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At least 37 records · Page 2Linked to original sources

PubMed1992

Minisatellite variant repeat (MVR) mapping: analysis of 'null' repeat units at D1S8.

Minisatellite variant repeat mapping by PCR (MVR-PCR) is a new approach to studying variation in human DNA which analyses interspersion patterns of variant repeats within minisatellite arrays. MVR-PCR has been applied to the hypervariable human minisatellite D1S8 which contains two major classes of variant 29bp repeat units designated a-type and t-type. The MVR-PCR assay uses a- or t-type specific primers, together with an amplimer at a fixed site in the DNA flanking the minisatellite, to reveal the interspersion patterns of variant repeats along an allele. Extreme levels of variation are seen both in the internal structures of individual alleles and in the digital code generated from the two superimposed alleles in total genomic DNA. However, occasional repeat units fail to amplify in MVR-PCR, signifying the existence of further repeat sequence variants termed 'null' or O-type repeats. Although not significant in individual identification, correct genotyping of null repeats is important when using MVR digital codes in parentage analysis. We have therefore characterised these null repeats and show that most null repeats share a common variant repeat sequence. We discuss the possible origins of null repeats and their application to paternity testing and the analysis of minisatellite evolution.

Alleles↗

PubMed1994

A CCG repeat polymorphism adjacent to the CAG repeat in the Huntington disease gene: implications for diagnostic accuracy and predictive testing.

The polymorphic CAG repeat that is expanded on Huntington disease (HD) chromosomes is flanked by a CCG repeat. Here we show that this CCG tract, previously assumed to be invariant at seven CCG repeats, is also polymorphic. We have identified five CCG alleles from 205 normal chromosomes, with 137 (67%) having alleles of seven repeats, five (2%) with nine repeats, 61 (30%) with 10 repeats, one (0.5%) with 11 repeats and one (0.5%) with 12 repeats. In contrast, analysis of 113 HD chromosomes revealed that the majority (105 chromosomes, 93%) contained seven CCG repeats, while the remaining eight chromosomes (7%) had allele sizes of 10 CCG repeats. Despite evidence that both CAG and CCG are polymorphic on normal chromosomes, we have found that it is only the CAG length that has a significant impact on age of onset. The discovery of larger sized CCG alleles, however, has significant implications for the assessment of CAG repeat length, particularly for persons with estimated CAG size of 36-42 repeats, since an overestimation of CAG length in this range could result in erroneous information being imparted to patients.

Adult↗

PubMed1996

Folding of proteins with WD-repeats: comparison of six members of the WD-repeat superfamily to the G protein beta subunit.

The family of WD-repeat proteins comprises over 30 different proteins that share a highly conserved repeating motif [Neer, E. J., Schmidt, C. J., Nambudripad, R., & Smith, T. F. (1994) Nature 371, 297-300]. Members of this family include the signal-transducing G protein beta subunit, as well as other proteins that regulate signal transduction, transcription, pre-mRNA splicing, cytoskeletal organization, and vesicular fusion. The crystal structure of one WD-repeat protein (G beta) has now been solved (Wall et al., 1995; Sondek et al, 1996) and reveals that the seven repeating units form a circular, propeller-like structure with seven blades each made up of four beta strands. It is very likely that all WD-repeat proteins form a similar structure. If so, it will be possible to use information about important surface regions of one family member to predict properties of another. If WD proteins form structures similar to G beta, their hydrodynamic properties should be those of compact, globular proteins, and they should be resistant to cleavage by trypsin. However, the only studied example of a WD-repeat protein, G beta, synthesized in vitro in a rabbit reticulocyte lysate, is unable to fold into a native structure without its partner protein G gamma. The non-WD-repeat amino terminal alpha helix of G beta does not inhibit folding because G beta does not fold even when this region is removed. It is not known whether all WD-repeat proteins are unable to fold when synthesized in an in vitro system. We synthesized seven members of the family in a rabbit reticulocyte lysate, determined their Stokes radius, sedimentation coefficient, and frictional ratio, and assayed their stability to trypsin. Our working definition of folding was that the proteins from globular, trypsin-resistant structures because, except for G beta gamma, their functions are not known or cannot be assayed in reticulocyte lysates. We chose proteins that include amino and carboxyl extensions as well as proteins that are made up entirely of WD-repeats. We show that unlike G beta, several proteins with WD-repeats are able to fold into globular proteins in a rabbit reticulocyte lysate. One protein, beta Trcp, formed large aggregates like G beta, suggesting that it may also require a partner protein. Despite the presence of many potential tryptic cleavage sites, all of the proteins that did fold gave stable large products on tryptic proteolysis, as predicted on the basis of the structure of G beta. These studies suggest that other WD-repeat proteins are likely to form propeller structures similar to G beta.

1-Alkyl-2-acetylglycerophosphocholine Esterase↗

PubMed1996

Novel proteins with binding specificity for DNA CTG repeats and RNA CUG repeats: implications for myotonic dystrophy.

While an unstable CTG triplet repeat expansion is responsible for myotonic dystrophy, the mechanism whereby this genetic defect induces the disease remains unknown. To detect proteins binding to CTG triplet repeats, we performed bandshift analysis using as probes double-stranded DNA fragments having CTG repeats [ds(CTG)6-10] and single-stranded oligonucleotides having CTG repeats ss(CTG)8 or RNA CUG triplet repeats (CUG)8. The source of protein was nuclear and cytoplasmic extracts of HeLa cells, fibroblasts and myotubes. Proteins binding to the double-stranded DNA repeat [ds(CTG)6-10], were inhibited by nonlabeled ds(CTG)6-10, but not by a non-specific DNA fragment (USF/AD-ML). Another protein binding to ssCTG probe and RNA CUG probe was inhibited by nonlabeled (CTG)8 and (CUG)8. Nonlabeled oligos with different triplet repeat sequences, ss(CAG)8 or ss(CGG)8, did not inhibit binding to the ss(CTG)8 probe. However, when labeled as probes, the (CAG)8 and (CGG)8 bound to proteins distinct from the CTG proteins and binding was inhibited by nonlabeled (CAG)8 or (CGG)8 respectively. The protein binding only to the RNA repeat (CUG)8 was inhibited by nonlabeled (CUG)8 but not by nonlabeled single- or double-stranded CTG repeats. Furthermore, the CUG-BP exhibited no binding to an RNA oligonucleotide of triplet repeats of the same length but having a different sequence, CGG. The CUG binding protein was localized to the cytoplasm, whereas dsDNA binding proteins were localized to the nuclear extract. Thus, several trinucleotide binding proteins exist and their specificity is determined by the triplet sequence. The novel protein, CUG-BP, is particularly interesting since it binds to triplet repeats known to be present in myotonin protein kinase mRNA which is responsible for myotonic dystrophy.

Base Sequence↗

PubMed1996

Analysis of CAG repeat of the Machado-Joseph gene in human, chimpanzee and monkey populations: a variant nucleotide is associated with the number of CAG repeats.

Machado-Joseph disease (MJD) is an autosomal dominant neurodegenerative disorder associated with an unstable and expanded CAG repeat. We analyzed this locus from various sources including MJD families, Acadian, African American, Caucasian, Greenland Inuit and Thai populations. The range of the CAG repeat size was 14-40 in the normal alleles while the MJD alleles contained 73-78 repeats in our studies. We found 25 different alleles on normal chromosomes with a heterozygosity of 0.86 in combined populations. The most common alleles were 23 (22.9%) and 14 (25.5%) repeats. We also examined 16 chimpanzees and various Old World monkeys: a pigtail macaque, a mangabey and 12 rhesus macaques. The DNA sequences surrounding the CAG repeat did not vary among species. The range of the number of the CAG repeats is 13-14 in macaques, 16 in mangabey and 14-20 in chimpanzees. Variant CAA or AAG triplets in the CAG repeat tracts were found in all 268 human, 28 monkey and 32 chimpanzee chromosomes. As reported in a previous study [Kawaguchi et al. (1994) Nature Genet. 8, 221-228] the common variant positions were the third (CAA), fourth (AAG) and sixth (CAA) positions. However, we found three human chromosomes containing CAG at the sixth position and the mangabey had AAG at the ninth position. In addition, we found CAG at the fourth position and AAG at the sixth position in all macaque chromosomes. The nucleotide following the CAG repeat tract was usually G in all species studied. However, we sometimes found C at this position in human and chimpanzee chromosomes. Interestingly, this variant C was found in all expanded chromosomes and in 54.5% of chromosomes with 27-40 CAG repeats but it was not found in any chromosomes with less than 20 CAG repeats. We hypothesize that the variant C may be associated with CAG repeat instability.

Animals↗

PubMed1996

Interaction of the trp RNA-Binding attenuation protein (TRAP) of Bacillus subtilis with RNA: effects of the number of GAG repeats, the nucleotides separating adjacent repeats, and RNA secondary structure.

The 11-subunit trp RNA-binding attenuation protein of Bacillus subtilis, TRAP, regulates transcription and translation by binding to several (G/U)AG repeats present in the trp leader and trpG transcripts. Filter binding assays were used to study interactions between L-tryptophan-activated TRAP and synthetic RNAs. RNAs that contained GAG and/or UAG repeats were tested while the length and sequence of the nucleotides separating adjacent trinucleotide repeats were altered. TRAP-RNA complexes formed with transcripts containing GAG repeats were more stable than those with transcripts containing UAG repeats or alternating GAG and UAG repeats. The stability of TRAP-RNA complexes also increased substantially when the number of GAG repeats was increased from five to six and from six to seven. A gradual increase in complex stability was observed when the number of GAG repeats was increased from 7 to 11. The optimal spacer between adjacent trinucleotide repeats was found to be 2 nucleotides, with A and U residues preferred over G and C residues. TRAP binding was specific for single-stranded RNA; TRAP could not bind to RNA containing GAG repeats base paired in a stable RNA duplex. Overall, our findings suggest that each L-tryptophan-activated TRAP subunit can bind one (G/U)AG repeat and that multiple TRAP subunit-RNA binding site interactions are required for stable TRAP-RNA association.

Bacillus subtilis↗

PubMed2001

Genetic effect of two APOA repeat polymorphisms (kringle 4 and pentanucleotide repeats) on plasma Lp(a) levels in American Samoans.

Elevated plasma lipoprotein(a) [Lp(a)] level has been established as an independent risk factor for atherosclerosis and coronary heart disease. Considerable ethnic group differences in the distribution of plasma Lp(a) levels have raised public health concerns. Recently, we have reported that Samoans have the lowest plasma Lp(a) levels of any population group. In the present investigation, we report the contribution of two apolipoprotein(a) (APOA) polymorphisms, the kringle 4 type 2 (K4) repeat and the pentanucleotide repeat (PNR), in affecting plasma Lp(a) levels in an American Samoan sample (n = 309). The K4 repeats ranged in size from 15 to 40. The common alleles contained repeats ranging from 26 to 36 with allele frequencies between 5.5% to 9.7%, and these accounted for 82% of all alleles. An inverse relationship between K4 repeat number and plasma Lp(a) level was observed for single-banded (r = -0.59, p = 0.0001) and double-banded phenotypes (r = -0.50, p = 0.0001). This polymorphism explained 60% of the variation in plasma Lp(a) level in American Samoans. For the PNR polymorphism, five different repeat alleles and eight different genotypes were identified; the most common allele was eight repeats. The *8 PNR allele was associated with a wide range of K4 repeats, the *9 PNR allele with larger K4 repeats (25-40), and the *10 PNR with smaller K4 repeats (15-24). Analysis of variance (ANOVA) revealed that the PNR polymorphism accounts for 2.1% of the variability in plasma Lp(a) levels in this sample, when the K4 repeat polymorphism was taken into account. Our data show that common polymorphisms in the APOA gene are major determinants of plasma Lp(a) variation in American Samoans.

Adult↗

PubMed2000

LPA gene: interaction between the apolipoprotein(a) size ('kringle IV' repeat) polymorphism and a pentanucleotide repeat polymorphism influences Lp(a) lipoprotein level.

OBJECTIVES: In order to search for factors influencing the Lp(a) lipoprotein level, we have examined the apolipoprotein(a) (apo(a)) size polymorphism as well as a pentanucleotide (TTTTA) repeat polymorphism in the 5' control region of the LPA gene. DESIGN: Lp(a) lipoprotein levels were compared between individuals with different genotypes as defined by pulsed field gel electrophoresis of DNA plugs, and PCR of DNA samples followed by polyacrylamide gel electrophoresis. DNA plugs and DNA were prepared from blood samples collected from blood donors. RESULTS: Twenty-seven different K IV repeat alleles were observed in the 71 women and 92 men from which apo(a) size polymorphism results were obtained. Alleles encoding 26-32 Kringle IV repeats were the most frequent. Alleles encoding seven to 11 TTTTA repeats were detected in the 84 women and 122 men included in the pentanucleotide polymorphism study, and homozygosity for eight TTTTA repeats was the most common genotype. The eight TTTTA repeat allele occurred with almost any apo(a) allele. An inverse relationship between number of K IV repeats and Lp(a) concentration was confirmed. The contributions of the apo(a) size polymorphism and the pentanucleotide repeat polymorphism to the interindividual variance of Lp(a) lipoprotein concentrations were 9.7 and 3.5%, respectively (type IV sum of squares). Nineteen per cent of the variance in Lp(a) lipoprotein level appeared to be the result of the multiplication product (interaction) between the apo(a) size polymorphism and the pentanucleotide repeat polymorphism. CONCLUSIONS: The contribution of the apo(a) size polymorphism alone to the variation in Lp(a) lipoprotein level was lower than previously reported. However, the multiplicative interaction effect between the K IV repeat polymorphism and the pentanucleotide repeat polymorphism may be an important factor explaining the variation in Lp(a) lipoprotein levels among the populations.

Adult↗

PubMed2002

Slipped-strand DNAs formed by long (CAG)*(CTG) repeats: slipped-out repeats and slip-out junctions.

The disease-associated expansion of (CTG)*(CAG) repeats is likely to involve slipped-strand DNAs. There are two types of slipped DNAs (S-DNAs): slipped homoduplex S-DNAs are formed between two strands having the same number of repeats; and heteroduplex slipped intermediates (SI-DNAs) are formed between two strands having different numbers of repeats. We present the first characterization of S-DNAs formed by disease-relevant lengths of (CTG)*(CAG) repeats which contained all predicted components including slipped-out repeats and slip-out junctions, where two arms of the three-way junction were composed of complementary paired repeats. In S-DNAs multiple short slip-outs of CTG or CAG repeats occurred throughout the repeat tract. Strikingly, in SI-DNAs most of the excess repeats slipped-out at preferred locations along the fully base-paired Watson-Crick duplex, forming defined three-way slip-out junctions. Unexpectedly, slipped-out CAG and slipped-out CTG repeats were predominantly in the random-coil and hairpin conformations, respectively. Both the junctions and the slip-outs could be recognized by DNA metabolizing proteins: only the strand with the excess repeats was hypersensitive to cleavage by the junction-specific T7 endonuclease I, while slipped-out CAG was preferentially bound by single-strand binding protein. An excellent correlation was observed for the size of the slip-outs in S-DNAs and SI-DNAs with the size of the tract length changes observed in quiescent and proliferating tissues of affected patients-suggesting that S-DNAs and SI-DNAs are mutagenic intermediates in those tissues, occurring during error-prone DNA metabolism and replication fork errors.

DNA↗

PubMed2007

Highly efficient concerted evolution in the ribosomal DNA repeats: total rDNA repeat variation revealed by whole-genome shotgun sequence data.

Repeat families within genomes are often maintained with similar sequences. Traditionally, this has been explained by concerted evolution, where repeats in an array evolve "in concert" with the same sequence via continual turnover of repeats by recombination. Another form of evolution, birth-and-death evolution, can also explain this pattern, although in this case selection is the critical force maintaining the repeats. The level of intragenomic variation is the key difference between these two forms of evolution. The prohibitive size and repetitive nature of large repeat arrays have made determination of the absolute level of intragenomic repeat variability difficult, thus there is little evidence to support concerted evolution over birth-and-death evolution for many large repeat arrays. Here we use whole-genome shotgun sequence data from the genome projects of five fungal species to reveal absolute levels of sequence variation within the ribosomal RNA gene repeats (rDNA). The level of sequence variation is remarkably low. Furthermore, the polymorphisms that are detected are not functionally constrained and seem to exist beneath the level of selection. These results suggest the rDNA is evolving via concerted evolution. Comparisons with a repeat array undergoing birth-and-death evolution provide a clear contrast in the level of repeat array variation between these two forms of evolution, confirming that the rDNA indeed does evolve via concerted evolution. These low levels of intra-genomic variation are consistent with a model of concerted evolution in which homogenization is very rapid and efficiently maintains highly similar repeat arrays.

Aspergillus nidulans↗

PubMedDate not supplied

Serum granulocyte-macrophage colony-stimulating factor and interleukin-1 levels in patients with repeated and non-repeated pulmonary infections.

Granulocyte-macrophage colony-stimulating factor (GM-CSF) has a stimulating effect on erythroid, megakaryocytic and granulocyte-macrophage progenitors. Activated T lymphocytes, monocytes, fibroblasts and endothelial cells release GM-CSF after stimulation by endotoxin and cytokines such as interleukin-1 (IL-1) and tumor necrosis factor. IL-1 is also released in response to bacterial infections and inflammation by phagocytic mononuclear cells. GM-CSF and IL-1 levels were examined in 10 patients with recurrent pulmonary infection (repeaters) and in 10 patients with acute pulmonary infection (non-repeaters) in the acute and recovery periods of infection. The mean serum GM-CSF and IL-1 levels of non-repeaters were significantly higher than those of repeaters in the acute period of infection (p < 0.002), but the same parameters of both groups were not different in the recovery period (p > 0.05). In addition, both the serum GM-CSF and IL-1 levels of repeaters and non-repeaters in the acute period of infection were higher than those in the recovery period (p < 0.05). There was a positive correlation between serum IL-1 and GM-CSF levels in non-repeaters (r = 0.746, p = 0.013), but no significant correlation between the same parameters in repeaters (r = 0.395, p = 0.259). In this study, we could not explain why the serum GM-CSF and IL-1 levels in repeaters did not increase as they did in non-repeaters; moreover, there was no significant correlation between serum IL-1 and GM-CSF levels in repeaters during the acute period of infection. These findings may be due to microenvironmental factors in bone marrow and/or other factors.

Acute Disease↗

PubMed2006

The intragenomic polymorphism of a partially inverted repeat (PIR) in Gallus gallus domesticus, potential role of inverted repeats in satellite DNAs evolution.

We report here the molecular characterization of the basic repeating unit of a novel repetitive family, partially inverted repeat (PIR), previously identified from chicken genome. This repetitive DNA family shares a close evolutionary relationship with XhoI/EcoRI repeats and chicken nuclear-membrane-associated (CNM) repeat. Sequence analyses reveal the 1430 bp basic repeating unit can be divided into two regions: the central region ( approximately 1000 bp) and the flanking region ( approximately 430 bp). Within the central region, a pair of repeats (86 bp) flanks the central core ( approximately 828 bp) in inversed orientation. Due to the tandem array feature shared by the repeating units, the inverted repeats fall between the central core and flanking region. Southern blot analyses further reveal the intragenomic polymorphism of PIR, and the molecular size of repeating units ranges from 1.1 kb to 1.6 kb. The identified monomer variants may result from multiple crossing-over events, implying the potential roles of inverted repeats in satellite DNAs variation.

Animals↗

PubMed2001

Modification of indium tin oxide electrodes with repeat polynucleotides: electrochemical detection of trinucleotide repeat expansion.

Genomic expansion of the triplet repeat sequences 5'-(CTG)n and 5'-(CGG)n leads to myotonic dystrophy and fragile X syndrome, respectively. Methods for determining the number of repeats in unprocessed nucleic acids would be useful in diagnosing diseases based on triplet repeat expansion. Electrochemical reactions based on the oxidation of guanine were expected to give larger signals per strand for expansion of repeats containing guanine. A novel PCR reaction was used to generate fragments containing 150, 230, 400, and 830 repeats of (CTG)n, which codes for myotonic dystrophy, and 130 and 600 repeats of (CGG)n, which codes for fragile X syndrome. These PCR fragments were immobilized to indium tin oxide electrodes, and oxidation of guanine in the fragments was realized using electrocatalysis by Ru(bpy)3(2+) (bpy = 2,2'-bipyridine). The catalytic currents due to oxidation of the immobilized guanines by Ru(bpy)3(3+) increased with the number of repeats and were a linear function of the repeat number when normalized to the number of strands immobilized. These results suggest a sensing strategy for repeat length based on the combination of the electrocatalytic strategy for determining the repeat length combined with existing methods for determining the number of strands.

DNA↗

PubMed1995

Linkage disequilibrium between the expanded (CAG)n repeat and an allele of the adjacent (CCG)n repeat in Huntington's disease patients of Greek origin.

Huntington's disease (HD) is associated with an expanded unstable (CAG)n repeat in the IT15 gene. This repeat was investigated in 44 HD patients and 59 of their relatives at risk who were members of 29 unrelated families from various parts of Greece. Abnormal elongation of the (CAG)n repeat ranging from 39 to 95 trinucleotide units was found in all but one of the 44 HD patients tested with 70% of these patients showing 42-47 repeats. The size of the expanded sequence correlated inversely with the age at disease onset (r = 0.77, p < 0.00001, n = 43). In a single sporadic case, de novo expansion of the (CAG)n repeat was detected. Twenty-four of 59 asymptomatic family members at risk showed expansion of the (CAG)n repeat in the HD range (39-56 trinucleotide units) while three had intermediate alleles (36-37 repeats). Evaluation of the adjacent polymorphic (CCG)n repeat showed a strong linkage disequilibrium between the 7-unit (CCG)n repeat allele and the HD mutation, with 51% of normal and 93% of HD chromosomes showing this allele (chi 2 = 15.55, p < 0.0001, n - 260). These data on HD patients of Greek origin are consistent with the thesis that the (CAG)n expansion is the primary gene defect of the disease and that this mutation occurred primarily on chromosomes with the (CCG)7 repeat haplotype.

Age of Onset↗

PubMed2002

Mutations in tetranucleotide repeats following DNA damage depend on repeat sequence and carcinogenic agent.

Sporadic microsatellite mutations are frequently observed in lung, bladder, and head and neck tumors with intact DNA mismatch repair. AAAG tetranucleotide repeats appear to be especially prone to the accumulation of these mutations. We hypothesized that occurrences of microsatellite mutations in these cancers may be linked to DNA damage caused by exposure to carcinogens in tobacco smoke. To test this hypothesis, we developed a model system based on reactivation of green fluorescent protein (GFP) in which a plasmid vector carries a microsatellite repeat that places the GFP sequence out of frame for protein translation. In this reporter system, DNA slippage mutations can restore the GFP reading frame and become detectable by flow cytometry as GFP-positive cells. Pools of stably transfected RKO cells were treated at four dose levels each of gamma-irradiation, benzo(a)pyrene diol epoxide, N-methyl-N-nitro-N-nitrosoguanidine (MNNG), t-butyl hydrogen peroxide, and UV irradiation and assayed for GFP-positive cells 48 h later. We studied the microsatellite repeats AAAG, ATAG, CAGT, and CA, as well as a control sequence lacking any repetitive elements. A log-linear regression approach was used to discriminate between the effects of repeat unit and dose for each agent. A statistically significant increase in GFP-positive cells was found with increasing dose with all agents, although repeat unit-specific response patterns were only observed with MNNG, t-butyl hydrogen peroxide, and UV irradiation. With MNNG, significant differences in response were observed between dinucleotide and tetranucleotide repeat units. The effects of UV irradiation were consistent with the predicted number of pyrimidine dimers/repeat unit, with higher GFP activation in repeats that had large numbers of adjacent pyrimidines. We found no evidence to indicate that the AAAG repeat responded to any of the DNA-damaging agents with higher levels of GFP activation than other repeat units. These results provide evidence that DNA damage can induce slippage mutations and increase mutation rates in repeated sequences and that there are sequence-specific responses to different types of DNA damage. Our results are compatible with the hypothesis that sporadic microsatellite mutations in human cancer may reflect DNA damage caused by carcinogen exposure.

7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide↗

PubMed1988

Terminal repeats in long repeat arrays are likely to reflect the early evolution of Balbiani ring genes.

Balbiani ring (BR) genes in Chironomus tentans are 35 to 40 kb (1 kb = 10(3) bases or basepairs) in length and encode secretory proteins of exceptional size. Each gene contains a large homogeneous core block consisting of approximately 100 tandemly arranged, highly homologous repeat units. The repeat unit has a constant (C) region and a subrepeat (SR) region. The various BR genes exhibit similar C regions, while the SR regions differ as to sequence, length and number of subrepeats. To study early steps in the evolution of the coding repeat arrays of the BR genes we have analyzed the 3' ends of the four BR genes in C. tentans: BR1, BR2.1, BR2.2 and BR6. In each gene the very end of the core block consists of two or three repeat unit variants; in each variant repeat the C region is linked to a Cys region, replacing the SR region. Sequence comparisons between the C regions of the closely related BR1 and BR2 genes show that during evolution the terminal repeat unit variants have to a large extent been isolated from the remainder of the core block and have probably been more conserved than the interior repeat units. Detailed analysis of the structure of the variant repeat units further supports this latter notion and suggests that the BR core blocks have evolved from an array of a simple 36 base-pair long sequence; larger, more complex repeat units containing subrepeats were gradually formed and spread in the block, mainly by homologous unequal recombination events. During this evolution the interior of the core blocks evolved as a homogeneous repetitive structure, while ancestor repeat units remained as sequence relicts in the terminal parts.

Animals↗

PubMed1991

The effect of the length of direct repeats and the presence of palindromes on deletion between directly repeated DNA sequences in bacteriophage T7.

The frequency of genetic deletion between directly repeated DNA sequences in bacteriophage T7 was measured as a function of the length of the direct repeat. The non-essential ligase gene (gene 1.3) of bacteriophage T7 was interrupted with pieces of synthetic DNA bracketed by direct repeats of various lengths. Deletion of these 76 bp long inserts was too low to be measured when the direct repeats were less than 6 bp long. However, the frequency of deletion of inserts with longer direct repeats increased exponentially as the length of the repeats increased from 8 to 20 bp. When inverted repeats (palindromes) were designed in the midst of the insert there was essentially no increase in deletion frequency between 10 bp direct repeats. But, the same palindromic sequences increased the deletion frequency between 5 bp direct repeats by at least two orders of magnitude. Thus, in this system homology at the endpoints is a more important determinant of deletion frequency than is the presence of palindromes between the direct repeats.

Base Sequence↗

PubMed1996

Risk of recurrence of repeat breeding in sows with a repeat breeding in the first parity.

Risk of recurrence of repeat breeding in sows with a repeat breeding in the 1st parity was investigated in 241 sow herds (1985-1990). The association between repeat breeding in the 1st and subsequent parities was examined using data on 9,120 sows. Each sow contributed only one pair of observations to the total data set. Occurrence of repeat breeding in the 1st and higher parities was presented in terms of recurrent risk rates (rRR), adjusted for different strata of herds. Sows with a repeat breeding in the 1st parity did not have a significantly higher risk rate for recurrence of a repeat breeding in the 2nd parity (rRR = 1.12, 95% confidence interval .97-1.29) and in the 3rd parity (rRR = 1.10, 95% confidence interval .86-1.41) compared to sows without a repeat breeding in the 1st parity. Sows with a repeat breeding in the 1st parity had a slightly higher risk rate for recurrence of a repeat breeding in the 4th or higher parity (rRR = 1.07, 95% confidence interval 1.03-1.10), compared to sows without a repeat breeding in the 1st parity. However, this risk is, in a biological sense, very small.

Animals↗