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PubMed2004

Mutations in Haemophilus influenzae mismatch repair genes increase mutation rates of dinucleotide repeat tracts but not dinucleotide repeat-driven pilin phase variation rates.

High-frequency, reversible switches in expression of surface antigens, referred to as phase variation (PV), are characteristic of Haemophilus influenzae. PV enables this bacterial species, an obligate commensal and pathogen of the human upper respiratory tract, to adapt to changes in the host environment. Phase-variable hemagglutinating pili are expressed by many H. influenzae isolates. PV involves alterations in the number of 5' TA repeats located between the -10 and -35 promoter elements of the overlapping, divergently orientated promoters of hifA and hifBCDE, whose products mediate biosynthesis and assembly of pili. Dinucleotide repeat tracts are destabilized by mismatch repair (MMR) mutations in Escherichia coli. The influence of mutations in MMR genes of H. influenzae strain Rd on dinucleotide repeat-mediated PV rates was investigated by using reporter constructs containing 20 5' AT repeats. Mutations in mutS, mutL, and mutH elevated rates approximately 30-fold, while rates in dam and uvrD mutants were increased 14- and 3-fold, respectively. PV rates of constructs containing 10 to 12 5' AT repeats were significantly elevated in mutS mutants of H. influenzae strains Rd and Eagan. An intact hif locus was found in 14 and 12% of representative nontypeable H. influenzae isolates associated with either otitis media or carriage, respectively. Nine or more tandem 5' TA repeats were present in the promoter region. Surprisingly, inactivation of mutS in two serotype b H. influenzae strains did not alter pilin PV rates. Thus, although functionally analogous to the E. coli MMR pathway and active on dinucleotide repeat tracts, defects in H. influenzae MMR do not affect 5' TA-mediated pilin PV.

5' Flanking Region↗
PubMed2001

The number of a U3 repeat box acting as an enhancer in long terminal repeats of polytropic replication-competent porcine endogenous retroviruses dynamically fluctuates during serial virus passages in human cells.

The organization and transcriptional regulation of porcine endogenous retrovirus (PERV) long terminal repeats (LTRs) are unknown. We have studied the activity of LTRs from replication-competent molecular clones by performing luciferase reporter assays. The LTRs differ in the presence and number of 39-bp repeats located in U3 that confer strong promoter activity in human, simian, canine, feline, and porcine cell lines, whereas for LTRs devoid of the repeats, the promoter strength was significantly reduced. As the activity of a heterologous simian virus 40 promoter and a homologous repeat-deficient LTR was elevated by four 39-bp repeats independently of its orientation and location, the repeat box complies with the definition of an enhancer. During serial virus passaging of molecular PERV clones on human 293 cells, proviral LTRs demonstrated adaptation of transcriptional activity by dynamic changes of the number of 39-bp repeats in the course of up to 12 passaging cycles.

Animals↗
PubMed2001

Sequence-specific recognition and cleavage of telomeric repeat (TTAGG)(n) by endonuclease of non-long terminal repeat retrotransposon TRAS1.

The telomere of the silkworm Bombyx mori consists of (TTAGG/CCTAA)(n) repeats and harbors a large number of telomeric repeat-specific non-long terminal repeat retrotransposons, such as TRAS1 and SART1. To understand how these retrotransposons recognize and integrate into the telomeric repeat in a sequence-specific manner, we expressed the apurinic-apryrimidinic endonuclease-like endonuclease domain of TRAS1 (TRAS1 EN), which is supposed to digest the target DNA, and characterized its enzymatic properties. Purified TRAS1 EN could generate specific nicks on both strands of the telomeric repeat sequence between T and A of the (TTAGG)(n) strand (bottom strand) and between C and T of the (CCTAA)(n) strand (top strand). These sites are consistent with insertion sites expected from the genomic structure of boundary regions of TRAS1. Time course studies of nicking activities on both strands revealed that the cleavages on the bottom strand preceded those on the top strand, supporting the target-primed reverse transcription model. TRAS1 EN could cleave the telomeric repeats specifically even if it was flanked by longer tracts of nontelomeric sequence, indicating that the target site specificity of the TRAS1 element was mainly determined by its EN domain. Based on mutation analyses, TRAS1 EN recognizes less than 10 bp around the initial cleavage site (upstream 7 bp and downstream 3 bp), and the GTTAG sequence especially is essential for the cleavage reaction on the bottom strand (5'. TTAGGTT downward arrow AGG. 3'). TRAS1 EN, the first identified endonuclease digesting telomeric repeats, may be used as a genetic tool to shorten the telomere in insects and some other organisms.

Amino Acid Sequence↗
PubMed2005

Sobo, a recently amplified satellite repeat of potato, and its implications for the origin of tandemly repeated sequences.

Highly repetitive satellite DNA sequences are main components of heterochromatin in higher eukaryotic genomes. It is well known that satellite repeats can expand and contract dramatically, which may result in significant genome size variation among genetically related species. The origin of satellite repeats, however, is elusive. Here we report a satellite repeat, Sobo, from a diploid potato species, Solanum bulbocastanum. The Sobo repeat is mapped to a single location in the pericentromeric region of chromosome 7. This single Sobo locus spans approximately 360 kb of a 4.7-kb monomer. Sequence analysis revealed that the major part of the Sobo monomer shares significant sequence similarity with the long terminal repeats (LTRs) of a retrotransposon. The Sobo repeat was not detected in other Solanum species and is absent in some S. bulbocastanum accessions. Sobo monomers are highly homogenized and share >99% sequence identity. These results suggest that the Sobo repeat is a recently emerged satellite and possibly originated by a sudden amplification of a genomic region including the LTR of a retrotransposon and its flanking genomic sequences.

Base Sequence↗
PubMed1987

Mini-exon gene repeats of Trypanosoma (Nannomonas) congolense have internal repeats of 190 base pairs.

Genomic DNA hybridizations reveal that the mini-exon gene repeats of Trypanosoma (Nannomonas) congolense contain from one to greater than 20 internal tandem repeats of 190 base pairs (bp). The sequences of two mini-exon gene repeats were determined, one with three internal 190 bp repeats and one with a single 190 bp sequence. These internal repeats appear just after a very dC/dT-rich region, in the non-transcribed spacer regions between adjacent mini-exon transcription units. They do not occur in the genomes of the three other Trypanosoma species nor in the mini-exon gene repeats of four other kinetoplastids previously investigated. The mini-exon coding region of T. congolense differs in four positions from the T. brucei mini-exon sequence and in one position from a consensus sequence of the mini-exons found in other trypanosomatids. Pulse field gradient gels show that the mini-exon gene repeats of T. congolense are on large, greater than 2 megabase pair, chromosome(s).

Animals↗
PubMed1992

Cluster of fibronectin type III repeats found in the human major histocompatibility complex class III region shows the highest homology with the repeats in an extracellular matrix protein, tenascin.

Walking and sequencing a genome portion centromeric of CYP21B in the human MHC class III region disclosed a cluster of fibronectin type III repeats in an approximately 50-kb DNA segment. Fibronectin type III repeats are known to consist of ca. 90 amino acid residues and exist in a wide range of protein species. Homology searches in protein databases showed that the repeats found had the highest homology with the repeats of human tenascin, an extracellular matrix protein. One cDNA sequence located immediately centromeric of CYP21B, the 3' portion of which is transcribed by the opposite strand of CYP21B, was found also to have six type III repeats followed by a fibrinogen domain. Pairwise homology comparison of these repeats in the MHC locus with those of human tenascin showed a general parallelism in their gene organization, indicating that the newly found repeats are elements of certain tenascin-like genea.

Amino Acid Sequence↗
PubMed2005

Xin-repeats and nebulin-like repeats bind to F-actin in a similar manner.

Xin and nebulette are striated muscle-specific actin-binding proteins that both contain multiple actin-binding repeats. The nature of these repeats is different: nebulette has nebulin-like repeats, while Xin contains its own unique repeats. However, the suggestion was made from biochemical data that the Xin-repeats may bind to multiple sites on the actin molecule as was found for nebulin. We have used electron microscopy and the iterative helical real space reconstruction to visualize complexes of F-actin with Xin fragments containing either three or six Xin-repeats, and with the CN5-nebulette fragment, containing five nebulin-like repeats. Our results indicate that Xin and nebulette fragments bind to F-actin in a similar manner and in two distinct modes: in one mode actin subdomain 1 is bound, while in the second mode the binding bridges between a different site on actin subdomains 1/2 of one protomer and subdomains 3/4 of an adjacent actin protomer. Taken together with published data about nebulin, tropomyosin and ADF/cofilin, our results suggest that the ability to bind in multiple modes to the actin protomer is a general property of many actin-binding proteins.

Actins↗
PubMed2005

Evaluation of a clinical aberrometer for lower-order accuracy and repeatability, higher-order repeatability, and instrument myopia.

BACKGROUND: Refractive surgery has stimulated the development of aberrometers, which are instruments that measure higher-order aberrations. The purpose of this study was to test one clinical aberrometer, the Complete Ophthalmic Analysis System (COAS), for its accuracy, repeatability, and instrument myopia for measuring sphere and astigmatism and its repeatability for measuring higher-order aberrations. METHODS: Aberrations of 56 normal eyes (28 subjects) were measured with and without cycloplegia using a COAS, a conventional autorefractor and by subjective refraction. We evaluated lower-order accuracy (sphere and astigmatism) of the COAS and autorefractor by comparing that data with that of subjective refraction. We also tested COAS lower- and higher-order repeatability for 5 measurements taken in less than 1 minute. We evaluated instrument myopia by comparing cycloplegic and noncycloplegic measurements of the same eye. Data were analyzed for a 5.0-mm-diameter pupil. RESULTS: Mean COAS spherical error was between -0.1 and +0.4 diopters (D), depending on cycloplegia and the kind of sphere power computation selected. Cylinder power errors were less than 0.1 D. COAS repeatability coefficients were better than 0.25 D, and instrument myopia was less than 0.4 D. These were comparable with those of autorefraction. Higher-order repeatability was sufficient to allow reliable measurement of normal third-order aberrations and spherical aberration. CONCLUSIONS: Accuracy, repeatability, and instrument myopia of the COAS are similar to those of a conventional autorefractor. Accuracy and repeatability are also similar to those of subjective refraction. Like an autorefractor, the COAS provides instantaneous, objective measurements of sphere and astigmatism, but it also measures higher-order aberrations. We found that it is capable of reliably measuring problematic higher-order aberrations and is therefore a valuable asset for modern clinical eye care.

Adult↗
PubMed1992

Highly repeated DNA sequences in birds: the structure and evolution of an abundant, tandemly repeated 190-bp DNA fragment in parrots.

Up to 6.8% of the parrot (Psittaciformes) genome consists of a tandemly repeated, 190-bp sequence (P1) located in the centromere of many if not all chromosomes. Monomer repeats from 10 different psittacine species representing four subfamilies were isolated and cloned. The intraspecific sequence variation ranged from 1.5 to 7%. The interspecific sequence variation ranged from less than 3% between two species of cockatoos to approximately 45% between cockatoos and other parrots. The monomer sequences of all 10 parrot species contained several conserved (> 90%) sequence elements at identical locations within the repeat. A comparison with tandemly repeated DNA sequences in other avian species showed that several of these conserved elements were also present at similar locations within the 184-bp repeat of the Chilean flamingo (Phoenicopterus chilensis), suggesting a great antiquity of the repeat. One of the elements was also found in the tandemly repeated sequences of the crane (Gruidae) and falcon (Falconidae) families. The data were used for the construction of a partial most parsimonious relationship that supports a regional subdivision of the Psittaciformes.

Animals↗
PubMed1995

Bovine gall-bladder mucin contains two distinct tandem repeating sequences: evidence for scavenger receptor cysteine-rich repeats.

Gall-bladder mucin is a densely glycosylated macromolecule which is the primary secretory product of the gall-bladder epithelium. It has been shown to bind cholesterol and other biliary lipids and to promote cholesterol crystal nucleation in vitro. In order to understand the molecular basis for mucin-lipid interactions, bovine gall-bladder mucin cDNAs were identified by expression cloning and were isolated and sequenced. The nucleotide sequences of these cDNAs revealed two distinct tandem repeating domains. One of these domains contained a 20-amino acid tandem repeating sequence enriched in threonine, serine and proline. This sequence was similar to, but not identical with, the short tandem repeating sequences identified previously in other mammalian mucins. The other domain contained a 127-amino acid tandem repeating sequence enriched in cysteine and glycine. This repeat displayed considerable sequence similarity to a family of receptor- and ligand-binding proteins containing scavenger receptor cysteine-rich repeats. By analogy with other proteins containing these cysteine-rich repeats, it is possible that, in gall-bladder mucin, this domain serves as a binding site for hydrophobic ligands such as bilirubin, cholesterol and other biliary lipids.

Amino Acid Sequence↗
PubMed1998

A PCR amplification method reveals instability of the dodecamer repeat in progressive myoclonus epilepsy (EPM1) and no correlation between the size of the repeat and age at onset.

Progressive myoclonus epilepsy of the Unverricht-Lundborg type (EPM1) is a rare, autosomal recessive disorder characterized by onset at age 6-16 years, generalized seizures, incapacitating myoclonus, and variable progression to cerebellar ataxia. The gene that causes EPM1, cystatin B, encodes a cysteine proteinase inhibitor. Only a minority of EPM1 patients carry a point mutation within the transcription unit. The majority of EPM1 alleles contain large expansions of a dodecamer repeat, CCC CGC CCC GCG, located upstream of the 5' transcription start site of the cystatin B gene; normal alleles contain two or three copies of this repeat. All EPM1 alleles with an expansion were resistant to standard PCR amplification. To precisely determine the size of the repeat in affected individuals, we developed a detection protocol involving PCR amplification and subsequent hybridization with an oligonucleotide containing the repeat. The largest detected expansion was approximately 75 copies; the smallest was approximately 30 copies. We identified affected siblings with repeat expansions, of different sizes, on the same haplotype, which confirms the repeat's instability during transmissions. Expansions were observed directly; contractions were deduced by comparison of allele sizes within a family. In a sample of 28 patients, we found no correlation between age at onset of EPM1 and the size of the expanded dodecamer. This suggests that once the dodecamer repeat expands beyond a critical threshold, cystatin B expression is reduced in certain cells, with pathological consequences.

Adolescent↗
PubMed2004

From masking repeats to identifying functional repeats in the mouse transcriptome.

The back-to-back release of the mouse genome and the functionally annotated RIKEN mouse full-length cDNA collection was an important milestone in mammalian genomics. Yet much of the data remain to be explored in terms of biological effects and mechanisms. For example, interspersed repeats account for 39 per cent of the mouse genome sequence and 11 per cent of representative transcripts. A considerable number of transposable repeat elements are still active and propagating in mouse compared with human. While existing repeat databases and tools assist the classification of repeats or identification of new repeats, there is little bioinformatic support towards exploring the extent and role of repeats in transcriptional variation, modulation of protein function, or gene regulatory events. Since the mouse is used as a model organism to study human genes and their disease associations, this review focuses on information extraction and collation that captures the functional context of repeats in mouse transcripts to facilitate the biological interpretation and extrapolation of findings to the human.

Animals↗
PubMed1984

A novel transposon-like repeat interrupted by an LTR element occurs in a cluster of B1 repeats in the mouse c-mos locus.

The mouse genomic locus containing the oncogene c-mos was analyzed for repetitive DNA sequences. We found a single B1 repeat 10 kb upstream and three B1 repeats 0.6 kb, 2.7 kb, and 5.4 kb, respectively, downstream from c-mos. The B1 repeat closest to c-mos contains an internal 7-bp duplication and a 18-bp insertion. Localized between the last two B1 repeats is a copy of a novel mouse repeat. Sequence comparison of three copies of this novel repeat family shows that they a) contain a conserved BglII site, b) are approximately 420 bp long, c) possess internal 50-bp polypurine tracts, and d) have structural characteristics of transposable elements. They are present in about 1500 copies per haploid genome in the mouse, but are not detectable in DNA of other mammals. The BglII repeat downstream from c-mos is interrupted by a single 632-bp LTR element. We estimate that approximately 1200 copies of this element are present per haploid genome in BALB/c mice. It shares sequence homology in the R-U5 region with an LTR element found in 129/J mice.

Animals↗
PubMed1991

The U1 snRNA gene repeat from the sea urchin (Strongylocentrotus purpuratus): the 70 kilobase tandem repeat ends directly 3' to a U1 gene.

Lambda phage clones containing multiple copies of the 1.1 kb tandemly repeated unit of the sea urchin (S. purpuratus) U1 RNA genes were isolated from a gene library. The 1.1 kb repeat unit encodes a single copy of the predominant U1 RNA expressed in oocytes and embryos prior to the blastula stage. The tandem repeat unit is about 80 kb in size and is probably present one time per haploid genome as judged by pulsed-field electrophoresis of sperm DNA digested with restriction enzymes which do not cut in the repeat unit. Two of the phage contained DNA flanking the repeat unit as well as several repeat units. The tandem repeat unit ends just 3' to the U1 coding region. There is only limited homology in the 5' flanking region with U1 snRNA genes from the sea urchin L. variegatus.

Animals↗
PubMed1998

Comparison of repeat videokeratography: repeatability and accuracy.

PURPOSE: We compared the repeatability and accuracy of four commercially available videokeratography instruments and a manual keratometer. METHODS: Ten optometry students and two university employees who had no history of rigid contact lens wear and no soft contact lens wear within 6 months of the study were measured. Two independent measurements were taken on the right eyes only using the Alcon EyeMap EH-290 topography system (both manual and automatic focus), the EyeSys System 2000 corneal topography system, the Humphrey Mastervue topography system, the Humphrey Atlas topography system, and a Marco manual keratometer. A three-factor repeated measures analysis of variance with all factors repeated was performed using SAS and BMDP statistical software. Separate analyses were conducted for paracentral and peripheral data. To test accuracy, measurements were taken with the Alcon EyeMap automatic focus system, the EyeSys System 2000, the Humphrey Atlas system, and the Humphrey Mastervue system using four calibration spheres. RESULTS: There were no statistically significant differences in the repeatability of the instruments. The EyeSys corneal topography system had the most narrow 95% limits of agreement around the mean difference. The two Humphrey instruments performed similarly to the EyeSys. Although the Alcon EyeMap EH-290 had the widest 95% limits of agreement around the mean difference, it showed better repeatability when the manual focus was used compared with the automatic focus. The instruments varied in their level of accuracy, but the highest percentage of data points within +/- 0.37 D of the known values of the calibration spheres was found with the Humphrey Atlas. CONCLUSIONS: Although there were no statistically significant differences in repeatability, the EyeSys System 2000 had the highest repeatability, which may have clinical relevance. The accuracy measured in this study varied tremendously; however, the Humphrey Atlas was found to be the most accurate of the instruments tested.

Cornea↗
PubMed1988

Accuracy of repeated single versus averages of repeated duplicates of probing depth measurements.

The present study aims to determine to which extent averages or deepest recordings of repeated duplicates of probing depth measurements may increase the accuracy as compared to repeated single measurements. In total, 1247 sites were recorded in 8 patients with advanced periodontitis. The patients had received initial treatment. Each site was probed 4 times with time intervals of 100 min. The standard deviation of differences between repeated single measurements of 0.97 mm decreased with a factor square root of 2 to 0.69 mm for differences between averages of repeated duplicates of measurements. Differences between the averages and the deepest recordings of repeated duplicates of measurements showed a non-Gaussian distribution. This implies that the type-I error can not be computed on the basis of the standard deviation of the error with the use of parametric statistical analysis. The best estimate for the type-I error is the observed frequency of differences. The type-I error for differences of 3 mm or more between repeated single measurements decreased from 1.5% to 0.9% and 0.2%, when deepest recordings and averages of repeated duplicates of measurements, respectively, were compared.

Adult↗
PubMed1982

Organization of the Epstein-Barr virus DNA molecule. II. Fine mapping of the boundaries of the internal repeat cluster of B95-8 and identification of additional small tandem repeats adjacent to the HR-1 deletion.

We used cloned BamHI fragments from Epstein-Barr virus strain B95-8 [EBV(B95-8)]DNA to obtain detailed restriction maps of the region of the genome adjacent to the large internal repeat cluster. These maps together with the results of hybridization experiments using a 3.1-kilobase repeat probe defined more precisely the location of the injection between the internal repeat cluster and the flanking unique-sequence DNA. On one side (UL), the repeat sequences extended 600 +/- 80 base pairs (bp) into BamHI-Y; on the other side (US), they extended 1,300 +/- 200 bp into BamHI-C. Therefore, EBV(B95-8) DNA contained a nonintegral number of 3.1-kilobase repeat units, namely, 12.6 copies. The mapping studies also revealed a second series of internal tandem repetitions in EBV(B95-8) DNA located within the BamHI-H fragment. This cluster comprised 11 copies of a 135-bp repeat unit which contained a single site for the NotI restriction endonuclease. Hybridization to these cloned EBV(B95-8) fragments using total EBV(HR-1) DNA as probe indicated that the deletion in EBV(HR-1) removed all 3,000 bp of unique-sequence DNA which lay between the large 3.1-kilobase and the small 135-bp repeat clusters. Thus, the deletion which destroyed the transforming ability in the EBV(HR-1) virus was bounded on either side by tandem repetitions.

Base Sequence↗
PubMedDate not supplied

Repeated gonorrhea in Sheffield: the size of the problem, epidemiologic significance, and personal characteristics of repeaters.

A retrospective study was made of patients in Sheffield who had had repeated gonorrhea infections during 1976-1979. Repeaters--defined as individuals with at least one gonococcal reinfection within 12 months of their index infection in any year--were a constant proportion of the absolute number of individuals infected in any calendar year. Thus, an average of 18.2% of individuals were repeaters who contributed 30.3% of the annual number of heterosexually acquired gonococcal infections. Repeaters of either sex were more likely to be young, unmarried, unemployed, and black; they more commonly had a history of preceding sexually transmitted infections, other sexually transmitted diseases accompanying their gonorrhea, and gonococcal isolates relatively resistant to penicillin. Discriminant analysis of their characteristics suggests that potential repeaters might be predicted. It is hypothesized that the local incidence of gonorrhea is directly proportional to the number of repeaters, and it is felt that control endeavors should be focused on potential repeaters if the incidence of this disease is to be reduced.

Adolescent↗