Journal articles: 'Tandem repeats'

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Matrajt, Mariana, Sergio O. Angel, Viviana Pszenny, Eduardo Guarnera, David S. Roos, and Juan C. Garberi. "Arrays of repetitive DNA elements in the largest chromosomes of Toxoplasma gondii." Genome 42, no. 2 (April 1, 1999): 265–69. http://dx.doi.org/10.1139/g98-120.

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A novel tandemly repeated DNA structure of Toxoplasma gondii that meets the requirements assigned for satellital DNA was characterized. A DNA fragment of 1002 bp contains two different elements of repetitive DNA families named ABGTg7 and ABGTg8.2. Both repeats are members of a more complex tandem structure where ABGTg7-like monomers can be arranged either as direct tandems or flanked by other related or non-related repeats. Pulse-field gel electrophoresis analysis showed that these repeats hybridize with the largest T. gondii chromosomes. Bal31 sensitivity assays indicated that these elements are located near the telomeres and along other regions too. Five genomic lambda phages were isolated and two different completed clusters of the repeated structure were analyzed.Key words: Toxoplasma gondii, tandem repeat, satellite DNA, molecular karyotype, telomere.

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Richard, Guy-Franck, Alix Kerrest, and Bernard Dujon. "Comparative Genomics and Molecular Dynamics of DNA Repeats in Eukaryotes." Microbiology and Molecular Biology Reviews 72, no. 4 (December 2008): 686–727. http://dx.doi.org/10.1128/mmbr.00011-08.

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SUMMARY Repeated elements can be widely abundant in eukaryotic genomes, composing more than 50% of the human genome, for example. It is possible to classify repeated sequences into two large families, “tandem repeats” and “dispersed repeats.” Each of these two families can be itself divided into subfamilies. Dispersed repeats contain transposons, tRNA genes, and gene paralogues, whereas tandem repeats contain gene tandems, ribosomal DNA repeat arrays, and satellite DNA, itself subdivided into satellites, minisatellites, and microsatellites. Remarkably, the molecular mechanisms that create and propagate dispersed and tandem repeats are specific to each class and usually do not overlap. In the present review, we have chosen in the first section to describe the nature and distribution of dispersed and tandem repeats in eukaryotic genomes in the light of complete (or nearly complete) available genome sequences. In the second part, we focus on the molecular mechanisms responsible for the fast evolution of two specific classes of tandem repeats: minisatellites and microsatellites. Given that a growing number of human neurological disorders involve the expansion of a particular class of microsatellites, called trinucleotide repeats, a large part of the recent experimental work on microsatellites has focused on these particular repeats, and thus we also review the current knowledge in this area. Finally, we propose a unified definition for mini- and microsatellites that takes into account their biological properties and try to point out new directions that should be explored in a near future on our road to understanding the genetics of repeated sequences.

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RIVALS, ERIC. "A SURVEY ON ALGORITHMIC ASPECTS OF TANDEM REPEATS EVOLUTION." International Journal of Foundations of Computer Science 15, no. 02 (April 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 genomic location in two individuals and a cost function for amplifications, contractions, and mutations, the purpose of TANDEM REPEAT ALLELE ALIGNMENT is to find an alignment of the sequences having minimal cost. We present a survey of these two problems that allow to investigate evolutionary mechanisms at work in tandem repeats.

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Kapila, Ritu, Sandip Das, Malathi Lakshmikumaran, and P. S. Srivastava. "A novel species-specific tandem repeat DNA family from Sinapis arvensis: detection of telomere-like sequences." Genome 39, no. 4 (August 1, 1996): 758–66. http://dx.doi.org/10.1139/g96-095.

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DNA sequences representing a tandemly repeated DNA family of the Sinapis arvensis genome were cloned and characterized. The 700-bp tandem repeat family is represented by two clones, pSA35 and pSA52, which are 697 and 709 bp in length, respectively. Dot matrix analysis of the sequences indicates the presence of repeated elements within each monomeric unit. Sequence analysis of the repetitive region of clones pSA35 and pSA52 shows that there are several copies of a 7-bp repeat element organized in tandem. The consensus sequence of this repeat element is 5′-TTTAGGG-3′. These elements are highly mutated and the difference in length between the two clones is due to different copy numbers of these elements. The repetitive region of clone pSA35 has 26 copies of the element TTTAGGG, whereas clone pSA52 has 28 copies. The repetitive region in both clones is flanked on either side by inverted repeats that may be footprints of a transposition event. Sequence comparison indicates that the element TTTAGGG is identical to telomeric repeats present in Arabidopsis, maize, tomato, and other plants. However, Bal31digestion kinetics indicates non-telomeric localization of the 700-bp tandem repeats. The clones represent a novel repeat family as (i) they contain telomere-like motifs as subrepeats within each unit; and (ii) they do not hybridize to related crucifers and are species-specific in nature. Key words : Brassica species, Sinapis arvensis, tandem repeats, telomeres.

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Subirana, Juan A., and Xavier Messeguer. "Tandem Repeats in Bacillus: Unique Features and Taxonomic Distribution." International Journal of Molecular Sciences 22, no. 10 (May 20, 2021): 5373. http://dx.doi.org/10.3390/ijms22105373.

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Little is known about DNA tandem repeats across prokaryotes. We have recently described an enigmatic group of tandem repeats in bacterial genomes with a constant repeat size but variable sequence. These findings strongly suggest that tandem repeat size in some bacteria is under strong selective constraints. Here, we extend these studies and describe tandem repeats in a large set of Bacillus. Some species have very few repeats, while other species have a large number. Most tandem repeats have repeats with a constant size (either 52 or 20–21 nt), but a variable sequence. We characterize in detail these intriguing tandem repeats. Individual species have several families of tandem repeats with the same repeat length and different sequence. This result is in strong contrast with eukaryotes, where tandem repeats of many sizes are found in any species. We discuss the possibility that they are transcribed as small RNA molecules. They may also be involved in the stabilization of the nucleoid through interaction with proteins. We also show that the distribution of tandem repeats in different species has a taxonomic significance. The data we present for all tandem repeats and their families in these bacterial species will be useful for further genomic studies.

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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 (July 1, 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 species with few repeats suggests length mutations are biased. Significant regressions of heteroplasmy, θ and π, on repeat number further suggest that repeat duplication rate increases with repeat number. Comparison of vespertilionine bat consensus repeats to mammal control region sequences revealed that tandem repeats of similar size, sequence and number also occur in shrews, cats and bighorn sheep. The presence of two conserved protein-binding sequences in all repeat units indicates that convergent evolution has occurred by duplication of functional units. We speculate that D-loop region tandem repeats may provide signal redundancy and a primitive repair mechanism in the event of somatic mutations to these binding sites.

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Horton, Richard. "Offline: Tandem repeats." Lancet 376, no. 9756 (December 2010): 1886. http://dx.doi.org/10.1016/s0140-6736(10)62193-9.

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8

Luby, Thomas M., Carol E. Schrader, Janet Stavnezer, and Erik Selsing. "The μ Switch Region Tandem Repeats Are Important, but Not Required, for Antibody Class Switch Recombination." Journal of Experimental Medicine 193, no. 2 (January 8, 2001): 159–68. http://dx.doi.org/10.1084/jem.193.2.159.

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Class switch DNA recombinations change the constant (C) region of the antibody heavy (H) chain expressed by a B cell and thereby change the antibody effector function. Unusual tandemly repeated sequence elements located upstream of H chain gene exons have long been thought to be important in the targeting and/or mechanism of the switch recombination process. We have deleted the entire switch tandem repeat element (Sμ) from the murine μ H chain gene. We find that the Sμ tandem repeats are not required for class switching in the mouse immunoglobulin H-chain locus, although the efficiency of switching is clearly reduced. Our data demonstrate that sequences outside of the Sμ tandem repeats must be capable of directing the class switch mechanism. The maintenance of the highly repeated Sμ element during evolution appears to reflect selection for a highly efficient switching process rather than selection for a required sequence element.

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Hernández-Ibarra, Norma Karina, Andrew R. Leitch, Pedro Cruz, and Ana M. Ibarra. "Fluorescent in situ hybridization and characterization of the SalI family of satellite repeats in the Haliotis L. species (abalone) of the Northeast Pacific." Genome 51, no. 8 (August 2008): 570–79. http://dx.doi.org/10.1139/g08-041.

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The SalI satellite repeat previously identified in Haliotis L. (abalone) was thought to be present in H. rufescens and absent in H. fulgens . However, we show here that SalI is also found in H. fulgens and is not useful for screening hybrid individuals bred in aquaculture or occurring naturally in the wild. SalI is a family of predominantly subtelomeric tandemly repeated sequences, and sequenced clones revealed clustering to species and little intraspecific variation. Analysis of SalI sequence divergence between Haliotis species of the Northeast Pacific revealed that evolutionary distances correlate well with bathymetric and latitudinal species distributions. Analysis of the structure of the tandem repeats revealed two regions of high sequence conservation that may contain conserved transcription factor binding sites, a surprise for an apparently “non-coding” tandem repeat. We speculate that these regions might be involved in heterochromatin silencing, perhaps mediated via transcriptional activity and RNA interference. The repeats show substantial differences in their chromosomal distributions, even between individuals of the same species, indicating a dynamic organization of repeats, perhaps mediated via sequence homogenization.

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Smith, Kirby D., Keith E. Young, C. Conover Talbot, and Barbara J. Schmeckpeper. "Repeated DNA of the human Y chromosome." Development 101, Supplement (March 1, 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 exception, can be distinguished from homologues elsewhere in the genome. These include the alphoid repeats, the major human SINE (Alu repeats) and several additional families of repeats which account for the majority of Y-chromosome repeated DNA. The alphoid sequences tandemly clustered near the centromere on the Y chromosome can be distinguished from those on other chromosomes by both sequence and repeat organization, while the majority of Y-chromosome Alu repeats have little homology with genomic consensus Alu sequences. In contrast, the Y-chromosome LINE repeats cannot be distinguished from LINEs found on other chromosomes. It has been proposed that both SINE and LINE repeats have been dispersed throughout the genome by mechanisms that involve RNA intermediates. The difference in the relationship of the Y-chromosome Alu and LINE repeats to their respective family members elsewhere in the genome makes it possible that their dispersal to the Y chromosome has occurred by different mechanisms or at different rates. In addition to the SINE and LINE repeats, the human Y chromosome contains a group of repeated DNA elements originally identified as 3·4 and 2·1 kb fragments in HaeIII digests of male genomic DNA. Although the 3·4 and 2·1 kb Y repeats do not crossreact, both exist as tandem clusters of alternating Yspecific and non-Y-specific sequences. The 3·4 kb Y repeats contain at least three distinct sequences with autosomal homologies interspersed in various ways with a collection of several different Yspecific repeat sequences. Individual recombinant clones derived from isolated 3·4 kb HaeIII Y fragments have been identified which do not cross-react. Thus, the 3·4 kb HaeIII Y fragments are a heterogeneous mixture of sequences which have in common the regular occurrence of HaeIII restriction sites at 3·4 kb intervals and an organization as tandem clusters at various sites along the Y-long arm. The 2·1 kb HaeIII Y fragment cross-reacts with a 1i9 kb HaeIII autosomal fragment. Both the Ychromosomal and autosomal fragments are part of tandem clusters which have a unit length of 2·4 kb. All of the 2·4 kb Y repeats are similar and contain a 1·6 kb Y-specific repeat and an 800 bp sequence which has homology with an 800 bp sequence in the autosomal 2·4 kb repeats. While this 800 bp sequence is common to both Y and autosomal 2·4 kb repeats and is associated with a single Y-specific repeat, it is associated with at least four non-cross-reacting autosome-specific sequences. Like the Y repeat, the autosomal repeats exist as tandem clusters of 2·4 kb units and are composed of an 800 bp common sequence alternating with a 1·6 kb autosome-specific sequence. Thus, in humans, the common sequence is associated with several different sequences yet always occurs as part of a tandem cluster of 2·4 kb repeats. The common and autosome-specific sequences of the 2·4 kb repeats are also present in gorillas as part of organized repeat units. However, in gorillas the two are not associated with each other. The Y-chromosome repeats described here are a heterogeneous mixture of sequences organized into specific sets of alternating Y-specific and non-Y-specific sequences. They do not have an identified function and the mechanisms by which they are generated are unknown. Nevertheless, their marked chromosomal speciticity and the regularity of the basic repeat unit in each type of repeat seem inconsistent with stochastic mechanisms of sequence diffusion between chromosomes.

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11

Gibbons, Richard J., and Douglas R. Higgs. "ATRX: Taming tandem repeats." Cell Cycle 9, no. 23 (December 2010): 4605–6. http://dx.doi.org/10.4161/cc.9.23.14164.

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12

Miura, Grant. "Counting short tandem repeats." Nature Methods 17, no. 1 (January 2020): 31. http://dx.doi.org/10.1038/s41592-019-0724-0.

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Broad, T. E., P. E. Lewis, S. H. Phua, A. J. Ede, J. W. Forrest, and P. A. Pugh. "Families of tandemly repeated DNA elements from horse: cloning, nucleotide sequence, and organization." Genome 38, no. 6 (December 1, 1995): 1285–89. http://dx.doi.org/10.1139/g95-169.

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DNA repeats, revealed initially by digestion of horse DNA with restriction enzymes, were cloned and characterized by cross-hybridization studies and nucleotide sequencing. The Sau-like family of tandem repeats contained two classes of repetitive elements with unit repeats of about 80 bp that shared no sequence similarity. Both unit repeats were present, frequently in tandem, in cloned segments of horse DNA of less than 600 bp. Evidence is presented, based on their ladderlike patterns of hybridization to horse DNA and their high level of similarity to published sequences of satellites from equine DNA, suggesting that they are centromerically located in the horse genome. The Sau-like tandem repeat families were specific to Equidae. Another class of repeats, GATA-like elements, which did not appear to have a centromeric distribution, was also cloned and sequenced.Key words: Equidae, Equus caballus, tandem DNA repeats, GATA-like repeats, Sau3AI repeats.

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Huang, Ying, Xin Huang, Xuming Zhou, Jialin Wang, Ruidong Zhang, Futong Ma, Kaiqiang Wang, et al. "Immune activation by a multigene family of lectins with variable tandem repeats in oriental river prawn ( Macrobrachium nipponense )." Open Biology 10, no. 9 (September 2020): 200141. http://dx.doi.org/10.1098/rsob.200141.

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Genomic regions with repeated sequences are unstable and prone to rapid DNA diversification. However, the role of tandem repeats within the coding region is not fully characterized. Here, we have identified a new hypervariable C-type lectin gene family with different numbers of tandem repeats (Rlecs; R means repeat) in oriental river prawn ( Macrobrachium nipponense ) . Two types of repeat units (33 or 30 bp) are identified in the second exon, and the number of repeat units vary from 1 to 9. Rlecs can be classified into 15 types through phylogenetic analysis. The amino acid sequences in the same type of Rlec are highly conservative outside the repeat regions. The main differences among the Rlec types are evident in exon 5. A variable number of tandem repeats in Rlecs may be produced by slip mispairing during gene replication. Alternative splicing contributes to the multiplicity of forms in this lectin gene family, and different types of Rlecs vary in terms of tissue distribution, expression quantity and response to bacterial challenge. These variations suggest that Rlecs have functional diversity. The results of experiments on sugar binding, microbial inhibition and clearance, regulation of antimicrobial peptide gene expression and prophenoloxidase activation indicate that the function of Rlecs with the motif of YRSKDD in innate immunity is enhanced when the number of tandem repeats increases. Our results suggest that Rlecs undergo gene expansion through gene duplication and alternative splicing, which ultimately leads to functional diversity.

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Taylor, John S., and Felix Breden. "Slipped-Strand Mispairing at Noncontiguous Repeats in Poecilia reticulata: A Model for Minisatellite Birth." Genetics 155, no. 3 (July 1, 2000): 1313–20. http://dx.doi.org/10.1093/genetics/155.3.1313.

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Abstract The standard slipped-strand mispairing (SSM) model for the formation of variable number tandem repeats (VNTRs) proposes that a few tandem repeats, produced by chance mutations, provide the “raw material” for VNTR expansion. However, this model is unlikely to explain the formation of VNTRs with long motifs (e.g., minisatellites), because the likelihood of a tandem repeat forming by chance decreases rapidly as the length of the repeat motif increases. Phylogenetic reconstruction of the birth of a mitochondrial (mt) DNA minisatellite in guppies suggests that VNTRs with long motifs can form as a consequence of SSM at noncontiguous repeats. VNTRs formed in this manner have motifs longer than the noncontiguous repeat originally formed by chance and are flanked by one unit of the original, noncontiguous repeat. SSM at noncontiguous repeats can therefore explain the birth of VNTRs with long motifs and the “imperfect” or “short direct” repeats frequently observed adjacent to both mtDNA and nuclear VNTRs.

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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 (March 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 IR3 and the cellular repeats is left unclear, the cellular repeats have many interesting features. The tandem arrays are about 1 to several kilobases long, much shorter than satellite tandem repeats and larger than other interspersed, tandem repeats. Each of the repeats is a distinct variation, perhaps diverged from a common sequence, (GGA)n. This family is present in the genomes of all species tested and appears to be a ubiquitous feature of all higher eucaryotic genomes.

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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 (March 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 IR3 and the cellular repeats is left unclear, the cellular repeats have many interesting features. The tandem arrays are about 1 to several kilobases long, much shorter than satellite tandem repeats and larger than other interspersed, tandem repeats. Each of the repeats is a distinct variation, perhaps diverged from a common sequence, (GGA)n. This family is present in the genomes of all species tested and appears to be a ubiquitous feature of all higher eucaryotic genomes.

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Singh, Dharam, and Mahipal Singh. "Organization of 5S ribosomal RNA genes in tea (Camellia sinensis)." Genome 44, no. 1 (February 1, 2001): 143–46. http://dx.doi.org/10.1139/g00-095.

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The 5S rRNA genes in the Camellia sinensis (L.) O. Kuntze (tea) genome are arranged as tandem repeat units of 300 and 325 bps. The 2 classes of tandem repeats were discovered by Southern hybridisation of tea genomic DNA with a 5S rRNA gene PCR product.Key words: Camellia species, 5S rDNA, multigene family, tandem repeats, spacers.

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Shaw, Brandon M., Warren L. Simmons, and Kevin Dybvig. "The Vsa Shield of Mycoplasma pulmonis Is Antiphagocytic." Infection and Immunity 80, no. 2 (November 14, 2011): 704–9. http://dx.doi.org/10.1128/iai.06009-11.

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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.

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Phillips, Melissa. "Tandem repeats take, make shape." Genome Biology 5 (2004): spotlight—20041215–01. http://dx.doi.org/10.1186/gb-spotlight-20041215-01.

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Gelfand, Y., A. Rodriguez, and G. Benson. "TRDB--The Tandem Repeats Database." Nucleic Acids Research 35, Database (January 3, 2007): D80—D87. http://dx.doi.org/10.1093/nar/gkl1013.

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de Jonge, Patrick A., F. A. Bastiaan von Meijenfeldt, Laura E. van Rooijen, Stan J. J. Brouns, and Bas E. Dutilh. "Evolution of BACON Domain Tandem Repeats in crAssphage and Novel Gut Bacteriophage Lineages." Viruses 11, no. 12 (November 21, 2019): 1085. http://dx.doi.org/10.3390/v11121085.

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The human gut contains an expanse of largely unstudied bacteriophages. Among the most common are crAss-like phages, which were predicted to infect Bacteriodetes hosts. CrAssphage, the first crAss-like phage to be discovered, contains a protein encoding a Bacteroides-associated carbohydrate-binding often N-terminal (BACON) domain tandem repeat. Because protein domain tandem repeats are often hotspots of evolution, BACON domains may provide insight into the evolution of crAss-like phages. Here, we studied the biodiversity and evolution of BACON domains in bacteriophages by analysing over 2 million viral contigs. We found a high biodiversity of BACON in seven gut phage lineages, including five known crAss-like phage lineages and two novel gut phage lineages that are distantly related to crAss-like phages. In three BACON-containing phage lineages, we found that BACON domain tandem repeats were associated with phage tail proteins, suggestive of a possible role of these repeats in host binding. In contrast, individual BACON domains that did not occur in tandem were not found in the proximity of tail proteins. In two lineages, tail-associated BACON domain tandem repeats evolved largely through horizontal transfer of separate domains. In the third lineage that includes the prototypical crAssphage, the tandem repeats arose from several sequential domain duplications, resulting in a characteristic tandem array that is distinct from bacterial BACON domains. We conclude that phage tail-associated BACON domain tandem repeats have evolved in at least two independent cases in gut bacteriophages, including in the widespread gut phage crAssphage.

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Cheng, Zhi-Jun, and Minoru Murata. "A Centromeric Tandem Repeat Family Originating From a Part of Ty3/gypsy-Retroelement in Wheat and Its Relatives." Genetics 164, no. 2 (June 1, 2003): 665–72. http://dx.doi.org/10.1093/genetics/164.2.665.

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AbstractFrom a wild diploid species that is a relative of wheat, Aegilops speltoides, a 301-bp repeat containing 16 copies of a CAA microsatellite was isolated. Southern blot and fluorescence in situ hybridization revealed that ∼250 bp of the sequence is tandemly arrayed at the centromere regions of A- and B-genome chromosomes of common wheat and rye chromosomes. Although the DNA sequence of this 250-bp repeat showed no notable homology in the databases, the flanking or intervening sequences between the repeats showed high homologies (>82%) to two separate sequences of the gag gene and its upstream region in cereba, a Ty3/gypsy-like retroelement of Hordeum vulgare. Since the amino acid sequence deduced from the 250 bp with seven CAAs showed some similarity (∼53%) to that of the gag gene, we concluded that the 250-bp repeats had also originated from the cereba-like retroelements in diploid wheat such as Ae. speltoides and had formed tandem arrays, whereas the 300-bp repeats were dispersed as a part of cereba-like retroelements. This suggests that some tandem repeats localized at the centromeric regions of cereals and other plant species originated from parts of retrotransposons.

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Liang, Yupu, Dina Sokol, Sarah Zelikovitz, and Sarah Ita Levitan. "Classification of Tandem Repeats in the Human Genome." International Journal of Knowledge Discovery in Bioinformatics 3, no. 3 (July 2012): 1–21. http://dx.doi.org/10.4018/jkdb.2012070101.

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Tandem repeats in DNA sequences are extremely relevant in biological phenomena and diagnostic tools. Computational programs that discover these tandem repeats generate a huge volume of data, which is often difficult to decipher without further organization. In this paper, the authors describe a new method for post-processing tandem repeats through clustering and classification. Their work presents multiple ways of expressing tandem repeats using the n-gram model with different clustering distance measures. Analysis of the clusters for the tandem repeats in the human genome shows that the method yields a well-defined grouping in which similarity among repeats is apparent. The authors’ new, alignment-free method facilitates the analysis of the myriad of tandem repeats that occur in the human genome and they believe that this work will lead to new discoveries on the roles, origins, and significance of tandem repeats.

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Ma, Z. Q., M. Röder, and M. E. Sorrells. "Frequencies and sequence characteristics of di-, tri-, and tetra-nucleotide microsatellites in wheat." Genome 39, no. 1 (February 1, 1996): 123–30. http://dx.doi.org/10.1139/g96-017.

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Microsatellites have emerged as an important source of genetic markers for eukaryotic genomes. In this report, two wheat (Triticum aestivum L.) genomic libraries were screened for several di-, tri-, and tetra-nucleotide tandem repeats. Clones containing (AC)n, (AG)n, (TCT)n, and (TTG)n repeats were isolated and sequenced. On average, there was one (AC)n microsatellite every 292 kbp and one (AG)n microsatellite every 212 kbp. The trinucleotide tandem repeats (TCT)n and (TTG)n were about 10 times less common than the two dinucleotide tandem repeats tested and tetranucleotide tandem repeats were rare. Many of the microsatellites had more than 10 repeats. The maximum repeat number found for (AC)n was 36 and for (TCT)n was more than 50. The prevailing category of (AG)n microsatellites from (AG)n isolates was perfect repeats. About half of the (AC)n microsatellites were compound repeats, while most of the (TCT)n microsatellites were imperfect repeats. In a small sample, (TTG)n microsatellites consisted mainly of compound repeats. The most frequently associated repeats were (AC)n with (AG)n, (TCT)n with (TCC)n, and (TTG)n with (TGG)n. Among 32 pairs of microsatellite primers surveyed, seven produced polymorphic products in the expected size range and these loci were mapped using a hexaploid wheat mapping population or aneuploid stocks. Key words : wheat, Triticum aestivum L., microsatellites, polymorphism, sequence characteristics.

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NYEO, SU-LONG, and JUI-PING YU. "LENGTH DISTRIBUTIONS OF SIMPLE TANDEM REPEATS IN GENOMES." Journal of Biological Systems 15, no. 03 (September 2007): 299–312. http://dx.doi.org/10.1142/s0218339007002246.

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The length distributions of simple tandem repeats in the genomes of several organisms are evaluated and found to exhibit long-range correlations in A and T nucleotide bases related repeats for most eukaryotes. In particular, the length distributions of the mononucleotide A/T repeat units have longer tails than those of the C/G repeat units. Also, the length distributions of the dinucleotide repeat unit CG show a simple monotonously fast decreasing behavior, while those of repeat units AT, AG and AC have complicated structures at larger repeat lengths, especially for human, mouse and rat chromosomes. These distributive behaviors are due to the CpG deficiency in different genomes with different methylation activities. Especially, methyltransferases in vertebrates appear to methylate specifically the cytosine in CpG dinucleotides, and the methylated cytosines is prone to mutate to thymine by spontaneous deamination. The dinucleotide CpG would gradually decay into TpG and CpA. In addition, there is a peak in the distributions of repeat unit A at repeat-repeat separation 153 nt for humans and chimpanzees. We show that the long-tail behavior of mononucleotide repeat unit A and the peak at repeat separation 153 nt are due to the interspersed repetitive DNA sequences in humans and chimpanzees.

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Jacob, S. S., R. Vanitharani, A. S. Karthikeyan, Y. Chinchore, P. Thillaichidambaram, and K. Veluthambi. "Mungbean yellow mosaic virus-Vi Agroinfection by Codelivery of DNA A and DNA B From One Agrobacterium Strain." Plant Disease 87, no. 3 (March 2003): 247–51. http://dx.doi.org/10.1094/pdis.2003.87.3.247.

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Agroinfection of bipartite geminiviruses is routinely done by mixing two Agrobacterium strains that independently harbor partial tandem repeats of DNA A and DNA B. We report here an improved agroinfection method for bipartite geminiviruses that utilizes one strain of Agrobacterium that harbors DNA A and DNA B partial tandem repeats on two compatible replicons. A cointegrate vector, pGV2260∷pGV1.3A, with the partial tandem repeat of Mungbean yellow mosaic virus-Vi (MYMV-Vi) DNA A and a binary vector, pGA1.9B, with the partial tandem repeat of MYMV-Vi DNA B gave an agroinfection efficiency of 24% when harbored in two Agrobacterium strains and an efficiency of 61% when harbored in one Agrobacterium strain. A combination of binary vectors, pGA1.9A with MYMV-Vi DNA A partial tandem repeat and pGA1.9B with DNA B partial tandem repeat, gave an agroinfection efficiency of 74% when harbored in two strains. But pGA1.9A and pPZP1.9B (a partial tandem repeat of DNA B), when present in the same Agrobacterium strain, gave 100% agroinfection. Accumulation of viral DNA was shown by Southern blotting. The single-strain method using two compatible replicons consistently gave 100% agroinfection efficiency.

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NOLLET, Séverine, Nicolas MONIAUX, Jacques MAURY, Danièle PETITPREZ, Pierre DEGAND, Anne LAINE, Nicole PORCHET, and Jean-Pierre AUBERT. "Human mucin gene MUC4: organization of its 5′-region and polymorphism of its central tandem repeat array." Biochemical Journal 332, no. 3 (June 15, 1998): 739–48. http://dx.doi.org/10.1042/bj3320739.

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In a previous study we isolated a partial cDNA with a tandem repeat of 48 bp, which allowed us to map a novel human mucin gene named MUC4to chromosome 3q29. Here we report the organization and sequence of the 5´-region and its junction with the tandem repeat array of MUC4. Analysis of three overlapping genomic clones allowed us to obtain a partial restriction map of MUC4 and to locate the complete 48 bp tandem repeat domain on a PstI/EcoRI genomic fragment that exhibits a very large variation in number of tandem repeats (7–19 kb). cDNA clonal extension allowed us to obtain the entire 5´ coding region of MUC4. Exon 1 consists of a 5´ untranslated region and an 82 bp fragment encoding the signal peptide. This latter shows a high degree of similarity to the signal peptide of another apomucin, ASGP-1. Exon 2 is extremely large and contains a unique sequence that is followed by the whole tandem repeat domain. It encodes only one cysteine residue, making MUC4 different from mucin genes belonging to the 11p15.5 family. Moreover, an intron downstream from the tandem repeat array consists mainly of a 15 bp tandem repeat that exhibits a polymorphism in having a variable number of tandem repeats.

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Mathema, Vivek Bhakta, Arjen M. Dondorp, and Mallika Imwong. "OSTRFPD: Multifunctional Tool for Genome-Wide Short Tandem Repeat Analysis for DNA, Transcripts, and Amino Acid Sequences with Integrated Primer Designer." Evolutionary Bioinformatics 15 (January 2019): 117693431984313. http://dx.doi.org/10.1177/1176934319843130.

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Microsatellite mining is a common outcome of the in silico approach to genomic studies. The resulting short tandemly repeated DNA could be used as molecular markers for studying polymorphism, genotyping and forensics. The omni short tandem repeat finder and primer designer (OSTRFPD) is among the few versatile, platform-independent open-source tools written in Python that enables researchers to identify and analyse genome-wide short tandem repeats in both nucleic acids and protein sequences. OSTRFPD is designed to run either in a user-friendly fully featured graphical interface or in a command line interface mode for advanced users. OSTRFPD can detect both perfect and imperfect repeats of low complexity with customisable scores. Moreover, the software has built-in architecture to simultaneously filter selection of flanking regions in DNA and generate microsatellite-targeted primers implementing the Primer3 platform. The software has built-in motif-sequence generator engines and an additional option to use the dictionary mode for custom motif searches. The software generates search results including general statistics containing motif categorisation, repeat frequencies, densities, coverage, guanine–cytosine (GC) content, and simple text-based imperfect alignment visualisation. Thus, OSTRFPD presents users with a quick single-step solution package to assist development of microsatellite markers and categorise tandemly repeated amino acids in proteome databases. Practical implementation of OSTRFPD was demonstrated using publicly available whole-genome sequences of selected Plasmodium species. OSTRFPD is freely available and open-sourced for improvement and user-specific adaptation.

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Levdansky, Emma, Jacob Romano, Yona Shadkchan, Haim Sharon, Kevin J. Verstrepen, Gerald R. Fink, and Nir Osherov. "Coding Tandem Repeats Generate Diversity in Aspergillus fumigatus Genes." Eukaryotic Cell 6, no. 8 (June 8, 2007): 1380–91. http://dx.doi.org/10.1128/ec.00229-06.

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ABSTRACT Genes containing multiple coding mini- and microsatellite repeats are highly dynamic components of genomes. Frequent recombination events within these tandem repeats lead to changes in repeat numbers, which in turn alters the amino acid sequence of the corresponding protein. In bacteria and yeasts, the expansion of such coding repeats in cell wall proteins is associated with alterations in immunogenicity, adhesion, and pathogenesis. We hypothesized that identification of repeat-containing putative cell wall proteins in the human pathogen Aspergillus fumigatus may reveal novel pathogenesis-related elements. Here, we report that the genome of A. fumigatus contains as many as 292 genes with internal repeats. Fourteen of 30 selected genes showed size variation of their repeat-containing regions among 11 clinical A. fumigatus isolates. Four of these genes, Afu3g08990, Afu2g05150 (MP-2), Afu4g09600, and Afu6g14090, encode putative cell wall proteins containing a leader sequence and a glycosylphosphatidylinositol anchor motif. All four genes are expressed and produce variable-size mRNA encoding a discrete number of repeat amino acid units. Their expression was altered during development and in response to cell wall-disrupting agents. Deletion of one of these genes, Afu3g08990, resulted in a phenotype characterized by rapid conidial germination and reduced adherence to extracellular matrix suggestive of an alteration in cell wall characteristics. The Afu3g08990 protein was localized to the cell walls of dormant and germinating conidia. Our findings suggest that a subset of the A. fumigatus cell surface proteins may be hypervariable due to recombination events in their internal tandem repeats. This variation may provide the functional diversity in cell surface antigens which allows rapid adaptation to the environment and/or elusion of the host immune system.

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Harris, Robert S., Monika Cechova, and Kateryna D. Makova. "Noise-cancelling repeat finder: uncovering tandem repeats in error-prone long-read sequencing data." Bioinformatics 35, no. 22 (July 10, 2019): 4809–11. http://dx.doi.org/10.1093/bioinformatics/btz484.

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Abstract Summary Tandem DNA repeats can be sequenced with long-read technologies, but cannot be accurately deciphered due to the lack of computational tools taking high error rates of these technologies into account. Here we introduce Noise-Cancelling Repeat Finder (NCRF) to uncover putative tandem repeats of specified motifs in noisy long reads produced by Pacific Biosciences and Oxford Nanopore sequencers. Using simulations, we validated the use of NCRF to locate tandem repeats with motifs of various lengths and demonstrated its superior performance as compared to two alternative tools. Using real human whole-genome sequencing data, NCRF identified long arrays of the (AATGG)n repeat involved in heat shock stress response. Availability and implementation NCRF is implemented in C, supported by several python scripts, and is available in bioconda and at https://github.com/makovalab-psu/NoiseCancellingRepeatFinder. Supplementary information Supplementary data are available at Bioinformatics online.

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Keil, R. L., and A. D. McWilliams. "A gene with specific and global effects on recombination of sequences from tandemly repeated genes in Saccharomyces cerevisiae." Genetics 135, no. 3 (November 1, 1993): 711–18. http://dx.doi.org/10.1093/genetics/135.3.711.

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Abstract The preservation of sequence homogeneity and copy number of tandemly repeated genes may require specific mechanisms or regulation of recombination. We have identified mutations that specifically affect recombination among natural repetitions in the yeast Saccharomyces cerevisiae. The rrm3 mutation stimulates mitotic recombination in the naturally occurring tandem repeats of the rDNA and copper chelatin (CUP1) genes. This mutation does not affect recombination of several other types of repeated genes tested including Ty elements, mating type information and duplications created by transformation. In addition to stimulating exchange among the multiple CUP1 repeats at their natural chromosomal location, rrm3 also increases recombination of a duplication of CUP1 units present at his4. This suggests that the RRM3 gene may encode a sequence-specific factor that contributes to a global suppression of mitotic exchange in sequences that can be maintained as tandem arrays.

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Danandeh, Mostafa, Seyed Reza Moadab, Mohammad Asgharzadeh, Naser Alizadeh, and Reza Ghotaslou. "Mycobacterium tuberculosis Diversity by Exact Tandem Repeats-Variable Number Tandem Repeat Method in Azerbaijan, Iran." Infectious Diseases in Clinical Practice 26, no. 2 (March 2018): 80–83. http://dx.doi.org/10.1097/ipc.0000000000000561.

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Paladin, Lisanna, and Silvio C. E. Tosatto. "Comparison of protein repeat classifications based on structure and sequence families." Biochemical Society Transactions 43, no. 5 (October 1, 2015): 832–37. http://dx.doi.org/10.1042/bst20150079.

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Tandem repeats (TR) in proteins are common in nature and have several unique functions. They come in various forms that are frequently difficult to recognize from a sequence. A previously proposed structural classification has been recently implemented in the RepeatsDB database. This defines five main classes, mainly based on repeat unit length, with subclasses representing specific folds. Sequence-based classifications, such as Pfam, provide an alternative classification based on evolutionarily conserved repeat families. Here, we discuss a detailed comparison between the structural classes in RepeatsDB and the corresponding Pfam repeat families and clans. Most instances are found to map one-to-one between structure and sequence. Some notable exceptions such as leucine-rich repeats (LRRs) and α-solenoids are discussed.

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Sokol, D., G. Benson, and J. Tojeira. "Tandem repeats over the edit distance." Bioinformatics 23, no. 2 (January 15, 2007): e30-e35. http://dx.doi.org/10.1093/bioinformatics/btl309.

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36

Waldron, Denise. "Tandem repeats and divergent gene expression." Nature Reviews Genetics 16, no. 12 (November 3, 2015): 686. http://dx.doi.org/10.1038/nrg4040.

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37

Weber, James L., and Carmen Wong. "Mutation of human short tandem repeats." Human Molecular Genetics 2, no. 8 (1993): 1123–28. http://dx.doi.org/10.1093/hmg/2.8.1123.

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Sharma, Anupma, Thomas K. Wolfgruber, and Gernot G. Presting. "Tandem repeats derived from centromeric retrotransposons." BMC Genomics 14, no. 1 (2013): 142. http://dx.doi.org/10.1186/1471-2164-14-142.

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Verstrepen, Kevin J., An Jansen, Fran Lewitter, and Gerald R. Fink. "Intragenic tandem repeats generate functional variability." Nature Genetics 37, no. 9 (August 7, 2005): 986–90. http://dx.doi.org/10.1038/ng1618.

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40

Landau, Gad M., Jeanette P. Schmidt, and Dina Sokol. "An Algorithm for Approximate Tandem Repeats." Journal of Computational Biology 8, no. 1 (February 2001): 1–18. http://dx.doi.org/10.1089/106652701300099038.

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Krishnan, A., and F. Tang. "Exhaustive whole-genome tandem repeats search." Bioinformatics 20, no. 16 (May 14, 2004): 2702–10. http://dx.doi.org/10.1093/bioinformatics/bth311.

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Parry, Simon, Mark Sutton-Smith, Paul Heal, Shih-Hsing Leir, Timea Palmai-Pallag, Howard R. Morris, Michael A. Hollingsworth, Anne Dell, and Ann Harris. "Evaluation of MUC6 mucin tandem repeats." Biochimica et Biophysica Acta (BBA) - General Subjects 1722, no. 1 (February 2005): 77–83. http://dx.doi.org/10.1016/j.bbagen.2004.11.010.

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Geiger-Schuller, Kathryn, Kevin Sforza, Max Yuhas, Fabio Parmeggiani, David Baker, and Doug Barrick. "Extreme stability in de novo-designed repeat arrays is determined by unusually stable short-range interactions." Proceedings of the National Academy of Sciences 115, no. 29 (June 29, 2018): 7539–44. http://dx.doi.org/10.1073/pnas.1800283115.

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Designed helical repeats (DHRs) are modular helix–loop–helix–loop protein structures that are tandemly repeated to form a superhelical array. Structures combining tandem DHRs demonstrate a wide range of molecular geometries, many of which are not observed in nature. Understanding cooperativity of DHR proteins provides insight into the molecular origins of Rosetta-based protein design hyperstability and facilitates comparison of energy distributions in artificial and naturally occurring protein folds. Here, we use a nearest-neighbor Ising model to quantify the intrinsic and interfacial free energies of four different DHRs. We measure the folding free energies of constructs with varying numbers of internal and terminal capping repeats for four different DHR folds, using guanidine-HCl and glycerol as destabilizing and solubilizing cosolvents. One-dimensional Ising analysis of these series reveals that, although interrepeat coupling energies are within the range seen for naturally occurring repeat proteins, the individual repeats of DHR proteins are intrinsically stable. This favorable intrinsic stability, which has not been observed for naturally occurring repeat proteins, adds to stabilizing interfaces, resulting in extraordinarily high stability. Stable repeats also impart a downhill shape to the energy landscape for DHR folding. These intrinsic stability differences suggest that part of the success of Rosetta-based design results from capturing favorable local interactions.

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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 (April 1, 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 > 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 decrease in monomer homogeneity that might be expected if homogeneity is maintained by recombination. However, just outside the last complete repeat at each end, there are a few fragments of sequence similar to the monomer. The sequences in these flanking regions are not those predicted for sequences decaying in the absence of recombination. Instead, the fragmentation of the sequence homology suggests that flanking regions have undergone more severe disruptions, possibly during an insertion or amplification event. Hsr-omega alleles differing in the number of repeats are detected and appear to be stable over a few thousand generations; however, both increases and decreases in repeat numbers have been observed. The new alleles appear to be as stable as their predecessors. No alleles of less than approximately 5 kb nor more than approximately 16 kb of repeats were seen in any stocks examined. The evidence that there is a limit on the minimum number of repeats is consistent with the suggestion that these repeats are important in the function of the unusual Hsr-omega nuclear RNA.

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Perez-Riba, Albert, Marie Synakewicz, and Laura S. Itzhaki. "Folding cooperativity and allosteric function in the tandem-repeat protein class." Philosophical Transactions of the Royal Society B: Biological Sciences 373, no. 1749 (May 7, 2018): 20170188. http://dx.doi.org/10.1098/rstb.2017.0188.

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The term allostery was originally developed to describe structural changes in one binding site induced by the interaction of a partner molecule with a distant binding site, and it has been studied in depth in the field of enzymology. Here, we discuss the concept of action at a distance in relation to the folding and function of the solenoid class of tandem-repeat proteins such as tetratricopeptide repeats (TPRs) and ankyrin repeats. Distantly located repeats fold cooperatively, even though only nearest-neighbour interactions exist in these proteins. A number of repeat-protein scaffolds have been reported to display allosteric effects, transferred through the repeat array, that enable them to direct the activity of the multi-subunit enzymes within which they reside. We also highlight a recently identified group of tandem-repeat proteins, the RRPNN subclass of TPRs, recent crystal structures of which indicate that they function as allosteric switches to modulate multiple bacterial quorum-sensing mechanisms. We believe that the folding cooperativity of tandem-repeat proteins and the biophysical mechanisms that transform them into allosteric switches are intimately intertwined. This opinion piece aims to combine our understanding of the two areas and develop ideas on their common underlying principles. This article is part of a discussion meeting issue ‘Allostery and molecular machines’.

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Paladin, Lisanna, Martina Bevilacqua, Sara Errigo, Damiano Piovesan, Ivan Mičetić, Marco Necci, Alexander Miguel Monzon, et al. "RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures." Nucleic Acids Research 49, no. D1 (November 25, 2020): D452—D457. http://dx.doi.org/10.1093/nar/gkaa1097.

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Abstract The RepeatsDB database (URL: https://repeatsdb.org/) provides annotations and classification for protein tandem repeat structures from the Protein Data Bank (PDB). Protein tandem repeats are ubiquitous in all branches of the tree of life. The accumulation of solved repeat structures provides new possibilities for classification and detection, but also increasing the need for annotation. Here we present RepeatsDB 3.0, which addresses these challenges and presents an extended classification scheme. The major conceptual change compared to the previous version is the hierarchical classification combining top levels based solely on structural similarity (Class > Topology > Fold) with two new levels (Clan > Family) requiring sequence similarity and describing repeat motifs in collaboration with Pfam. Data growth has been addressed with improved mechanisms for browsing the classification hierarchy. A new UniProt-centric view unifies the increasingly frequent annotation of structures from identical or similar sequences. This update of RepeatsDB aligns with our commitment to develop a resource that extracts, organizes and distributes specialized information on tandem repeat protein structures.

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Sulovari, Arvis, Ruiyang Li, Peter A. Audano, David Porubsky, Mitchell R. Vollger, Glennis A. Logsdon, Wesley C. Warren, Alex A. Pollen, Mark J. P. Chaisson, and Evan E. Eichler. "Human-specific tandem repeat expansion and differential gene expression during primate evolution." Proceedings of the National Academy of Sciences 116, no. 46 (October 28, 2019): 23243–53. http://dx.doi.org/10.1073/pnas.1912175116.

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Short tandem repeats (STRs) and variable number tandem repeats (VNTRs) are important sources of natural and disease-causing variation, yet they have been problematic to resolve in reference genomes and genotype with short-read technology. We created a framework to model the evolution and instability of STRs and VNTRs in apes. We phased and assembled 3 ape genomes (chimpanzee, gorilla, and orangutan) using long-read and 10x Genomics linked-read sequence data for 21,442 human tandem repeats discovered in 6 haplotype-resolved assemblies of Yoruban, Chinese, and Puerto Rican origin. We define a set of 1,584 STRs/VNTRs expanded specifically in humans, including large tandem repeats affecting coding and noncoding portions of genes (e.g., MUC3A, CACNA1C). We show that short interspersed nuclear element–VNTR–Alu (SVA) retrotransposition is the main mechanism for distributing GC-rich human-specific tandem repeat expansions throughout the genome but with a bias against genes. In contrast, we observe that VNTRs not originating from retrotransposons have a propensity to cluster near genes, especially in the subtelomere. Using tissue-specific expression from human and chimpanzee brains, we identify genes where transcript isoform usage differs significantly, likely caused by cryptic splicing variation within VNTRs. Using single-cell expression from cerebral organoids, we observe a strong effect for genes associated with transcription profiles analogous to intermediate progenitor cells. Finally, we compare the sequence composition of some of the largest human-specific repeat expansions and identify 52 STRs/VNTRs with at least 40 uninterrupted pure tracts as candidates for genetically unstable regions associated with disease.

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Masárová, Veronika, Daniel Mihálik, and Ján Kraic. "In Silico Retrieving of Opium Poppy (Papaver Somniferum L.) Microsatellites." Agriculture (Polnohospodárstvo) 61, no. 4 (December 1, 2015): 149–56. http://dx.doi.org/10.1515/agri-2015-0020.

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Abstract Repetitive tandem sequences were retrieved within nucleotide sequences of opium poppy (Papaver somniferum L.) genomic DNA available in the GenBank® database. Altogether 538 different microsatellites with the desired length characteristics of tandem repeats have been identified within 450 sequences of opium poppy DNA available in the database. The most frequented were mononucleotide repeats (246); nevertheless, 44 dinucleotide, 148 trinucleotide, 62 tetranucleotide, 28 pentanucleotide and 5 hexanucleotide tandem repeats have also been found. The most abundant were trinucleotide motifs (27.50%), and the most abundant motifs within each group of tandem repeats were TA/AT, TTC/GAA, GGTT/AACC and TTTTA/ TAAAA. Five hexanucleotide repeats contained four different motifs.

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Jackson, Colin J., Takashi Mochizuki, and Richard C. Barton. "PCR fingerprinting of Trichophyton mentagrophytes var. interdigitale using polymorphic subrepeat loci in the rDNA nontranscribed spacer." Journal of Medical Microbiology 55, no. 10 (October 1, 2006): 1349–55. http://dx.doi.org/10.1099/jmm.0.46691-0.

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The sequence of the nontranscribed spacer (NTS) region of the rDNA of Trichophyton mentagrophytes var. interdigitale strain 2111 was determined, and three individual subrepeat loci identified. The first repeat region contained eight tandem copies of a degenerate 33–43 bp sequence, whilst the second had two complete and two partial 300 bp repeats. The third locus contained six tandemly repetitive elements of between 67 and 89 bp, which showed sequence identity to the TrS2 repeats of Trichophyton rubrum. PCR amplification of the individual repetitive regions from 42 random isolates of T. mentagrophytes var. interdigitale identified fragment length polymorphisms at each locus. Sequence analysis of the PCR products revealed that the size variations resulted from differences in the copy number of each of the three sets of subrepeat elements, TmiS0, TmiS1 and TmiS2. In addition, some indels were present in the flanking regions of the TmiS1 repeats. Combining PCR fingerprints from each of the three polymorphic loci produced a total of 19 individual strain profiles. The method was rapid, reproducible and discriminatory, and the fragment patterns simple to interpret. PCR fingerprint analysis of variable tandem repeat loci in the T. mentagrophytes var. interdigitale NTS represents a valuable molecular typing method for future epidemiological investigations in this species.

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Halman, Andreas, and Alicia Oshlack. "Accuracy of short tandem repeats genotyping tools in whole exome sequencing data." F1000Research 9 (March 23, 2020): 200. http://dx.doi.org/10.12688/f1000research.22639.1.

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Background: Short tandem repeats are an important source of genetic variation. They are highly mutable and repeat expansions are associated dozens of human disorders, such as Huntington's disease and spinocerebellar ataxias. Technical advantages in sequencing technology have made it possible to analyse these repeats at large scale; however, accurate genotyping is still a challenging task. We compared four different short tandem repeats genotyping tools on whole exome sequencing data to determine their genotyping performance and limits, which will aid other researchers in choosing a suitable tool and parameters for analysis. Methods: The analysis was performed on the Simons Simplex Collection dataset, where we used a novel method of evaluation with accuracy determined by the rate of homozygous calls on the X chromosome of male samples. In total we analysed 433 samples and around a million genotypes for evaluating tools on whole exome sequencing data. Results: We determined a relatively good performance of all tools when genotyping repeats of 3-6 bp in length, which could be improved with coverage and quality score filtering. However, genotyping homopolymers was challenging for all tools and a high error rate was present across different thresholds of coverage and quality scores. Interestingly, dinucleotide repeats displayed a high error rate as well, which was found to be mainly caused by the AC/TG repeats. Overall, LobSTR was able to make the most calls and was also the fastest tool, while RepeatSeq and HipSTR exhibited the lowest heterozygous error rate at low coverage. Conclusions: All tools have different strengths and weaknesses and the choice may depend on the application. In this analysis we demonstrated the effect of using different filtering parameters and offered recommendations based on the trade-off between the best accuracy of genotyping and the highest number of calls.

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Journal articles on the topic 'Tandem repeats'

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