Self-amplification of satellite DNA in vitro

Genome ◽  
1998 ◽  
Vol 41 (3) ◽  
pp. 429-434 ◽  
Author(s):  
J B Buntjer ◽  
J A Lenstra
Keyword(s):  
Tandem Repeat ◽  
Satellite Dna ◽  
Genomic Dna ◽  
Tandem Repeats ◽  
Repeat Unit ◽  
Dna Amplification ◽  
Repeat Units ◽  
Rapid Amplification ◽  
Species Specific

We describe a PCR-like reaction in which genomic DNA acts as a template as well as a primer. Interaction between genomic tandem repeat units leads to self-amplification of satellite DNA. This genomic self-priming PCR (GSP-PCR) allowed the rapid amplification of species-specific tandem repeats of horse, cattle, dolphin, and chicken. A novel specific satellite of ostrich with a repeat unit of 60 bp was isolated using this method.Key words: satellite DNA, amplification, isolation, species-specific probes.

scholarly journals The Vsa Shield of Mycoplasma pulmonis Is Antiphagocytic

2011 ◽  
Vol 80 (2) ◽  
pp. 704-709 ◽  
Author(s):  
Brandon M. Shaw ◽  
Warren L. Simmons ◽  
Kevin Dybvig
Keyword(s):  
Tandem Repeat ◽  
Tandem Repeats ◽  
Repeat Unit ◽  
Mycoplasma Pulmonis ◽  
Content Type ◽  
Tandem Repeat Region ◽  
Chronic Respiratory Infection

ABSTRACTThe infection of mice withMycoplasma pulmonisis a model for studying chronic mycoplasmal respiratory disease. Manyin vivoandin vitrostudies have used the organism to gain a better understanding of host-pathogen interactions in chronic respiratory infection. The organism's Vsa proteins contain an extensive tandem repeat region. The length of the tandem repeat unit varies from as few as 11 amino acids to as many as 19. The number of tandem repeats can be as high as 60. The number of repeats varies at a high frequency due to slipped-strand mispairing events that occur during DNA replication. When the number of repeats is high, e.g., 40, the mycoplasma is resistant to lysis by complement but does not form a robust biofilm. When the number of repeats is low, e.g., 5, the mycoplasma is killed by complement when the cells are dispersed but has the capacity to form a biofilm that resists complement. Here, we examine the role of the Vsa proteins in the avoidance of phagocytosis and find that cells producing a protein with many tandem repeats are relatively resistant to killing by macrophages. These results may be pertinent to understanding the functions of similar proteins that have extensive repeat regions in other microbes.

A species-specific satellite DNA from the entomopathogenic nematode Heterorhabditis indicus

Genome ◽  
1998 ◽  
Vol 41 (2) ◽  
pp. 148-153 ◽  
Author(s):  
Monique Abadon ◽  
Eric Grenier ◽  
Christian Laumond ◽  
Pierre Abad
Keyword(s):  
Dna Sequence ◽  
Satellite Dna ◽  
Tandem Repeats ◽  
Sequence Data ◽  
Entomopathogenic Nematode ◽  
Consensus Sequence ◽  
Repeated Sequence ◽  
Nucleotide Sequence Analysis ◽  
Specific Sequence ◽  
Species Specific

An AluI satellite DNA family has been cloned from the entomopathogenic nematode Heterorhabditis indicus. This repeated sequence appears to be an unusually abundant satellite DNA, since it constitutes about 45% of the H. indicus genome. The consensus sequence is 174 nucleotides long and has an A + T content of 56%, with the presence of direct and inverted repeat clusters. DNA sequence data reveal that monomers are quite homogeneous. Such homogeneity suggests that some mechanism is acting to maintain the homogeneity of this satellite DNA, despite its abundance, or that this repeated sequence could have appeared recently in the genome of H. indicus. Hybridization analysis of genomic DNAs from different Heterorhabditis species shows that this satellite DNA sequence is specific to the H. indicus genome. Considering the species specificity and the high copy number of this AluI satellite DNA sequence, it could provide a rapid and powerful tool for identifying H. indicus strains.Key words: AluI repeated DNA, tandem repeats, species-specific sequence, nucleotide sequence analysis.

scholarly journals Isolation of a Pericentromeric Satellite DNA Family in Chnootriba argus (Henosepilachna argus) with an Unusual Short Repeat Unit (TTAAAA) for Beetles

Insects ◽  
2019 ◽  
Vol 10 (9) ◽  
pp. 306 ◽  
Author(s):  
Pablo Mora ◽  
Jesús Vela ◽  
Areli Ruiz-Mena ◽  
Teresa Palomeque ◽  
Pedro Lorite
Keyword(s):  
Repetitive Dna ◽  
Satellite Dna ◽  
Repeat Unit ◽  
Pericentromeric Region ◽  
Fish Analysis ◽  
Agricultural Pests ◽  
Base Pairs ◽  
Satellite Dnas ◽  
Repeat Units

Ladybird beetles (Coccinellidae) are one of the largest groups of beetles. Among them, some species are of economic interest since they can act as a biological control for some agricultural pests whereas other species are phytophagous and can damage crops. Chnootriba argus (Coccinellidae, Epilachnini) has large heterochromatic pericentromeric blocks on all chromosomes, including both sexual chromosomes. Classical digestion of total genomic DNA using restriction endonucleases failed to find the satellite DNA located on these heterochromatic regions. Cloning of C0t-1 DNA resulted in the isolation of a repetitive DNA with a repeat unit of six base pairs, TTAAAA. The amount of TTAAAA repeat in the C. argus genome was about 20%. Fluorescence in situ hybridization (FISH) analysis and digestion of chromosomes with the endonuclease Tru9I revealed that this repetitive DNA could be considered as the putative pericentromeric satellite DNA (satDNA) in this species. The presence of this satellite DNA was tested in other species of the tribe Epilachnini and it is also present in Epilachna paenulata. In both species, the TTAAAA repeat seems to be the main satellite DNA and it is located on the pericentromeric region on all chromosomes. The size of this satDNA, which has only six base pairs is unusual in Coleoptera satellite DNAs, where satDNAs usually have repeat units of a much larger size. Southern hybridization and FISH proved that this satDNA is conserved in some Epilachnini species but not in others. This result is in concordance with the controversial phylogenetic relationships among the genera of the tribe Epilachnini, where the limits between genera are unclear.

scholarly journals Human homologs of TU transposon sequences: polypurine/polypyrimidine sequence elements that can alter DNA conformation in vitro and in vivo.

1986 ◽  
Vol 6 (11) ◽  
pp. 3632-3642 ◽  
Author(s):  
B Hoffman-Liebermann ◽  
D Liebermann ◽  
A Troutt ◽  
L H Kedes ◽  
S N Cohen
Keyword(s):  
Tandem Repeats ◽  
Base Pairs ◽  
S1 Nuclease ◽  
Human Dna ◽  
Outer Domain ◽  
Sequence Elements ◽  
Dna Strands ◽  
Species Specific

We previously have shown that homologs of the outer domain segment of the inverted repeat termini (IVR-OD) of the sea urchin TU transposons are conserved among multiple eucaryotic species, including humans. We report here that two cloned human DNA IVR-OD homologs, Hut2 and Hut17, consist of a series of tandem repeats of the trimer AGG/TCC, forming segments (313 and 221 base pairs in length, respectively) of polypurine/polypyrimidine (pPu/pPy or "Puppy") asymmetry in the two DNA strands; these are punctuated at certain sites with variant trimers, which are different for the two clones. Sequences homologous to the Hut2 pPu/pPy tract exist at multiple sites in the DNA of a wide variety of eucaryotes. Hybridization of human DNA with a Hut2 probe or with a previously described chicken DNA pPu/pPy sequence indicates that pPu/pPy sequences can be grouped into families distinguishable by the extent of their homology with each probe at different hybridization stringencies. Moreover, particular pPu/pPy tracts show species-specific differences in their distribution. Both the Hut2 and Hut17 pPu/pPy tracts are cleaved by S1 nuclease when tested on supercoiled plasmids. Most if not all of the 313-base-pair Hut2 pPu/pPy tract is also sensitive to S1 in its native location in HeLa cell chromatin, indicating that the sequence contains conformational information that can be expressed in vivo. This view is supported by evidence that exogenously derived Hut2 pPu/pPy tracts introduced into mouse L cells and integrated in chromatin can assume an S1-sensitive conformation.

scholarly journals Finding Long Tandem Repeats In Long Noisy Reads

2020 ◽  
Author(s):  
Shinichi Morishita ◽  
Kazuki Ichikawa ◽  
Gene Myers
Keyword(s):  
Tandem Repeat ◽  
Error Rate ◽  
Tandem Repeats ◽  
Repeat Unit ◽  
Error Rates ◽  
De Bruijn Graph ◽  
Frequency Distributions ◽  
Sequencing Technologies ◽  
Long Reads ◽  
Repeat Expansions

Abstract Motivation Long tandem repeat expansions of more than 1000 nt have been suggested to be associated with diseases, but remain largely unexplored in individual human genomes because read lengths have been too short. However, new long-read sequencing technologies can produce single reads of 10,000 nt or more that can span such repeat expansions, although these long reads have high error rates, of 10%-20%, which complicates the detection of repetitive elements. Moreover, most traditional algorithms for finding tandem repeats are designed to find short tandem repeats (< 1000 nt) and cannot effectively handle the high error rate of long reads in a reasonable amount of time. Results Here, we report an efficient algorithm for solving this problem that takes advantage of the length of the repeat. Namely, a long tandem repeat has hundreds or thousands of approximate copies of the repeated unit, so despite the error rate, many short k-mers will be error-free in many copies of the unit. We exploited this characteristic to develop a method for first estimating regions that could contain a tandem repeat, by analyzing the k-mer frequency distributions of fixed-size windows across the target read, followed by an algorithm that assembles the k-mers of a putative region into the consensus repeat unit by greedily traversing a de Bruijn graph. Experimental results indicated that the proposed algorithm largely outperformed Tandem Repeats Finder (TRF), a widely used program for finding tandem repeats, in terms of sensitivity. Software availability https://github.com/morisUtokyo/mTR

scholarly journals Satellite DNA at the Centromere is Dispensable for Segregation Fidelity

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 469 ◽  
Author(s):  
Roberti ◽  
Bensi ◽  
Mazzagatti ◽  
Piras ◽  
Nergadze ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Satellite Dna ◽  
Tandem Repeats ◽  
Micronucleus Assay ◽  
Chromosome 11 ◽  
Chromosome 13 ◽  
Primary Fibroblasts ◽  
Mitotic Stress ◽  
And Behavior

The typical vertebrate centromeres contain long stretches of highly repeated DNA sequences (satellite DNA). We previously demonstrated that the karyotypes of the species belonging to the genus Equus are characterized by the presence of satellite-free and satellite-based centromeres and represent a unique biological model for the study of centromere organization and behavior. Using horse primary fibroblasts cultured in vitro, we compared the segregation fidelity of chromosome 11, whose centromere is satellite-free, with that of chromosome 13, which has similar size and a centromere containing long stretches of satellite DNA. The mitotic stability of the two chromosomes was compared under normal conditions and under mitotic stress induced by the spindle inhibitor, nocodazole. Two independent molecular-cytogenetic approaches were used—the interphase aneuploidy analysis and the cytokinesis-block micronucleus assay. Both assays were coupled to fluorescence in situ hybridization with chromosome specific probes in order to identify chromosome 11 and chromosome 13, respectively. In addition, we tested if the lack of centromeric satellite DNA affected chromatid cohesion under normal and stress conditions. We demonstrated that, in our system, the segregation fidelity of a chromosome is not influenced by the presence of long stretches of tandem repeats at its centromere. To our knowledge, the present study is the first analysis of the mitotic behavior of a natural satellite-free centromere.

scholarly journals Conservation of k-mer Composition and Correlation Contribution between Introns and Intergenic Regions of Animalia Genomes

Genes ◽  
2018 ◽  
Vol 9 (10) ◽  
pp. 482 ◽  
Author(s):  
Aaron Sievers ◽  
Frederik Wenz ◽  
Michael Hausmann ◽  
Georg Hildenbrand
Keyword(s):  
Dna Sequences ◽  
Tandem Repeats ◽  
Repeat Unit ◽  
Full Range ◽  
Correlation Coefficients ◽  
Strong Correlations ◽  
Sequence Structure ◽  
Conserved Sequence ◽  
Repeat Units ◽  
Intergenic Regions

In this study, we pairwise-compared multiple genome regions, including genes, exons, coding DNA sequences (CDS), introns, and intergenic regions of 39 Animalia genomes, including Deuterostomia (27 species) and Protostomia (12 species), by applying established k-mer-based (alignment-free) comparison methods. We found strong correlations between the sequence structure of introns and intergenic regions, individual organisms, and within wider phylogenetical ranges, indicating the conservation of certain structures over the full range of analyzed organisms. We analyzed these sequence structures by quantifying the contribution of different sets of DNA words to the average correlation value by decomposing the correlation coefficients with respect to these word sets. We found that the conserved structures within introns, intergenic regions, and between the two were mainly a result of conserved tandem repeats with repeat units ≤ 2 bp (e.g., (AT)n), while other conserved sequence structures, such as those found between exons and CDS, were dominated by tandem repeats with repeat unit sizes of 3 bp in length and more complex DNA word patterns. We conclude that the conservation between intron and intergenic regions indicates a shared function of these sequence structures. Also, the similar differences in conserved structures with known origin, especially to the conservation between exons and CDS resulting from DNA codons, indicate that k-mer composition-based functional properties of introns and intergenic regions may differ from those of exons and CDS.

Comparative analysis of 1.688 satellite DNA on D. melanogaster species subgroup provides new insights of its pervasive presence throughout both chromatin domains and reveals a recent horizontal transfer event.

2018 ◽  
Author(s):  
Leonardo Gomes De Lima ◽  
Gustavo C. S. Kuhn
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Analysis ◽  
X Chromosome ◽  
Satellite Dna ◽  
Horizontal Transfer ◽  
Tandem Repeats ◽  
Specific Pattern ◽  
Chromosome X ◽  
Transfer Event ◽  
Species Specific

The 1.688 satellite DNA is present in the genome of Drosophila species from the melanogaster subgroup and has never been detected in species outside this subgroup. We investigated the presence and evolution of the 1.688 satDNA in all Drosophila genomes sequenced so far. Blast searches showed that 1.688 repeats are virtually confined to species from the melanogaster subgroup. Phylogenetic analysis of ~6,500 repeats extracted from D. melanogaster , D. simulans , D. sechellia , D. yakuba and D. erecta revealed the presence of 1.688 family on heterochromatin and euchromatin of all five species. Heterochromatic copies revealed a concerted mode of evolution and a species-specific pattern. Oppositely, euchromatic copies lack species-specific or array-specific pattern. Euchromatic arrays also showed a high number of insertions on 5Kb upstream/downstream of genes and in intronic regions. Unexpectedly, we found an array with at least three full 1.688 tandem repeats in the genome of D. willistoni . These repeats were highly similar to the ones present in the chromosome X of D. melanogaster , although both species have diverged from each other more than 35Mya, suggesting that 1.688 repeats from the X chromosome of D. melanogaster moved to D. willistoni by a recent horizontal transfer event.

scholarly journals Tyrosine-Phosphorylated Ehrlichia chaffeensis and Ehrlichia canis Tandem Repeat Orthologs Contain a Major Continuous Cross-Reactive Antibody Epitope in Lysine-Rich Repeats

2011 ◽  
Vol 79 (8) ◽  
pp. 3178-3187 ◽  
Author(s):  
Jere W. McBride ◽  
Xiaofeng Zhang ◽  
Abdul Wakeel ◽  
Jeeba A. Kuriakose
Keyword(s):  
Amino Acids ◽  
Tandem Repeat ◽  
Tandem Repeats ◽  
Ehrlichia Canis ◽  
Small Subset ◽  
Ehrlichia Chaffeensis ◽  
Whole Cell ◽  
Content Type ◽  
Cell Lysates ◽  
Species Specific

ABSTRACTA small subset of major immunoreactive proteins have been identified inEhrlichia chaffeensisandEhrlichia canis, including three molecularly and immunologically characterized pairs of immunoreactive tandem repeat protein (TRP) orthologs with major continuous species-specific epitopes within acidic tandem repeats (TR) that stimulate strong antibody responses during infection. In this study, we identified a fourth major immunoreactive TR-containing ortholog pair and defined a major cross-reactive epitope in homologous nonidentical 24-amino-acid lysine-rich TRs. Antibodies from patients and dogs with ehrlichiosis reacted strongly with recombinant TR regions, and epitopes were mapped to the N-terminal TR region (18 amino acids) inE. chaffeensisand the complete TR (24 amino acids) inE. canis. Two less-dominant epitopes were mapped to adjacent glutamate/aspartate-rich and aspartate/tyrosine-rich regions in the acidic C terminus ofE. canisTRP95 but not inE. chaffeensisTRP75. Major immunoreactive proteins inE. chaffeensis(75-kDa) andE. canis(95-kD) whole-cell lysates and supernatants were identified with TR-specific antibodies. Consistent with other ehrlichial TRPs, the TRPs identified in ehrlichial whole-cell lysates and the recombinant proteins migrated abnormally slow electrophoretically a characteristic that was demonstrated with the positively charged TR and negatively charged C-terminal domains.E. chaffeensisTRP75 andE. canisTRP95 were immunoprecipitated with anti-pTyr antibody, demonstrating that they are tyrosine phosphorylated during infection of the host cell.

Suitability of loci for multiple-locus variable-number of tandem-repeats analysis of Cryptosporidium parvum for inter-laboratory surveillance and outbreak investigations

Parasitology ◽  
2016 ◽  
Vol 144 (1) ◽  
pp. 37-47 ◽  
Author(s):  
RACHEL M. CHALMERS ◽  
GUY ROBINSON ◽  
EMILY HOTCHKISS ◽  
CLAIRE ALEXANDER ◽  
SOPHIE MAY ◽  
...  
Keyword(s):  
Cryptosporidium Parvum ◽  
Tandem Repeats ◽  
Repeat Unit ◽  
Unit Length ◽  
Variable Number ◽  
Multiple Locus ◽  
Chain Reactions ◽  
Outbreak Investigations ◽  
Laboratory Surveillance

SUMMARYCryptosporidium parvum is the major cause of livestock and zoonotically-acquired human cryptosporidiosis. The ability to track sources of contamination and routes of transmission by further differentiation of isolates would assist risk assessment and outbreak investigations. Multiple-locus variable-number of tandem-repeats (VNTR) analysis provides a means for rapid characterization by fragment sizing and estimation of copy numbers, but structured, harmonized development has been lacking for Cryptosporidium spp. To investigate potential for application in C. parvum surveillance and outbreak investigations, we studied nine commonly used VNTR loci (MSA, MSD, MSF, MM5, MM18, MM19, MS9-Mallon, GP60 and TP14) for chromosome distribution, repeat unit length and heterogeneity, and flanking region proximity and conservation. To investigate performance in vitro, we compared these loci in 14 C. parvum samples by capillary electrophoresis in three laboratories. We found that many loci did not contain simple repeat units but were more complex, hindering calculations of repeat unit copy number for standardized reporting nomenclature. However, sequenced reference DNA enabled reproducible fragment sizing and inter-laboratory allele assignation based on size normalized to that of the sequenced fragments by both single round and nested polymerase chain reactions. Additional Cryptosporidium loci need to be identified and validated for robust inter-laboratory surveillance and outbreak investigations.

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