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PubMed1994

The genome of the THE I human transposable repetitive elements is composed of a basic motif homologous to an ancestral immunoglobulin gene sequence.

Amplification of rearranged human immunoglobulin heavy-chain genes using the polymerase chain reaction resulted unexpectedly in the amplification of human transposable repetitive element genomes. These were identified as members of the THE I (transposon-like human element I) transposable element family. Analysis of the THE I sequences revealed the presence of several copies of the ancestral building block described > 10 years ago by Ohno and coworkers as the primordial immunoglobulin sequence. The frequency and degree of homology of the repeats of the basic unit were similar for the two genes, as well as for two murine intracisternal A particles. These findings suggest that both the transposable genetic elements and the immunoglobulin genes originated from a common ancestral building block.

Animals↗
PubMed1997

Duplication and distribution of repetitive elements and non-unique regions in the human genome.

Genome mapping efforts and the initial sequencing of large segments of human DNA permit ongoing assessment of the patterns and extent of sequence duplication and divergence in the human genome. Initial sequence data indicate that the most highly repetitive sequences show isochore-related enrichment and clustering produced by successive insertional recombination and local duplication of particular repetitive elements. Regional duplication is also observed for a number of otherwise unique genomic sequences and thereby makes these segments become repetitive. The consequences of these duplication events are: (1) clustering of related genes, along with a variety of coregulatory mechanisms; and (2) recombinations between the nearby homologous sequences, which can delete genes in individuals and account for a significant fraction of human genetic disease.

Genetic Diseases, Inborn↗
PubMed1998

Molecular fingerprinting of mycobacterium tuberculosis isolates obtained in havana, cuba, by IS6110 restriction fragment length polymorphism analysis and by the double-repetitive-element PCR method.

Mycobacterium tuberculosis sputum isolates from 38 patients, obtained in the first 6 months of 1997 in Havana, Cuba, were characterized by IS6110 restriction fragment length polymorphism (RFLP) analysis and the double-repetitive-element PCR (DRE-PCR) method. Among 41 strains from 38 patients, 24 and 25 unique patterns, and 5 and 4 cluster patterns, were found by the RFLP and DRE-PCR methods, respectively. Patients within two of these clusters were found to be epidemiologically related, while no relation was observed in patients in the other clusters. The DRE-PCR method is rapid, and it was as discriminating as IS6110 RFLP analysis in identifying an epidemiological association. Its simplicity makes the technique accessible for subtyping of M. tuberculosis strains in laboratories not equipped to perform RFLP analysis.

Cluster Analysis↗
PubMed2019

Discovering human transcription factor physical interactions with genetic variants, novel DNA motifs, and repetitive elements using enhanced yeast one-hybrid assays.

Identifying transcription factor (TF) binding to noncoding variants, uncharacterized DNA motifs, and repetitive genomic elements has been technically and computationally challenging. Current experimental methods, such as chromatin immunoprecipitation, generally test one TF at a time, and computational motif algorithms often lead to false-positive and -negative predictions. To address these limitations, we developed an experimental approach based on enhanced yeast one-hybrid assays. The first variation of this approach interrogates the binding of >1000 human TFs to repetitive DNA elements, while the second evaluates TF binding to single nucleotide variants, short insertions and deletions (indels), and novel DNA motifs. Using this approach, we detected the binding of 75 TFs, including several nuclear hormone receptors and ETS factors, to the highly repetitive Alu elements. Further, we identified cancer-associated changes in TF binding, including gain of interactions involving ETS TFs and loss of interactions involving KLF TFs to different mutations in the TERT promoter, and gain of a MYB interaction with an 18-bp indel in the TAL1 superenhancer. Additionally, we identified TFs that bind to three uncharacterized DNA motifs identified in DNase footprinting assays. We anticipate that these enhanced yeast one-hybrid approaches will expand our capabilities to study genetic variation and undercharacterized genomic regions.

Algorithms↗
PubMed2004

Evolutionary impact of human Alu repetitive elements.

Early studies of human Alu retrotransposons focused on their origin, evolution and biological properties, but current focus is shifting toward the effect of Alu elements on evolution of the human genome. Recent analyses indicate that numerous factors have affected the chromosomal distribution of Alu elements over time, including male-driven insertions, deletions and rapid CpG mutations after their retrotransposition. Unequal crossing over between Alu elements can lead to local mutations or to large segmental duplications responsible for genetic diseases and long-term evolutionary changes. Alu elements can also affect human (primate) evolution by introducing alternative splice sites in existing genes. Studying the Alu family in a human genomic context is likely to have general significance for our understanding of the evolutionary impact of other repetitive elements in diverse eukaryotic genomes.

Alu Elements↗
PubMed1995

Epidemiological investigation of infections due to Alcaligenes species in children and patients with cystic fibrosis: use of repetitive-element-sequence polymerase chain reaction.

Twenty-one isolates of Alcaligenes species were recovered from the respiratory tract of 16 patients at Texas Children's Hospital over a 1-year period. All but one were identified as Alcaligenes xylosoxidans; the remaining isolate was identified as Alcaligenes faecalis (formerly Alcaligenes odorans). Thirteen of 21 isolates were from the sputum of eight patients with cystic fibrosis (CF), two of whom were persistently colonized. The remaining isolates were recovered from intubated children. Patterns produced by repetitive-element-sequence polymerase chain reaction (rep-PCR), with use of either repetitive extragenic palindromic (REP) or enterobacterial repetitive intergenic consensus (ERIC) primers, showed that strains from different patients were distinct. This observation ruled out a common-source outbreak. Strains repeatedly cultured from the two persistently colonized patients over several months had identical rep-PCR patterns. We conclude that, similar to Pseudomonas aeruginosa, Alcaligenes species (most often A. xylosoxidans) colonize the respiratory tract of intubated children and of patients with CF. Colonization of patients with CF was associated with an exacerbation of pulmonary symptoms.

Adolescent↗
PubMed1990

The polydeoxyadenylate tract of Alu repetitive elements is polymorphic in the human genome.

To identify DNA polymorphisms that are abundant in the human genome and are detectable by polymerase chain reaction amplification of genomic DNA, we tested the hypothesis that the polydeoxyadenylate tract of the Alu family of repetitive elements is polymorphic among human chromosomes. We analyzed the 3' ends of three specific Alu sequences and found that two (in the adenosine deaminase gene and the beta-globin pseudogene) were polymorphic. This novel class of polymorphisms, termed AluVpA [Alu variable poly(A)] may represent one of the most useful and informative group of DNA markers in the human genome.

Alleles↗
PubMed1986

In vitro transcription of RU, a middle repetitive element of the rat genome.

Repetitive DNA sequences have been found within as well as adjacent to the rat growth hormone (rGH) gene (1,2). In vitro transcription of the rGH gene yields transcripts predominantly from a tandemly duplicated repeat (RU) in the second intron of the gene. The relative alpha-amanitin sensitivity of this transcription indicates that it is carried out by RNA polymerase III. Transcription initiates within a 5' flanking 15 base-pair repeat, and terminates within a stretch of A residues at the end of each repeat, a termination site that is notably unlike most of those used by polymerase III. Approximately 75% of the transcripts stop at the end of the first repeat; the remainder "read-through" to a homologous termination region at the end of the second repeat.

Animals↗
PubMed1995

Comparison of repetitive elements in the third intron of human and rodent mitochondrial benzodiazepine receptor-encoding genes.

The third intron of the mitochondrial benzodiazepine receptor (MBR)-encoding gene was sequenced from hamster, mouse and human. The rodent species were found to include an Alu-like sequence, as was first discovered in the rat gene. Differences with the rat intron were evident by an insertion of an additional B1 element in the hamster and the introduction of a complete and two partial B2 sequences in the mouse intron. The human intron contained a cluster of four Alu sequences; however, all of these repetitive elements were found to be in the opposite orientation relative to the Alu-like sequence present in the rodent genes. These findings support the possibility that the rodent Alu-like sequence is a remnant of a retropositional insertion in this gene prior to the divergence of rodent species. Because the human intron does not contain the same Alu remnant, it cannot be concluded that the rodent sequence represents an insertion of a primordial Alu element prior to the divergence of rodent and primate lineages.

Animals↗
PubMed2006

Repetitive elements in imprinted genes.

Genomic imprinting in mammals results in mono-allelic expression of about 80 genes depending on the parental origin of the alleles. Though the epigenetic mechanisms underlying imprinting are rather clear, little is known about the genetic basis for these epigenetic mechanisms. It is still rather enigmatic which sequence features discriminate imprinted from non-imprinted genes/regions and why and how certain sequence elements are recognized and differentially marked in the germlines. It seems likely that specific DNA elements serve as signatures that guide the necessary epigenetic modification machineries to the imprinted regions. Inter- and intraspecific comparative genomic studies suggest that the unusual occurrence and distribution of various types of repetitive elements within imprinted regions may represent such genomic imprinting signatures. In this review we summarize the various observations made and discuss them in light of experimental data.

Animals↗
PubMed1983

Simple DNA sequences and dispersed repetitive elements in the vicinity of mouse immunoglobulin K light chain genes.

The simple DNA sequences (T-G)20, (T-T-T-G-C)20 and (G-C-C-T-C-T)30 were found in the vicinity of mouse immunoglobulin genes and of dispersed repetitive elements as the R, B1 and B2 sequences. On the basis of sequence data, blot hybridizations with salmon and mouse DNA and with defined mouse DNA fragments, possible functional and evolutionary aspects of simple DNA sequences are discussed.

Animals↗
PubMed2004

First application of the SINE (short interspersed repetitive element) method to infer phylogenetic relationships in reptiles: an example from the turtle superfamily Testudinoidea.

Although turtles (order Testudines) constitute one of the major reptile groups, their phylogenetic relationships remain largely unresolved. Hence, we attempted to elucidate their phylogeny using the SINE (short interspersed repetitive element) method, in which the sharing of a SINE at orthologous loci is indicative of synapomorphy. First, a detailed characterization of the tortoise polIII/SINE was conducted using 10 species from eight families of hidden-necked turtles (suborder Cryptodira). Our analysis of 382 SINE sequences newly isolated in the present study revealed two subgroups, namely Cry I and Cry II, which were distinguishable according to diagnostic nucleotides in the 3' region. Furthermore, four (IA-ID) and five (IIA-IIE) different SINE types were identified within Cry I and Cry II subgroups, respectively, based on features of insertions/deletions located in the middle of the SINE sequences. The relative frequency of occurrence of the subgroups and the types of SINEs in this family were highly variable among different lineages of turtles, suggesting active differential retroposition in each lineage. Further application of the SINE method using the most retrotranspositionally active types, namely IB and IC, challenged the established phylogenetic relationships of Bataguridae and its related families. The data for 11 orthologous loci demonstrated a close relationship between Bataguridae and Testudinidae, as well as the presence of the three clades within Bataguridae. Although the SINE method has been used to infer the phylogenies of a number of vertebrate groups, it has never been applied to reptiles. The present study represents the first application of this method to a phylogenetic analysis of this class of vertebrates, and it provides detailed information on the SINE subgroups and types. This information may be applied to the phylogenetic resolution of relevant turtle lineages.

Amino Acid Sequence↗
PubMed1992

A human dopamine transporter cDNA predicts reduced glycosylation, displays a novel repetitive element and provides racially-dimorphic TaqI RFLPs.

We describe a cDNA for the human dopamine transporter, which has been implicated in several human disorders linked to dopaminergic function. The cDNA predicts reduced glycosylation of the protein with respect to the rat transporter, as well as a novel repetitive element in the 3' untranslated region of the cDNA. A TaqI RFLP is also reported that shows a race-specific difference in allelic frequencies.

Blotting, Southern↗
PubMed1996

Genetic diversity of Neisseria gonorrhoeae IB-2 and IB-6 isolates revealed by whole-cell repetitive element sequence-based PCR.

Phenotypic characterization of 19 Neisseria gonorrhoeae serovar IB-2 and 8 serovar IB-6 isolates by the combined use of auxotypes, serological characterization, and penicillin susceptibility testing indicated intraserovar genetic diversity. In the present study, we applied whole-cell repetitive element sequence-based PCR (rep-PCR) analysis which allows a rapid assessment of the clonal relationships of IB-2 and IB-6 isolates. DNA templates were prepared by boiling cells harvested directly from plate cultures, eliminating the need for time-consuming phenol extraction. Six different rep-PCR profiles were established among the 19 IB-2 isolates. Rep-PCR typing results had a good correlation with pulsed-field gel electrophoresis patterns. It is slightly less discriminatory than BglII-generated macrorestriction pattern analysis by pulsed-field gel electrophoresis. It is capable of discriminating epidemiologically related from epidemiologically unrelated IB-2 isolates. It should serve as a rapid and useful subtyping tool for epidemiologic investigations in which there is a predominance of major serovar groups.

Bacterial Typing Techniques↗
PubMed1998

Typing of Bacillus sporothermodurans and other Bacillus species isolated from milk by repetitive element sequence based PCR.

When analysing raw milk for the presence of Bacillus sporothermodurans, 11 Bacillus strains were isolated which could be differentiated from known Bacillus, Brevibacillus and Paenibacillus spp. by different primer specificity in PCR experiments, indicating that they probably belong to Bacillus species as yet undescribed. Using repetitive element sequence based PCR (REP-PCR), these 11 strains could be clearly distinguished from B. sporothermodurans as well as from each other. Eighty-five B. sporothermodurans strains were characterized by a typical REP-pattern. Using REP-PCR combined with separation on non-denaturing polyacrylamide gel electrophoresis and silver staining, individual B. sporothermodurans strains could be discriminated, which was not possible by methods previously published.

Animals↗
PubMed2005

Molecular characterization of Mycobacterium tuberculosis isolates from Łódź, Poland: analysis by IS6110 restriction fragment length polymorphism and double-repetitive-element PCR.

OBJECTIVES: The aim of the present study was to characterize Mycobacterium tuberculosis strains isolated in the area of Łódź, Poland, from 1996 to 2000. METHODS: Two hundred sixty three isolates from 250 patients with tuberculosis were analysed by IS6110 restriction fragment length polymorphism (RFLP) and the double-repetitive-element PCR (DRE-PCR) method when indicated. RESULTS: The isolates were found to show a great heterogeneity and only 52 strains (20.8%) occurred in 20 clusters of 2-5 identical clones. Despite this diversity of IS6110 RFLP patterns, a computer analysis of similarities revealed a high level of relatedness (at least 90%) among 38.4% of different patterns. Most of the patients with clustered strains showed no apparent epidemiologic links with other patients whose strains had the same pattern. Utilisation of the DRE-PCR analysis as an additional typing test allowed to differentiate M. tuberculosis strains with a discriminating capacity similar to that of the IS6110 RFLP. Also, DRE-PCR differentiated nine strains that were indistinguishable by the RFLP analysis. CONCLUSIONS: Both methods used for the molecular characterization of M. tuberculosis clinical isolates showed similar discriminating ability. DRE-PCR analysis proved a simple, rapid and cost-effective adjunct to the IS6110 RFLP reference method. It could be applied as a screening test, thus, reducing the number of isolates that need further subtyping with the IS6110 RFLP to those initially clustered.

Adolescent↗
PubMed1996

The rate of CpG mutation in Alu repetitive elements within the p53 tumor suppressor gene in the primate germline.

Cytosine to thymine transition mutations at the CpG dinucleotide are the most common point mutations in cancer and genetic disease. We calculated the in vivo rate of CpG mutation in the primate germline by deriving a primordial consensus sequence for an Alu repetitive element which inserted into intron 6 of the primate p53 gene 35 to 55 million years ago. Comparison of this primordial sequence to the Alu sequence in intron 6 of present-day primates was used to determine the nature and rate of mutations which occurred during evolution. We estimate the half-life of a CpG nucleotide to be 24 to 60 million years, and the rate constant for mutation at this dinucleotide to be 1.2 x 1O(-8) to 2.9 x 1O(-8) years(-1). These results were confirmed by the analysis of a second Alu sequence in intron 10 of the p53 gene. The in vivo mutation rate is at least 1250-fold slower than the in vitro chemical rate of 5-methylcytosine deamination in double-stranded DNA, showing that current estimates of CpG mutation repair have been significantly underestimated. Furthermore, the mutability of the CpG dinucleotide has led to the depletion of this dinucleotide from the vertebrate genome, and calculations in this study suggest that current levels of the CpG dinucleotide in the primate genome are very close to a steady state equilibrium in which the rate of CpG mutation is equal to the rate of CpG formation by random mutation.

Animals↗
PubMed2003

DNA fingerprinting of Lactobacillus crispatus strain CTV-05 by repetitive element sequence-based PCR analysis in a pilot study of vaginal colonization.

Lactobacillus crispatus is one of the predominant hydrogen peroxide (H(2)O(2))-producing species found in the vagina and is under development as a probiotic for the treatment of bacterial vaginosis. In this study, we assessed whether DNA fingerprinting by repetitive element sequence-based PCR (rep-PCR) can be used to distinguish the capsule strain of L. crispatus (CTV-05) from other endogenous strains as well as other species of vaginal lactobacilli. Vaginal and rectal lactobacilli were identified to the species level by using whole-chromosome probe DNA hybridization. The DNAs from L. crispatus, L. jensenii, L. gasseri, and an as-yet-unnamed H(2)O(2)-negative Lactobacillus species designated 1086V were subjected to rep-PCR. The results of gel electrophoresis and ethidium bromide staining of the DNA fingerprints obtained were compared. L. crispatus CTV-05 had a unique DNA fingerprint compared to all other lactobacilli. DNA fingerprints for 27 production lots of L. crispatus sampled from 1994 through 2001 were identical to that of the original strain isolated in 1993, suggesting strain stability. In a pilot study of nine women, this DNA fingerprinting method distinguished CTV-05 from other endogenous vaginal lactobacilli prior to and after vaginal capsule use. rep-PCR DNA fingerprinting is useful for strain typing and for evaluating longitudinal loss or acquisition of vaginal lactobacilli used as probiotics.

Bacterial Typing Techniques↗