene, either in an intron or in the 5' or 3' flanking regions. It did not share any similarities with known short interspersed nucleotide elements (SINEs) or presently known gene regulatory elements. This element was highly conserved at the same position within the corresponding human and mouse genes for myoglobin and N-myc, indicating evolutionary conservation and possible functional importance. Preliminary DNase I footprinting data suggested that the element or its adjacent sequences may bind nuclear factors to generate specific DNase I hypersensitive sites. The size, structure, and evolutionary conservation of this sequence indicates that it is distinct from other types of short interspersed repetitive elements. It is possible that the element may have a cis-acting functional role in the genome.

Animals↗

PubMed1994

Expression of (cac)n/(gtg)n simple repetitive sequences in mRNA of human lymphocytes.

Di- and trinucleotide tandem repeat sequences are ubiquitously interspersed and are often polymorphic in the human genome. We have analyzed the transcription of simple (cac)n/(gtg)n repeats in the cDNA of RNA from human lymphocytes. When using such motifs as probes in RNA hybridization experiments, distinct signals are scarcely demonstrable. In order to investigate mRNA sequences that contain such simple repeats, 1 million phage clones from cDNA libraries were screened with the probe (CAC)5. From 50 hybridizing phages, 38 clones were successfully isolated and characterized. The lengths of the transcripts ranged from 120 bp to 3.5 kb. More than 15 different additional simple repeat motifs were found immediately next to or distant to the (cac)n/(gtg)n repeat. In 12 clones, significant homologies were identified with a wide variety of unrelated genes, such as a processed pseudogene of human ubiquitin, serin protease inhibitor genes, a gene candidate from yeast, and sequence-tagged sites of man and mouse. Of the clones, 18% represented mRNA of MHC class I promotor binding protein; 79% displayed novel single copy sequences or partial similarity to many different organelle and nuclear genomes of animal, fungal, bacterial, and viral sequences. These data indicate that short (cac)n/(gtg)n stretches (n < or = 6) are sometimes contained in open reading frames, but more often in the 3' and 5' untranslated portions of mature mRNAs. Longer stretches of perfect simple (cac)n/(gtg)n repeats can rarely be recovered, even from the hnRNA of human lymphocytes.

Amino Acid Sequence↗

PubMed2005

Species- and strain-specific probes derived from repetitive DNA for distinguishing Entamoeba histolytica and Entamoeba dispar.

Entamoeba histolytica and Entamoeba dispar are two morphologically indistinguishable species that are found in the human gut. Of the two, E. histolytica is considered to be pathogenic while E. dispar is nonpathogenic. To generate molecular probes to detect and distinguish between the two species, we utilized repeat sequences present in Entamoeba genome. We have developed probes and primers from rDNA episomes, and unidentified Entamoeba EST1 repeat for this purpose, and used them for dot blot hybridization and PCR amplification. To investigate the possible existence of invasive and noninvasive strains of E. histolytica, the ability to differentiate individual isolates is necessary. For this purpose, we have utilized a modification of the AFLP procedure called 'Transposon display,' which generates and displays large number of genomic bands associated with a transposon. We have used the abundant retrotransposon, EhSINE1, for this purpose,and demonstrated its potential as a marker to study strain variation in E. histolytica. This technique could suitably be employed in carrying out significant molecular epidemiological studies and large-scale typing of this parasite.

Animals↗

PubMed1984

The mouse globin pseudogene beta h3 is descended from a premammalian delta-globin gene.

The beta h3 pseudogene of the BALB/c mouse contains sequence defects which prevent transcription and translation to produce a beta-globin. Comparison with other globin gene sequences indicates that beta h3 arose by recombination between an adult beta-globin gene and some significantly diverged globin sequence. Analysis of noncoding sequences shows that the 3' end of mouse beta h3 and the human delta-globin gene are both descended from an ancestral gene, which we call proto-delta. The origin of proto-delta must predate the mammalian radiation. A member of the L1 family of interspersed repetitive elements is inserted into the 3' untranslated delta-homologous sequence in beta h3 from BALB/c. beta h3 is a widespread feature of the rodent beta-globin complex, which has been fixed in the genome for 35 million years. Independent inactivation events produced pseudogenes located between the adult and nonadult beta-globin genes in the rodent, primate, rabbit, and goat lineages. One model to explain the abundance and evolutionary persistence of pseudogenes postulates that the mammalian genome simply has no efficient mechanism for deleting nonessential sequences. Consequently, the genomes of higher eukaryotes have been growing, by the accumulation of duplications, with doubling times of 200 +/- 100 million years.

Animals↗

PubMed2005

Genome size and organization in the blacklegged tick, Ixodes scapularis and the Southern cattle tick, Boophilus microplus.

Genome sizes and the organization of repetitive DNA were determined in the hard ticks Ixodes scapularis and Boophilus microplus using reassociation kinetics. The I. scapularis genome contains approximately 2.15 pg (2.1x10(3) Mbp) of DNA and consists of no foldback (FB), 27% highly repetitive (HR), 39% moderately repetitive (MR), and 34% unique DNA. The B. microplus genome contains 7.5 pg (7.1x10(3) Mbp) DNA, and consists of 0.82% FB, 31% HR, 38% MR, and 30% unique DNA. In both species, repetitive sequences occur in a mixture of long and short period interspersion but most (65-80%) of the DNA follows a pattern of short period interspersion. Genome size and organization in the three tick species so far examined are distinct from other arthropods in having a greater proportion of MR, a lower proportion of unique and HR DNA of very low sequence complexity.

Animals↗

PubMed1993

Characterization of tomato DNA clones with sequence similarity to human minisatellites 33.6 and 33.15.

A tomato lambda genomic library was screened with the human minisatellites 33.6 and 33.15. Similar tomato sequences are estimated to occur on average every 4000 kb. In thirteen hybridizing clones characterized, the size of minisatellite arrays varied between 100 bp and 3 kb. The structure of the repetitive elements is complex as the human core sequence is interspersed with other elements. In three cases, sequences similar to the human minisatellites were part of a higher-order tandem repeat. The chromosomal position of these sequences was established by ascertaining linkage to previously mapped RFLP markers. In contrast to the human genome, no clustering of minisatellite loci was observed in tomato. The fingerprints generated by hybridizing tomato minisatellites to genomic DNA of a set of cultivars were, in two cases, more variable than those obtained with 33.6 or 33.15. Two of the characterized probes detected 4-8 alleles of a single locus, which displayed 10-15 times more polymorphism than random RFLP clones. Some minisatellites contain di- and tri-nucleotide microsatellite repeated motifs which may account for the high level of polymorphism detected with these clones.

Base Sequence↗

PubMed1993

Bacterial interspersed mosaic elements (BIMEs) are present in the genome of Klebsiella.

Bacterial interspersed mosaic elements (BIMEs) constitute a family of highly repetitive sequences containing palindromic units (PUs), also called repetitive extragenic palindromes (REPs). BIMEs were originally described in Escherichia coli and Salmonella typhimurium. We show here, by determining the nucleotide sequence of two intergenic regions of Klebsiella pneumoniae, by computer searches, and by hybridization, that sequences with similar characteristics are found in the genome of several Klebsiella species. This reinforces the idea that BIMEs play general and important roles in enterobacteria such as in the organization of the bacterial chromosome.

Base Sequence↗

PubMed1980

An unusual pattern of genome organization in two Phaseolus plant species.

The modes of DNA sequence organization in the nuclear genomes of French bean and green gram are studied. The reassociation kinetics of DNAs of increasing fragment lengths have revealed that approximately 60% of the genomes of French bean and green gram consist of interspersed repeated and single copy sequences. The hyperchromicity and S1-nuclease-resistance of the reassociated long DNA fragments have further confirmed the occurrence of interspersion and have shown the actual proportion of repetitive DNA to be 35-40% in each species. These experiments have also yielded the size of interspersed repeated sequences as 1900-2350 nucleotide pairs. The fragment length of the interspersed single copy DNA sequences is estimated from a curve relating the fraction of DNA fragments binding to hydroxyapatite and the DNA fragment length and is 1300 nucleotides in both plant species. Approximately 35-40% of the single copy sequences are interspersed in this manner in French bean and green gram. Since the lengths of the interspersed repeated sequences are significantly different from those in other plant species, the DNA sequence organization patterns in French bean and green gram are considered to be unusual.

Base Sequence↗

PubMed2002

Cooperativity between DNA methyltransferases in the maintenance methylation of repetitive elements.

We used mouse embryonic stem (ES) cells with systematic gene knockouts for DNA methyltransferases to delineate the roles of DNA methyltransferase 1 (Dnmt1) and Dnmt3a and -3b in maintaining methylation patterns in the mouse genome. Dnmt1 alone was able to maintain methylation of most CpG-poor regions analyzed. In contrast, both Dnmt1 and Dnmt3a and/or Dnmt3b were required for methylation of a select class of sequences which included abundant murine LINE-1 promoters. We used a novel hemimethylation assay to show that even in wild-type cells these sequences contain high levels of hemimethylated DNA, suggestive of poor maintenance methylation. We showed that Dnmt3a and/or -3b could restore methylation of these sequences to pretreatment levels following transient exposure of cells to 5-aza-CdR, whereas Dnmt1 by itself could not. We conclude that ongoing de novo methylation by Dnmt3a and/or Dnmt3b compensates for inefficient maintenance methylation by Dnmt1 of these endogenous repetitive sequences. Our results reveal a previously unrecognized degree of cooperativity among mammalian DNA methyltransferases in ES cells.

Animals↗

PubMed2003

Differential organization of a LINE-1 family in Indian pygmy field mice.

Southern blot hybridization analysis of genomic DNAs digested with restriction endonuclease EcoR I and Ava II from Mus musculus domesticus, Mus booduga and Mus terricolor with a cloned repetitive DNA fragment of Mus booduga as a probe showed difference in restriction pattern of this DNA in these three species. Further Southern analysis of the BamH I digested genomic DNAs from these species hybridized with cloned DNA fragment as a probe and sequencing of the cloned DNA revealed that this 252 bp cloned DNA fragment is a part of BamHI repeat element of genus Mus and is 87% homologous to the contiguous portion of the Mus musculus domesticus LINE-1 element. The species specific fragment pattern generated by different restriction endonucleases using this DNA as a probe revealed difference in the organization of LINE-1 repetitive element in the three species of genus Mus.

Animals↗

PubMed1997

Characterization of an interspersed repetitive DNA element in the genome of Trypanosoma cruzi.

We report the molecular characterization of a middle repetitive DNA sequence, named C6, isolated from the Trypanosoma cruzi genome. C6 appears to be a composite repeated element since 3 subregions may be defined within it on the basis of sequence similarities with other T. cruzi genomic sequences. Sequences homologous to C6 are interspersed in the genome and can be mapped out on most chromosomal bands of different T. cruzi. strains. The copy number of the C6 element is about 1000 per haploid genome. Given the species specificity and different genomic distribution of C6 homologous sequences among the T. cruzi strains the C6 element could be a useful probe for diagnosis and typing of parasites. C6 is a polymorphic marker with potential as a tool for physical mapping of the T. cruzi genome.

Animals↗