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Journal articles on the topic 'Repeat sequences'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

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1

Russ, Brendan, Friedhelm Pfeiffer, and Mike Dyall-Smith. "Halovirus HF2 Intergenic Repeat Sequences Carry Promoters." Viruses 13, no. 12 (2021): 2388. http://dx.doi.org/10.3390/v13122388.

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Halovirus HF2 was the first member of the Haloferacalesvirus genus to have its genome fully sequenced, which revealed two classes of intergenic repeat (IR) sequences: class I repeats of 58 bp in length, and class II repeats of 29 bp in length. Both classes of repeat contain AT-rich motifs that were conjectured to represent promoters. In the present study, nine IRs were cloned upstream of the bgaH reporter gene, and all displayed promoter activity, providing experimental evidence for the previous conjecture. Comparative genomics showed that IR sequences and their relative genomic positions were

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2

Baum, Bernard R., and D. A. Johnson. "The molecular diversity of the 5S rRNA gene in barley (Hordeum vulgare)." Genome 37, no. 6 (1994): 992–98. http://dx.doi.org/10.1139/g94-140.

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The 5S rDNA genes from several accessions of cultivated barley, Hordeum vulgare L., were amplified by the polymerase chain reaction, cloned, and sequenced. Analysis of the aligned sequences, followed by principal coordinate analysis, support the recognition of at least two distinct classes of 5S rDNA genes. The short repeat class corresponds to the 300-bp tandem repeat defined by E.V. Ananiev as containing several TAG repeating units. The long repeat class contains long tandem repeats and lacks the TAG repeating unit. Sequences in each class can be further subdivided, with the long repeat clas

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3

Whiteford, Nava E., Niall J. Haslam, Gerald Weber, Adam Prügel-Bennett, Jonathan W. Essex, and Cameron Neylon. "Visualizing the Repeat Structure of Genomic Sequences." Complex Systems 17, no. 4 (2008): 381–98. http://dx.doi.org/10.25088/complexsystems.17.4.381.

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Repeats are a common feature of genomic sequences and much remains to be understood of their origin and structure. The identification of repeated strings in genomic sequences is therefore of importance for a variety of applications in biology. In this paper a new method for finding all repeats and visualizing them in a two-dimensional plot is presented. The method is first applied to a set of constructed sequences in order to develop a comparative framework. Several complete genomes are then analyzed, including the whole human genome. The technique reveals the complex repeat structure of genom

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Hannan, Anthony J. "Expanding horizons of tandem repeats in biology and medicine: Why ‘genomic dark matter’ matters." Emerging Topics in Life Sciences 7, no. 3 (2023): 239–47. http://dx.doi.org/10.1042/etls20230075.

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Approximately half of the human genome includes repetitive sequences, and these DNA sequences (as well as their transcribed repetitive RNA and translated amino-acid repeat sequences) are known as the repeatome. Within this repeatome there are a couple of million tandem repeats, dispersed throughout the genome. These tandem repeats have been estimated to constitute ∼8% of the entire human genome. These tandem repeats can be located throughout exons, introns and intergenic regions, thus potentially affecting the structure and function of tandemly repetitive DNA, RNA and protein sequences. Over m

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5

ZHU, YONG, JOAN E. STRASSMANN, and DAVID C. QUELLER. "Insertions, substitutions, and the origin of microsatellites." Genetical Research 76, no. 3 (2000): 227–36. http://dx.doi.org/10.1017/s001667230000478x.

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This paper uses data from the Human Gene Mutation Database to contrast two hypotheses for the origin of short DNA repeats: substitutions and insertions that duplicate adjacent sequences. Because substitutions are much more common than insertions, they are the dominant source of new 2-repeat loci. Insertions are rarer, but over 70% of the 2–4 base insertion mutations are duplications of adjacent sequences, and over half of these generate new repeat regions. Insertions contribute fewer new repeat loci than substitutions, but their relative importance increases rapidly with repeat number so that

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6

Luo, Xiaomei, Charlene P. Wight, Yonghong Zhou, and Nicholas A. Tinker. "Characterization of chromosome-specific genomic DNA from hexaploid oat." Genome 55, no. 4 (2012): 265–68. http://dx.doi.org/10.1139/g2012-011.

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We have sequenced, assembled, and characterized a set of complexity-reduced genomic clones derived from a chromosome 18D-specific library from hexaploid oat ( Avena sativa L.). Sequences from 314 clones were assembled into 99 contigs of identical or nearly identical sequence. The Censor tool was used to identify similarity to known and characterized repeat sequences in RepBase. Eight repeat classes were scattered throughout 50 contigs, with most repeats belonging to seven transposon and retrotransposon classes. After accounting for known repeats, additional matches to orthologous genes from ot

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7

Yu, Xue-jie, Jere W. McBride, C. Marcela Diaz, and David H. Walker. "Molecular Cloning and Characterization of the 120-Kilodalton Protein Gene of Ehrlichia canis and Application of the Recombinant 120-Kilodalton Protein for Serodiagnosis of Canine Ehrlichiosis." Journal of Clinical Microbiology 38, no. 1 (2000): 369–74. http://dx.doi.org/10.1128/jcm.38.1.369-374.2000.

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ABSTRACT The 120-kDa outer membrane protein (p120) is a potential adhesin of Ehrlichia chaffeensis , and recombinant p120 is very useful for serodiagnosis of human monocytotropic ehrlichiosis. The analogous gene of p120 in Ehrlichia canis was cloned, sequenced, and expressed. Like the E. chaffeensis p120, the E. canis p120 contains tandem repeat units. However, neither the repeat number nor the amino acid sequences in the repeats are identical in the two Ehrlichia species. The repeat units are hydrophilic and by probability analysis are predicted to be surface exposed in both species. The repe

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8

Franck, Jens P. C., and Jonathan M. Wright. "Conservation of a satellite DNA sequence (SATB) in the tilapiine and haplochromine genome (Pisces: Cichlidae)." Genome 36, no. 1 (1993): 187–94. http://dx.doi.org/10.1139/g93-025.

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We have cloned and sequenced a 1900-bp EcoRI fragment (SATB) from the tilapiine fish Oreochromis niloticus. The SATB sequence is highly reiterated in the tilapiine genome and organized in long tandem arrays. A 760-bp HindIII fragment, an internal component of SATB, has also been cloned and sequenced from the related tilapiine species Oreochromis hornorum. Hybridization of the radiolabeled 760-bp HindIII repeat detected the presence of the SATB repeat in the genomes of several tilapiine species as well as the haplochromine species Haplochromis (Protomelas) similis. The 760-bp HindIII fragment d

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9

Ojkic, Davor, and éva Nagy. "The complete nucleotide sequence of fowl adenovirus type 8." Microbiology 81, no. 7 (2000): 1833–37. http://dx.doi.org/10.1099/0022-1317-81-7-1833.

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The fowl adenovirus type 8 (FAdV-8) genome was sequenced and found to be 45063 nucleotides in length, the longest adenovirus (AdV) genome for which the complete nucleotide sequence has been determined so far. No regions homologous to early regions 1, 3 and 4 (E1, E3 and E4) of mastadenoviruses were recognized. Gene homologues for early region 2 (E2) proteins, intermediate protein IVa2 and late proteins were found by their similarities to protein sequences from other AdVs. However, sequences homologous to intermediate protein IX and late protein V could not be identified. Sequences for virus-as

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10

Biessmann, Harald, and James M. Mason. "Telomeric repeat sequences." Chromosoma 103, no. 3 (1994): 154–61. http://dx.doi.org/10.1007/s004120050019.

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11

Biessmann, Harald, and James M. Mason. "Telomeric repeat sequences." Chromosoma 103, no. 3 (1994): 154–61. http://dx.doi.org/10.1007/bf00368007.

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12

Wilkinson, Gerald S., Frieder Mayer, Gerald Kerth, and Barbara Petri. "Evolution of Repeated Sequence Arrays in the D-Loop Region of Bat Mitochondrial DNA." Genetics 146, no. 3 (1997): 1035–48. http://dx.doi.org/10.1093/genetics/146.3.1035.

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Analysis of mitochondrial DNA control region sequences from 41 species of bats representing 11 families revealed that repeated sequence arrays near the tRNA-Pro gene are present in all vespertilionine bats. Across 18 species tandem repeats varied in size from 78 to 85 bp and contained two to nine repeats. Heteroplasmy ranged from 15% to 63%. Fewer repeats among heteroplasmic than homoplasmic individuals in a species with up to nine repeats indicates selection may act against long arrays. A lower limit of two repeats and more repeats among heteroplasmic than homoplasmic individuals in two speci

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13

Gyohda, Atsuko, and Teruya Komano. "Purification and Characterization of the R64 Shufflon-Specific Recombinase." Journal of Bacteriology 182, no. 10 (2000): 2787–92. http://dx.doi.org/10.1128/jb.182.10.2787-2792.2000.

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ABSTRACT The shufflon, a multiple DNA inversion system in plasmid R64, consists of four invertible DNA segments which are separated and flanked by seven 19-bp repeat sequences. The product of a site-specific recombinase gene, rci, promotes site-specific recombination between any two of the inverted 19-bp repeat sequences of the shufflon. To analyze the molecular mechanism of this recombination reaction, Rci protein was overproduced and purified. The purified Rci protein promoted the in vitro recombination reaction between the inverted 19-bp repeats of supercoiled DNA of a plasmid carrying segm

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14

Smith, Kirby D., Keith E. Young, C. Conover Talbot, and Barbara J. Schmeckpeper. "Repeated DNA of the human Y chromosome." Development 101, Supplement (1987): 77–92. http://dx.doi.org/10.1242/dev.101.supplement.77.

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A significant fraction of the human Y chromosome is composed of DNA sequences which have homologues on the X chromosome or autosomes in humans and non-human primates. However, most human Ychromosome sequences so far examined do not have homologues on the Y chromosomes of other primates. This observation suggests that a significant proportion of the human Y chromosome is composed of sequences that have acquired their Y-chromosome association since humans diverged from other primates. More than 50 % of the human Y chromosome is composed of a variety of repeated DNAs which, with one known excepti

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15

RIVALS, ERIC. "A SURVEY ON ALGORITHMIC ASPECTS OF TANDEM REPEATS EVOLUTION." International Journal of Foundations of Computer Science 15, no. 02 (2004): 225–57. http://dx.doi.org/10.1142/s012905410400239x.

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Local repetitions in genomes are called tandem repeats. A tandem repeat contains multiple, but slightly different copies of a repeated unit. It changes over time as the copies are altered by mutations, when additional copies are created by amplification of an existing copy, or when a copy is removed by contraction. Theses changes let tandem repeats evolve dynamically. From this statement follow two problems. TANDEM REPEAT HISTORY aims at recovering the history of amplifications and mutations that produced the tandem repeat sequence given as input. Given the tandem repeat sequences at the same

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16

Trees, David L., Abbigail J. Schultz, and Joan S. Knapp. "Use of the Neisserial Lipoprotein (Lip) for Subtyping Neisseria gonorrhoeae." Journal of Clinical Microbiology 38, no. 8 (2000): 2914–16. http://dx.doi.org/10.1128/jcm.38.8.2914-2916.2000.

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The pathogenic Neisseria species N. meningitidis and N. gonorrhoeae possess an outer membrane lipoprotein, designated Lip, which is present in all strains tested. The predicted protein sequence of Lip consists of a consensus AAEAP amino acid repeat. The objective of this study was to determine the feasibility of using the Lip repeat number and sequence for subtyping of Neisseria gonorrhoeae. Thelip genes of each isolate were amplified by PCR and sequenced to determine the repeat number and sequence. Among the 46 strains we examined, eight different Lip repeat numbers were identified, with leng

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17

Miret, J. J., L. Pessoa-Brandão, and R. S. Lahue. "Instability of CAG and CTG trinucleotide repeats in Saccharomyces cerevisiae." Molecular and Cellular Biology 17, no. 6 (1997): 3382–87. http://dx.doi.org/10.1128/mcb.17.6.3382.

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A quantitative genetic assay was developed to monitor alterations in tract lengths of trinucleotide repeat sequences in Saccharomyces cerevisiae. Insertion of (CAG)50 or (CTG)50 repeats into a promoter that drives expression of the reporter gene ADE8 results in loss of expression and white colony color. Contractions within the trinucleotide sequences to repeat lengths of 8 to 38 restore functional expression of the reporter, leading to red colony color. Reporter constructs including (CAG)50 or (CTG)50 repeat sequences were integrated into the yeast genome, and the rate of red colony formation

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18

Falistocco, E., V. Passeri, and G. Marconi. "Investigations of 5S rDNA of Vitis vinifera L.: sequence analysis and physical mapping." Genome 50, no. 10 (2007): 927–38. http://dx.doi.org/10.1139/g07-070.

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Here we report the first results of a study of 5S rDNA of Vitis vinifera . 5S rDNA sequences from seven genotypes were amplified by PCR, cloned, and sequenced. Three types of repeats were found. Two variants, denominated long repeat and short repeat, appeared to be the main components of the 5S rDNA of this species, since they were found in all genotypes analyzed. They differed markedly from each other in both the length and the nucleotide composition of the spacers. The third variant, classified as DEL short repeat, differs from the short repeat owing to a large deletion in the spacer region.

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Dvořák, J., D. Jue, and M. Lassner. "Homogenization of Tandemly Repeated Nucleotide Sequences by Distance-Dependent Nucleotide Sequence Conversion." Genetics 116, no. 3 (1987): 487–98. http://dx.doi.org/10.1093/genetics/116.3.487.

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ABSTRACT Previous work revealed that recurrent mutations (=mutation occurring more than once) in the tandemly repeated arrays present in nontranscribed spacers (NTS) of ribosomal RNA genes (rDNA) are clustered, i.e., they most frequently occur in repeats with adjacent or alternate distribution. A possible explanation is that the likelihood of heteroduplex formation, a prerequisite of gene conversion, decreases with the distance between repeats. To test this possibility, evolution of an array of 11 initially homogeneous repeats was computer simulated using three models, two assuming that the li

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20

Peng, Xu, Kim Brügger, Biao Shen, Lanming Chen, Qunxin She, and Roger A. Garrett. "Genus-Specific Protein Binding to the Large Clusters of DNA Repeats (Short Regularly Spaced Repeats) Present in Sulfolobus Genomes." Journal of Bacteriology 185, no. 8 (2003): 2410–17. http://dx.doi.org/10.1128/jb.185.8.2410-2417.2003.

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ABSTRACT Short regularly spaced repeats (SRSRs) occur in multiple large clusters in archaeal chromosomes and as smaller clusters in some archaeal conjugative plasmids and bacterial chromosomes. The sequence, size, and spacing of the repeats are generally constant within a cluster but vary between clusters. For the crenarchaeon Sulfolobus solfataricus P2, the repeats in the genome fall mainly into two closely related sequence families that are arranged in seven clusters containing a total of 441 repeats which constitute ca. 1% of the genome. The Sulfolobus conjugative plasmid pNOB8 contains a s

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21

Rubinsztein, David C., Bill Amos, and Gillian Cooper. "Microsatellite and trinucleotide-repeat evolution: evidence for mutational bias and different rates of evolution in different lineages." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 354, no. 1386 (1999): 1095–99. http://dx.doi.org/10.1098/rstb.1999.0465.

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Microsatellites are stretches of repetitive DNA, where individual repeat units comprise one to six bases. These sequences are often highly polymorphic with respect to repeat number and include trinucleotide repeats, which are abnormally expanded in a number of diseases. It has been widely assumed that microsatellite loci are as likely to gain and lose repeats when they mutate. In this review, we present population genetic and empirical data arguing that microsatellites, including normal alleles at trinucleotide repeat disease loci, are more likely to expand in length when they mutate. In addit

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22

Feng, Suping, Helin Tong, You Chen, et al. "Development of Pineapple Microsatellite Markers and Germplasm Genetic Diversity Analysis." BioMed Research International 2013 (2013): 1–11. http://dx.doi.org/10.1155/2013/317912.

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Two methods were used to develop pineapple microsatellite markers. Genomic library-based SSR development: using selectively amplified microsatellite assay, 86 sequences were generated from pineapple genomic library. 91 (96.8%) of the 94 Simple Sequence Repeat (SSR) loci were dinucleotide repeats (39 AC/GT repeats and 52 GA/TC repeats, accounting for 42.9% and 57.1%, resp.), and the other three were mononucleotide repeats. Thirty-six pairs of SSR primers were designed; 24 of them generated clear bands of expected sizes, and 13 of them showed polymorphism. EST-based SSR development: 5659 pineapp

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23

Fishel, B., H. Amstutz, M. Baum, J. Carbon, and L. Clarke. "Structural organization and functional analysis of centromeric DNA in the fission yeast Schizosaccharomyces pombe." Molecular and Cellular Biology 8, no. 2 (1988): 754–63. http://dx.doi.org/10.1128/mcb.8.2.754-763.1988.

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Centromeric DNA in the fission yeast Schizosaccharomyces pombe was isolated by chromosome walking and by field inversion gel electrophoretic fractionation of large genomic DNA restriction fragments. The centromere regions of the three chromosomes were contained on three SalI fragments (120 kilobases [kb], chromosome III; 90 kb, chromosome II; and 50 kb, chromosome I). Each fragment contained several repetitive DNA sequences, including repeat K (6.4 kb), repeat L (6.0 kb), and repeat B, that occurred only in the three centromere regions. On chromosome II, these repeats were organized into a 35-

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Fishel, B., H. Amstutz, M. Baum, J. Carbon, and L. Clarke. "Structural organization and functional analysis of centromeric DNA in the fission yeast Schizosaccharomyces pombe." Molecular and Cellular Biology 8, no. 2 (1988): 754–63. http://dx.doi.org/10.1128/mcb.8.2.754.

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Centromeric DNA in the fission yeast Schizosaccharomyces pombe was isolated by chromosome walking and by field inversion gel electrophoretic fractionation of large genomic DNA restriction fragments. The centromere regions of the three chromosomes were contained on three SalI fragments (120 kilobases [kb], chromosome III; 90 kb, chromosome II; and 50 kb, chromosome I). Each fragment contained several repetitive DNA sequences, including repeat K (6.4 kb), repeat L (6.0 kb), and repeat B, that occurred only in the three centromere regions. On chromosome II, these repeats were organized into a 35-

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Li, Zhan, Xiong Liu, Nianzhi Ning, Tao Li, and Hui Wang. "Diversity, Distribution, and Chromosomal Rearrangements of TRIP1 Repeat Sequences in Escherichia coli." Genes 15, no. 2 (2024): 236. http://dx.doi.org/10.3390/genes15020236.

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The bacterial genome contains numerous repeated sequences that greatly affect its genomic plasticity. The Escherichia coli K-12 genome contains three copies of the TRIP1 repeat sequence (TRIP1a, TRIP1b, and TRIP1c). However, the diversity, distribution, and role of the TRIP1 repeat sequence in the E. coli genome are still unclear. In this study, after screening 6725 E. coli genomes, the TRIP1 repeat was found in the majority of E. coli strains (96%: 6454/6725). The copy number and direction of the TRIP1 repeat sequence varied in each genome. Overall, 2449 genomes (36%: 2449/6725) had three cop

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Stupar, Robert M., Junqi Song, Ahmet L. Tek, Zhukuan Cheng, Fenggao Dong, and Jiming Jiang. "Highly Condensed Potato Pericentromeric Heterochromatin Contains rDNA-Related Tandem Repeats." Genetics 162, no. 3 (2002): 1435–44. http://dx.doi.org/10.1093/genetics/162.3.1435.

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Abstract The heterochromatin in eukaryotic genomes represents gene-poor regions and contains highly repetitive DNA sequences. The origin and evolution of DNA sequences in the heterochromatic regions are poorly understood. Here we report a unique class of pericentromeric heterochromatin consisting of DNA sequences highly homologous to the intergenic spacer (IGS) of the 18S•25S ribosomal RNA genes in potato. A 5.9-kb tandem repeat, named 2D8, was isolated from a diploid potato species Solanum bulbocastanum. Sequence analysis indicates that the 2D8 repeat is related to the IGS of potato rDNA. Thi

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Bornet, B., C. Muller, F. Paulus, and M. Branchard. "Highly informative nature of inter simple sequence repeat (ISSR) sequences amplified using tri- and tetra-nucleotide primers from DNA of cauliflower (Brassica oleracea var. botrytis L.)." Genome 45, no. 5 (2002): 890–96. http://dx.doi.org/10.1139/g02-061.

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Inter simple sequence repeat (ISSR) sequences as molecular markers can lead to the detection of polymorphism and also be a new approach to the study of SSR distribution and frequency. In this study, ISSR amplification with nonanchored primer was performed in closely related cauliflower lines. Fourty-four different amplified fragments were sequenced. Sequences of PCR products are delimited by the expected motifs and number of repeats, which validates the ISSR nonanchored primer amplification technique. DNA and amino acids homology search between internal sequences and databases (i) show that th

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Hogan, N. C., F. Slot, K. L. Traverse, J. C. Garbe, W. G. Bendena, and M. L. Pardue. "Stability of tandem repeats in the Drosophila melanogaster Hsr-omega nuclear RNA." Genetics 139, no. 4 (1995): 1611–21. http://dx.doi.org/10.1093/genetics/139.4.1611.

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Abstract The Drosophila melanogaster Hsr-omega locus produces a nuclear RNA containing &gt; 5 kb of tandem repeat sequences. These repeats are unique to Hsr-omega and show concerted evolution similar to that seen with classical satellite DNAs. In D. melanogaster the monomer is approximately 280 bp. Sequences of 19 1/2 monomers differ by 8 +/- 5% (mean +/- SD), when all pairwise comparisons are considered. Differences are single nucleotide substitutions and 1-3 nucleotide deletions/insertions. Changes appear to be randomly distributed over the repeat unit. Outer repeats do not show the decr

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Sultana, Nusrat, Samsunnahar Oishi, Tanzena Tanny, and Mohammad Abdur Rahim. "GENETIC DIVERSITY ANALYSIS OF CULTIVATED AND WILD MANGOES FROM BANGLADESH BASED ON PCR AMPLIFICATION PATTERN OF TANDEMLY ORGANIZED REPEAT SEQUENCES." Journal of Applied Biological Sciences 17, no. 3 (2023): 510–19. https://doi.org/10.71336/jabs.1246.

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Mangifera is an economically important genus mainly because of the delicious fruit produced by many species of this genus. Wild species available in Bangladesh of this genus are often misidentified and have ambiguous taxonomic leveling, due to the difficulty of getting the appropriate sample for plant identification. Tandem repeat diversity was analyzed from the Mangifera genome, to understand their impact on the genomic diversity of different species and cultivars available in Bangladesh. We use tandem repeats amplification pattern for mango diversity analysis because of the fact that satelli

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Heller, M., E. Flemington, E. Kieff, and P. Deininger. "Repeat arrays in cellular DNA related to the Epstein-Barr virus IR3 repeat." Molecular and Cellular Biology 5, no. 3 (1985): 457–65. http://dx.doi.org/10.1128/mcb.5.3.457-465.1985.

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We isolated clones and determined the sequence of portions of mouse and human cellular DNA which cross-hybridize strongly with the IR3 repetitive region of Epstein-Barr virus. The sequences were found to be tandem arrays of a simple sequence based on the triplet GGA, very similar to the IR3 repeat. The cellular repeats have distinct differences from the viral repeat region, however, and their sequences do not appear capable of being translated into a purely glycine-plus-alanine protein domain like the portion of the Epstein-Barr nuclear antigen coded by IR3. Although the relationship between I

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Heller, M., E. Flemington, E. Kieff, and P. Deininger. "Repeat arrays in cellular DNA related to the Epstein-Barr virus IR3 repeat." Molecular and Cellular Biology 5, no. 3 (1985): 457–65. http://dx.doi.org/10.1128/mcb.5.3.457.

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We isolated clones and determined the sequence of portions of mouse and human cellular DNA which cross-hybridize strongly with the IR3 repetitive region of Epstein-Barr virus. The sequences were found to be tandem arrays of a simple sequence based on the triplet GGA, very similar to the IR3 repeat. The cellular repeats have distinct differences from the viral repeat region, however, and their sequences do not appear capable of being translated into a purely glycine-plus-alanine protein domain like the portion of the Epstein-Barr nuclear antigen coded by IR3. Although the relationship between I

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Bowater, Richard P., Natália Bohálová, and Václav Brázda. "Interaction of Proteins with Inverted Repeats and Cruciform Structures in Nucleic Acids." International Journal of Molecular Sciences 23, no. 11 (2022): 6171. http://dx.doi.org/10.3390/ijms23116171.

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Cruciforms occur when inverted repeat sequences in double-stranded DNA adopt intra-strand hairpins on opposing strands. Biophysical and molecular studies of these structures confirm their characterization as four-way junctions and have demonstrated that several factors influence their stability, including overall chromatin structure and DNA supercoiling. Here, we review our understanding of processes that influence the formation and stability of cruciforms in genomes, covering the range of sequences shown to have biological significance. It is challenging to accurately sequence repetitive DNA

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Barik, Sailen. "The Nature and Arrangement of Pentatricopeptide Domains and the Linker Sequences Between Them." Bioinformatics and Biology Insights 14 (January 2020): 117793222090643. http://dx.doi.org/10.1177/1177932220906434.

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The tricopeptide (amino acid number in the 30s) repeats constitute some of the most common amino acid repeats in proteins of diverse organisms. The most important representatives of this class are the 34-residue and 35-residue repeats, eponymously known as tetratricopeptide repeat (TPR) and pentatricopeptide repeat (PPR), respectively. The unit motif of both consists of a pair of alpha helices. As members of the large, all-helical repeat classes, TPR and PPR share structural similarities, but also play specific roles in protein function. In this study, a comprehensive bioinformatic analysis of

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Polley, Spencer D., Kevin K. A. Tetteh, David R. Cavanagh, et al. "Repeat Sequences in Block 2 of Plasmodium falciparum Merozoite Surface Protein 1 Are Targets of Antibodies Associated with Protection from Malaria." Infection and Immunity 71, no. 4 (2003): 1833–42. http://dx.doi.org/10.1128/iai.71.4.1833-1842.2003.

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ABSTRACT Human antibodies to the block 2 region of Plasmodium falciparum merozoite surface protein 1 (MSP1) are associated with a reduced prospective risk of clinical malaria. Block 2 is highly polymorphic, but all known alleles can be grouped into three major types. Two of these types (the K1-like and MAD20-like types) contain type-specific sequences (found in all alleles of a particular type) that flank polymorphic tripeptide repeats. These repeats contain both type-specific and subtype-specific sequences. To evaluate the antibody recognition of these parts of block 2, a new panel of six rec

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Baum, M., V. K. Ngan, and L. Clarke. "The centromeric K-type repeat and the central core are together sufficient to establish a functional Schizosaccharomyces pombe centromere." Molecular Biology of the Cell 5, no. 7 (1994): 747–61. http://dx.doi.org/10.1091/mbc.5.7.747.

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The DNA requirements for centromere function in fission yeast have been investigated using a minichromosome assay system. Critical elements of Schizosaccharomyces pombe centromeric DNA are portions of the centromeric central core and sequences within a 2.1-kilobase segment found on all three chromosomes as part of the K-type (K/K"/dg) centromeric repeat. The S. pombe centromeric central core contains DNA sequences that appear functionally redundant, and the inverted repeat motif that flanks the central core in all native fission yeast centromeres is not essential for centromere function in cir

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Macas, Jiří, Pavel Neumann, Petr Novák, and Jiming Jiang. "Global sequence characterization of rice centromeric satellite based on oligomer frequency analysis in large-scale sequencing data." Bioinformatics 26, no. 17 (2010): 2101–8. http://dx.doi.org/10.1093/bioinformatics/btq343.

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Abstract Motivation: Satellite DNA makes up significant portion of many eukaryotic genomes, yet it is relatively poorly characterized even in extensively sequenced species. This is, in part, due to methodological limitations of traditional methods of satellite repeat analysis, which are based on multiple alignments of monomer sequences. Therefore, we employed an alternative, alignment-free, approach utilizing k-mer frequency statistics, which is in principle more suitable for analyzing large sets of satellite repeat data, including sequence reads from next generation sequencing technologies. R

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Nusrat, Sultana, Oishi Samsunnahar, Tanny Tanzena, and Abdur Rahim Mohammad. "GENETIC DIVERSITY ANALYSIS OF CULTIVATED AND WILD MANGOES FROM BANGLADESH BASED ON PCR AMPLIFICATION PATTERN OF TANDEMLY ORGANIZED REPEAT SEQUENCES." Journal of Applied Biological Sciences 17, no. 3 (2023): 510–19. https://doi.org/10.5281/zenodo.10035513.

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<i>Mangifera</i> is an economically important genus mainly because of the delicious fruit produced by many species of this genus. Wild species available in Bangladesh of this genus are often misidentified and have ambiguous taxonomic leveling, due to the difficulty of getting the appropriate sample for plant identification. Tandem repeat diversity was analyzed from the <i>Mangifera</i> genome, to understand their impact on the genomic diversity of different species and cultivars available in Bangladesh. We use tandem repeats amplification pattern for mango diversity analysis because of the fac

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38

Cohen, J. B., D. Liebermann, and L. Kedes. "Tsp transposons: a heterogeneous family of mobile sequences in the genome of the sea urchin Strongylocentrotus purpuratus." Molecular and Cellular Biology 5, no. 10 (1985): 2814–25. http://dx.doi.org/10.1128/mcb.5.10.2814-2825.1985.

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In the preceding paper (J.B. Cohen, B. Hoffman-Liebermann, and L. Kedes, Mol. Cell. Biol., 5:2804-2813, 1985), we described the nucleotide sequence of ISTU4, which is a member of a new family of repetitive sequences, the Tsp family, present in a higher eucaryote, the sea urchin Strongylocentrotus purpuratus. We provided evidence that individual members of this family can act as transposable elements. Here we describe our structural analysis of the Tsp element family, which numbers about 1,000 members per haploid genome. Hybridization and nucleotide sequence analysis of several genomic Tsp clon

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39

Cohen, J. B., D. Liebermann, and L. Kedes. "Tsp transposons: a heterogeneous family of mobile sequences in the genome of the sea urchin Strongylocentrotus purpuratus." Molecular and Cellular Biology 5, no. 10 (1985): 2814–25. http://dx.doi.org/10.1128/mcb.5.10.2814.

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In the preceding paper (J.B. Cohen, B. Hoffman-Liebermann, and L. Kedes, Mol. Cell. Biol., 5:2804-2813, 1985), we described the nucleotide sequence of ISTU4, which is a member of a new family of repetitive sequences, the Tsp family, present in a higher eucaryote, the sea urchin Strongylocentrotus purpuratus. We provided evidence that individual members of this family can act as transposable elements. Here we describe our structural analysis of the Tsp element family, which numbers about 1,000 members per haploid genome. Hybridization and nucleotide sequence analysis of several genomic Tsp clon

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40

Mizuguchi, Takeshi, Tomoko Toyota, Satoko Miyatake, et al. "Complete sequencing of expanded SAMD12 repeats by long-read sequencing and Cas9-mediated enrichment." Brain 144, no. 4 (2021): 1103–17. http://dx.doi.org/10.1093/brain/awab021.

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Abstract A pentanucleotide TTTCA repeat insertion into a polymorphic TTTTA repeat element in SAMD12 causes benign adult familial myoclonic epilepsy. Although the precise determination of the entire SAMD12 repeat sequence is important for molecular diagnosis and research, obtaining this sequence remains challenging when using conventional genomic/genetic methods, and even short-read and long-read next-generation sequencing technologies have been insufficient. Incomplete information regarding expanded repeat sequences may hamper our understanding of the pathogenic roles played by varying numbers

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41

Pidpala, O. V., and L. L. Lukash. "Distribution of the macaques genus-specific Alu repeat AluMacYa3 in the MGMT gene orthologs of old world monkeys." Faktori eksperimental'noi evolucii organizmiv 32 (September 1, 2023): 148–54. http://dx.doi.org/10.7124/feeo.v32.1552.

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Aim. To follow the distribution and evolution of the macaques genus-specific Alu repeat AluMacYa3 in Cercopithecidae MGMT gene orthologs. Methods. The homology between nucleotide sequences has been determined by the BLAST 2.6.1 program. The results of the search and identification of MGE have been obtained by the CENSOR program. Results. It has been shown on the example of Cercopithecidae MGMT gene orthologs that the genus-specific Alu repeat AluMacYa3 is present not only in the intron sequences of macaques, but also in other representatives of the Old World monkeys and in its evolutionary his

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Sui, Xin, Fu Juan Feng, Dan Zhao, Min Min Chen, and Shi Jie Han. "Development of Pinus koraiensis SSR Primers Based on EST-SSR Information Technology." Advanced Materials Research 183-185 (January 2011): 259–66. http://dx.doi.org/10.4028/www.scientific.net/amr.183-185.259.

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A total 408 SSRs were distributed in 18,181 ESTs sequences in Pinaceae in NCBI (National Center for Biotechnology Information) searched by SSRIT software, accounting for 2.24% of the whole EST sequences. We designed 132 pairs of EST-SSR primers by primer3. Of the designed 132 pairs, 29 pairs were able to produce an amplification product in the 10 Pinus koraiensis DNA samples, but only five primers in the 29 pairs exhibited polymorphism. Dinucleotide repeats were the most common repeat class. The repeated primitives of dinucleotide were 10, accounting for 52.73% of the whole repeated primitives

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Maurer, D. J., B. L. O'Callaghan, and D. M. Livingston. "Orientation dependence of trinucleotide CAG repeat instability in Saccharomyces cerevisiae." Molecular and Cellular Biology 16, no. 12 (1996): 6617–22. http://dx.doi.org/10.1128/mcb.16.12.6617.

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To examine the chromosomal stability of repetitions of the trinucleotide CAG, we have cloned CAG repeat tracts onto the 3' end of the Saccharomyces cerevisiae ADE2 gene and placed the appended gene into the ARO2 locus of chromosome VII. Examination of chromosomal DNA from sibling colonies arising from clonal expansion of strains harboring repeat tracts showed that repeat tracts often change in length. Most changes in tract length are decreases, but rare increases also occur. Longer tracts are more unstable than smaller tracts. The most unstable tracts, of 80 to 90 repeats, undergo changes at r

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Saint, R. B., R. L. Coppel, A. F. Cowman, et al. "Changes in repeat number, sequence, and reading frame in S-antigen genes of Plasmodium falciparum." Molecular and Cellular Biology 7, no. 8 (1987): 2968–73. http://dx.doi.org/10.1128/mcb.7.8.2968-2973.1987.

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The S antigens from different isolates of Plasmodium falciparum exhibit extensive size, charge, and serological diversity. We show here that the S-antigen genes behave as multiple alleles of a single locus. The size heterogeneity results from different numbers, lengths, and/or sequences of tandem repeat units encoded within the S-antigen genes. Two genes studied here encode antigenically different S antigens but nevertheless have closely related tandem repeat sequences. We show that antigenic differences can arise because repeats are translated in different reading frames.

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Saint, R. B., R. L. Coppel, A. F. Cowman, et al. "Changes in repeat number, sequence, and reading frame in S-antigen genes of Plasmodium falciparum." Molecular and Cellular Biology 7, no. 8 (1987): 2968–73. http://dx.doi.org/10.1128/mcb.7.8.2968.

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The S antigens from different isolates of Plasmodium falciparum exhibit extensive size, charge, and serological diversity. We show here that the S-antigen genes behave as multiple alleles of a single locus. The size heterogeneity results from different numbers, lengths, and/or sequences of tandem repeat units encoded within the S-antigen genes. Two genes studied here encode antigenically different S antigens but nevertheless have closely related tandem repeat sequences. We show that antigenic differences can arise because repeats are translated in different reading frames.

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Murray, A. W., T. E. Claus, and J. W. Szostak. "Characterization of two telomeric DNA processing reactions in Saccharomyces cerevisiae." Molecular and Cellular Biology 8, no. 11 (1988): 4642–50. http://dx.doi.org/10.1128/mcb.8.11.4642-4650.1988.

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We have investigated two reactions that occur on telomeric sequences introduced into Saccharomyces cerevisiae cells by transformation. The elongation reaction added repeats of the yeast telomeric sequence C1-3A to telomeric sequences at the end of linear DNA molecules. The reaction worked on the Tetrahymena telomeric sequence C4A2 and also on the simple repeat CA. The reaction was orientation specific: it occurred only when the GT-rich strand ran 5' to 3' towards the end of the molecule. Telomere elongation occurred by non-template-directed DNA synthesis rather than any type of recombination w

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47

Murray, A. W., T. E. Claus, and J. W. Szostak. "Characterization of two telomeric DNA processing reactions in Saccharomyces cerevisiae." Molecular and Cellular Biology 8, no. 11 (1988): 4642–50. http://dx.doi.org/10.1128/mcb.8.11.4642.

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Abstract:

We have investigated two reactions that occur on telomeric sequences introduced into Saccharomyces cerevisiae cells by transformation. The elongation reaction added repeats of the yeast telomeric sequence C1-3A to telomeric sequences at the end of linear DNA molecules. The reaction worked on the Tetrahymena telomeric sequence C4A2 and also on the simple repeat CA. The reaction was orientation specific: it occurred only when the GT-rich strand ran 5' to 3' towards the end of the molecule. Telomere elongation occurred by non-template-directed DNA synthesis rather than any type of recombination w

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48

Waye, J. S., S. B. England, and H. F. Willard. "Genomic organization of alpha satellite DNA on human chromosome 7: evidence for two distinct alphoid domains on a single chromosome." Molecular and Cellular Biology 7, no. 1 (1987): 349–56. http://dx.doi.org/10.1128/mcb.7.1.349-356.1987.

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A complete understanding of chromosomal disjunction during mitosis and meiosis in complex genomes such as the human genome awaits detailed characterization of both the molecular structure and genetic behavior of the centromeric regions of chromosomes. Such analyses in turn require knowledge of the organization and nature of DNA sequences associated with centromeres. The most prominent class of centromeric DNA sequences in the human genome is the alpha satellite family of tandemly repeated DNA, which is organized as distinct chromosomal subsets. Each subset is characterized by a particular mult

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49

Waye, J. S., S. B. England, and H. F. Willard. "Genomic organization of alpha satellite DNA on human chromosome 7: evidence for two distinct alphoid domains on a single chromosome." Molecular and Cellular Biology 7, no. 1 (1987): 349–56. http://dx.doi.org/10.1128/mcb.7.1.349.

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A complete understanding of chromosomal disjunction during mitosis and meiosis in complex genomes such as the human genome awaits detailed characterization of both the molecular structure and genetic behavior of the centromeric regions of chromosomes. Such analyses in turn require knowledge of the organization and nature of DNA sequences associated with centromeres. The most prominent class of centromeric DNA sequences in the human genome is the alpha satellite family of tandemly repeated DNA, which is organized as distinct chromosomal subsets. Each subset is characterized by a particular mult

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50

Delviks, Krista A., and Vinay K. Pathak. "Effect of Distance between Homologous Sequences and 3′ Homology on the Frequency of Retroviral Reverse Transcriptase Template Switching." Journal of Virology 73, no. 10 (1999): 7923–32. http://dx.doi.org/10.1128/jvi.73.10.7923-7932.1999.

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ABSTRACT Deletion of direct repeats in retroviral genomes provides an in vivo system for analysis of reverse transcriptase (RT) template switching. The effect of distance between direct repeats on the rate of deletion was determined for 16 murine leukemia virus (MLV)-based vectors containing a 701-bp direct repeat of overlapping fragments of the herpes simplex virus thymidine kinase gene (HTK). The direct repeats were separated by spacer fragments of various lengths (0.1 to 3.5 kb). Southern analysis of infected cells after one replication cycle indicated that all vectors in which the distance

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