Journal articles: 'Tandem duplication'

1

Pluciennik, Anna, Ravi R. Iyer, Pawel Parniewski, and Robert D. Wells. "Tandem Duplication." Journal of Biological Chemistry 275, no. 37 (June 30, 2000): 28386–97. http://dx.doi.org/10.1074/jbc.m000154200.

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Takahashi, Tadashi, Atsushi Sato, Masahiro Ogawa, Yoshiki Hanya, and Tetsuya Oguma. "Targeted Tandem Duplication of a Large Chromosomal Segment in Aspergillus oryzae." Applied and Environmental Microbiology 80, no. 15 (May 16, 2014): 4547–58. http://dx.doi.org/10.1128/aem.00300-14.

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ABSTRACTWe describe here the first successful construction of a targeted tandem duplication of a large chromosomal segment inAspergillus oryzae. The targeted tandem chromosomal duplication was achieved by using strains that had a 5′-deletedpyrGupstream of the region targeted for tandem chromosomal duplication and a 3′-deletedpyrGdownstream of the target region. Consequently, strains bearing a 210-kb targeted tandem chromosomal duplication near the centromeric region of chromosome 8 and strains bearing a targeted tandem chromosomal duplication of a 700-kb region of chromosome 2 were successfully constructed. The strains bearing the tandem chromosomal duplication were efficiently obtained from the regenerated protoplast of the parental strains. However, the generation of the chromosomal duplication did not depend on the introduction of double-stranded breaks (DSBs) by I-SceI. The chromosomal duplications of these strains were stably maintained after five generations of culture under nonselective conditions. The strains bearing the tandem chromosomal duplication in the 700-kb region of chromosome 2 showed highly increased protease activity in solid-state culture, indicating that the duplication of large chromosomal segments could be a useful new breeding technology and gene analysis method.

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Pan, Deng, and Liqing Zhang. "Tandemly Arrayed Genes in Vertebrate Genomes." Comparative and Functional Genomics 2008 (2008): 1–11. http://dx.doi.org/10.1155/2008/545269.

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Tandemly arrayed genes (TAGs) are duplicated genes that are linked as neighbors on a chromosome, many of which have important physiological and biochemical functions. Here we performed a survey of these genes in 11 available vertebrate genomes. TAGs account for an average of about 14% of all genes in these vertebrate genomes, and about 25% of all duplications. The majority of TAGs (72–94%) have parallel transcription orientation (i.e., they are encoded on the same strand) in contrast to the genome, which has about 50% of its genes in parallel transcription orientation. The majority of tandem arrays have only two members. In all species, the proportion of genes that belong to TAGs tends to be higher in large gene families than in small ones; together with our recent finding that tandem duplication played a more important role than retroposition in large families, this fact suggests that among all types of duplication mechanisms, tandem duplication is the predominant mechanism of duplication, especially in large families. Finally, several species have a higher proportion of large tandem arrays that are species-specific than random expectation.

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Lin, Ming-Tseh, Li-Hui Tseng, Katie Beierl, Antony Hsieh, Michele Thiess, Nadine Chase, Amanda Stafford, Mark J. Levis, James R. Eshleman, and Christopher D. Gocke. "Tandem Duplication PCR." Diagnostic Molecular Pathology 22, no. 3 (September 2013): 149–55. http://dx.doi.org/10.1097/pdm.0b013e31828308a1.

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Broughton, R. E., and T. E. Dowling. "Length variation in mitochondrial DNA of the minnow Cyprinella spiloptera." Genetics 138, no. 1 (September 1, 1994): 179–90. http://dx.doi.org/10.1093/genetics/138.1.179.

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Abstract Length differences in animal mitochondrial DNA (mtDNA) are common, frequently due to variation in copy number of direct tandem duplications. While such duplications appear to form without great difficulty in some taxonomic groups, they appear to be relatively short-lived, as typical duplication products are geographically restricted within species and infrequently shared among species. To better understand such length variation, we have studied a tandem and direct duplication of approximately 260 bp in the control region of the cyprinid fish, Cyprinella spiloptera. Restriction site analysis of 38 individuals was used to characterize population structure and the distribution of variation in repeat copy number. This revealed two length variants, including individuals with two or three copies of the repeat, and little geographic structure among populations. No standard length (single copy) genomes were found and heteroplasmy, a common feature of length variation in other taxa, was absent. Nucleotide sequence of tandem duplications and flanking regions localized duplication junctions in the phenylalanine tRNA and near the origin of replication. The locations of these junctions and the stability of folded repeat copies support the hypothesized importance of secondary structures in models of duplication formation.

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Naseeb, Samina, Ryan M. Ames, Daniela Delneri, and Simon C. Lovell. "Rapid functional and evolutionary changes follow gene duplication in yeast." Proceedings of the Royal Society B: Biological Sciences 284, no. 1861 (August 23, 2017): 20171393. http://dx.doi.org/10.1098/rspb.2017.1393.

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Duplication of genes or genomes provides the raw material for evolutionary innovation. After duplication a gene may be lost, recombine with another gene, have its function modified or be retained in an unaltered state. The fate of duplication is usually studied by comparing extant genomes and reconstructing the most likely ancestral states. Valuable as this approach is, it may miss the most rapid evolutionary events. Here, we engineered strains of Saccharomyces cerevisiae carrying tandem and non-tandem duplications of the singleton gene IFA38 to monitor (i) the fate of the duplicates in different conditions, including time scale and asymmetry of gene loss, and (ii) the changes in fitness and transcriptome of the strains immediately after duplication and after experimental evolution. We found that the duplication brings widespread transcriptional changes, but a fitness advantage is only present in fermentable media. In respiratory conditions, the yeast strains consistently lose the non-tandem IFA38 gene copy in a surprisingly short time, within only a few generations. This gene loss appears to be asymmetric and dependent on genome location, since the original IFA38 copy and the tandem duplicate are retained. Overall, this work shows for the first time that gene loss can be extremely rapid and context dependent.

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Fernandes, Gustavo, Mirela Souto, Frederico Costa, Edite Oliveira, and Bernardo Garicochea. "Familial Lymphoproliferative Malignancies and Tandem Duplication of NF1 Gene." Case Reports in Oncological Medicine 2014 (2014): 1–4. http://dx.doi.org/10.1155/2014/685857.

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Background. Neurofibromatosis type 1 is a genetic disorder caused by loss-of-function mutations in a tumor suppressor gene (NF1) which codifies the protein neurofibromin. The frequent genetic alterations that modify neurofibromin function are deletions and insertions. Duplications are rare and phenotype in patients bearing duplication of NF1 gene is thought to be restricted to developmental abnormalities, with no reference to cancer susceptibility in these patients. We evaluated a patient who presented with few clinical signs of neurofibromatosis type 1 and a conspicuous personal and familiar history of different types of cancer, especially lymphoproliferative malignancies. The coding region of the NF-1 gene was analyzed by real-time polymerase chain reaction and direct sequencing. Multiplex ligation-dependent probe amplification was performed to detect the number of mutant copies. The NF1 gene analysis showed the following alterations: mosaic duplication of NF1, TRAF4, and MYO1D. Fluorescence in situ hybridization using probes (RP5-1002G3 and RP5-92689) flanking NF1 gene in 17q11.2 and CEP17 for 17q11.11.1 was performed. There were three signals (RP5-1002G3conRP5-92689) in the interphases analyzed and two signals (RP5-1002G3conRP5-92689) in 93% of cells. These findings show a tandem duplication of 17q11.2.Conclusion. The case suggests the possibility that NF1 gene duplication may be associated with a phenotype characterized by lymphoproliferative disorders.

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8

BENSON, GARY. "Sequence Alignment with Tandem Duplication." Journal of Computational Biology 4, no. 3 (January 1997): 351–67. http://dx.doi.org/10.1089/cmb.1997.4.351.

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9

Yang, J. "On Counting Tandem Duplication Trees." Molecular Biology and Evolution 21, no. 6 (February 12, 2004): 1160–63. http://dx.doi.org/10.1093/molbev/msh115.

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10

Penso-Dolfin, L., T. Wu, and C. D. Greenman. "The combinatorics of tandem duplication." Discrete Applied Mathematics 194 (October 2015): 1–22. http://dx.doi.org/10.1016/j.dam.2015.05.014.

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11

Jackson, Jennifer A., and Gerald R. Fink. "MEIOTIC RECOMBINATION BETWEEN DUPLICATED GENETIC ELEMENTS IN SACCHAROMYCES CEREVISIAE." Genetics 109, no. 2 (February 1, 1985): 303–32. http://dx.doi.org/10.1093/genetics/109.2.303.

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ABSTRACT We have studied the meiotic recombination behavior of strains carrying two types of duplications of an 18.6-kilobase HIS4 BamHI fragment. The first type is a direct duplication of the HIS4 BamHI fragment in which the repeated sequences are separated by Escherichia coli plasmid sequences. The second type, a tandem duplication, has no sequences intervening between the repeated yeast DNA. The HIS4 genes in each region were marked genetically so that recombination events between the duplicated segments could be identified. Meiotic progeny of the strains carrying the duplication were analyzed genetically and biochemically to determine the types of recombination events that had occurred. Analysis of the direct vs. tandem duplication suggests that the E. coli plasmid sequences are recombinogenic in yeast when homozygous. In both types of duplications recombination between the duplicated HIS4 regions occurs at high frequency and involves predominantly interchromosomal reciprocal exchanges (equal and unequal crossovers). The striking observation is that intrachromosomal reciprocal recombination is very rare in comparison with interchromosomal reciprocal recombination. However, intrachromosomal gene conversion occurs at about the same frequency as interchromosomal gene conversion. Reciprocal recombination events between regions on the same chromatid are the most infrequent exchanges. These data suggest that intrachromosomal reciprocal exchanges are suppressed.

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12

Stanton, D. J., L. L. Daehler, C. C. Moritz, and W. M. Brown. "Sequences with the potential to form stem-and-loop structures are associated with coding-region duplications in animal mitochondrial DNA." Genetics 137, no. 1 (May 1, 1994): 233–41. http://dx.doi.org/10.1093/genetics/137.1.233.

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Abstract Tandem duplications of gene-encoding regions occur in the mitochondrial DNA (mt DNA) of some individuals belonging to several species of whiptail lizards (genus Cnemidophorus). All or part of the duplicated regions of the mtDNAs from five different species were sequenced. In all, the duplication endpoints were within or immediately adjacent to sequences in tRNA, rRNA or protein genes that are capable of forming energetically stable stem-and-loop structures. In two of these mtDNAs, the duplication endpoints were also associated with a direct sequence repeat of 13 bp. The consistent association of stem-and-loop structures with duplication endpoints suggests that these structures may play a role in the duplication process. These data, combined with the absence of direct or palindromic repeats at three of the pairs of duplication endpoints, also suggest the existence of a mechanism for generating de novo duplications that is qualitatively different from those previously modeled.

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13

Loehlin, David W., and Sean B. Carroll. "Expression of tandem gene duplicates is often greater than twofold." Proceedings of the National Academy of Sciences 113, no. 21 (May 9, 2016): 5988–92. http://dx.doi.org/10.1073/pnas.1605886113.

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Tandem gene duplication is an important mutational process in evolutionary adaptation and human disease. Hypothetically, two tandem gene copies should produce twice the output of a single gene, but this expectation has not been rigorously investigated. Here, we show that tandem duplication often results in more than double the gene activity. A naturally occurring tandem duplication of the Alcohol dehydrogenase (Adh) gene exhibits 2.6-fold greater expression than the single-copy gene in transgenic Drosophila. This tandem duplication also exhibits greater activity than two copies of the gene in trans, demonstrating that it is the tandem arrangement and not copy number that is the cause of overactivity. We also show that tandem duplication of an unrelated synthetic reporter gene is overactive (2.3- to 5.1-fold) at all sites in the genome that we tested, suggesting that overactivity could be a general property of tandem gene duplicates. Overactivity occurs at the level of RNA transcription, and therefore tandem duplicate overactivity appears to be a previously unidentified form of position effect. The increment of surplus gene expression observed is comparable to many regulatory mutations fixed in nature and, if typical of other genomes, would shape the fate of tandem duplicates in evolution.

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14

Aluru, Chaitanya, and Mona Singh. "Improved inference of tandem domain duplications." Bioinformatics 37, Supplement_1 (July 1, 2021): i133—i141. http://dx.doi.org/10.1093/bioinformatics/btab329.

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Abstract Motivation Protein domain duplications are a major contributor to the functional diversification of protein families. These duplications can occur one at a time through single domain duplications, or as tandem duplications where several consecutive domains are duplicated together as part of a single evolutionary event. Existing methods for inferring domain-level evolutionary events are based on reconciling domain trees with gene trees. While some formulations consider multiple domain duplications, they do not explicitly model tandem duplications; this leads to inaccurate inference of which domains duplicated together over the course of evolution. Results Here, we introduce a reconciliation-based framework that considers the relative positions of domains within extant sequences. We use this information to uncover tandem domain duplications within the evolutionary history of these genes. We devise an integer linear programming approach that solves our problem exactly, and a heuristic approach that works well in practice. We perform extensive simulation studies to demonstrate that our approaches can accurately uncover single and tandem domain duplications, and additionally test our approach on a well-studied orthogroup where lineage-specific domain expansions exhibit varying and complex domain duplication patterns. Availability and implementation Code is available on github at https://github.com/Singh-Lab/TandemDuplications. Supplementary information Supplementary data are available at Bioinformatics online.

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15

Foss, E. J., P. W. Garrett, J. A. Kinsey, and E. U. Selker. "Specificity of repeat-induced point mutation (RIP) in Neurospora: sensitivity of non-Neurospora sequences, a natural diverged tandem duplication, and unique DNA adjacent to a duplicated region." Genetics 127, no. 4 (April 1, 1991): 711–17. http://dx.doi.org/10.1093/genetics/127.4.711.

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Abstract The process designated RIP (repeat-induced point mutation) alters duplicated DNA sequences in the sexual cycle of Neurospora crassa. We tested whether non-Neurospora sequences are susceptible to RIP, explored the basis for the observed immunity to this process of a diverged tandem duplication that probably arose by a natural duplication followed by RIP (the Neurospora zeta-eta region), and investigated whether RIP extends at all into unique sequences bordering a duplicated region. Bacterial sequences of the plasmid pUC8 and of a gene conferring resistance to hygromycin B were sensitive to RIP in N. crassa when repeated in the genome. When the entire 1.6-kb zeta-eta region was duplicated, it was susceptible to RIP, but was affected by it to a lesser extent than other duplications. Only three of 62 progeny from crosses harboring unlinked duplications of the region showed evidence of changes. We attribute the low level of alterations to depletion of mutable sites. The stability of the zeta-eta region in strains having single copies of the region suggests that the 14% divergence of the tandem elements is sufficient to prevent RIP. DNA sequence analysis of unduplicated pUC8 sequences adjacent to a duplication revealed that RIP continued at least 180 bp beyond the boundary of the duplication. Three mutations occurred in the 200-bp segment of bordering sequences examined.

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16

Dill, F. J., M. Schertzer, J. Sandercock, B. Tischler, and S. Wood. "Inverted tandem duplication generates a duplication deficiency of chromosome 8p." Clinical Genetics 32, no. 2 (June 28, 2008): 109–13. http://dx.doi.org/10.1111/j.1399-0004.1987.tb03335.x.

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17

Lan, Tianying, Tanya Renner, Enrique Ibarra-Laclette, Kimberly M. Farr, Tien-Hao Chang, Sergio Alan Cervantes-Pérez, Chunfang Zheng, et al. "Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome." Proceedings of the National Academy of Sciences 114, no. 22 (May 15, 2017): E4435—E4441. http://dx.doi.org/10.1073/pnas.1702072114.

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Utricularia gibba, the humped bladderwort, is a carnivorous plant that retains a tiny nuclear genome despite at least two rounds of whole genome duplication (WGD) since common ancestry with grapevine and other species. We used a third-generation genome assembly with several complete chromosomes to reconstruct the two most recent lineage-specific ancestral genomes that led to the modern U. gibba genome structure. Patterns of subgenome dominance in the most recent WGD, both architectural and transcriptional, are suggestive of allopolyploidization, which may have generated genomic novelty and led to instantaneous speciation. Syntenic duplicates retained in polyploid blocks are enriched for transcription factor functions, whereas gene copies derived from ongoing tandem duplication events are enriched in metabolic functions potentially important for a carnivorous plant. Among these are tandem arrays of cysteine protease genes with trap-specific expression that evolved within a protein family known to be useful in the digestion of animal prey. Further enriched functions among tandem duplicates (also with trap-enhanced expression) include peptide transport (intercellular movement of broken-down prey proteins), ATPase activities (bladder-trap acidification and transmembrane nutrient transport), hydrolase and chitinase activities (breakdown of prey polysaccharides), and cell-wall dynamic components possibly associated with active bladder movements. Whereas independently polyploid Arabidopsis syntenic gene duplicates are similarly enriched for transcriptional regulatory activities, Arabidopsis tandems are distinct from those of U. gibba, while still metabolic and likely reflecting unique adaptations of that species. Taken together, these findings highlight the special importance of tandem duplications in the adaptive landscapes of a carnivorous plant genome.

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Gascuel, Olivier, Michael D. Hendy, Alain Jean-Marie, and Robert McLachlan. "The Combinatorics of Tandem Duplication Trees." Systematic Biology 52, no. 1 (February 1, 2003): 110–18. http://dx.doi.org/10.1080/10635150390132821.

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Zeraatpisheh, Mohamadbagher, Morteza Esmaeili, and T. Aaron Gulliver. "Construction of tandem duplication correcting codes." IET Communications 13, no. 15 (September 17, 2019): 2217–25. http://dx.doi.org/10.1049/iet-com.2018.6053.

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Martinez Gomez, Laura, Fernando Pozo, Thomas A. Walsh, Federico Abascal, and Michael L. Tress. "The clinical importance of tandem exon duplication-derived substitutions." Nucleic Acids Research 49, no. 14 (July 24, 2021): 8232–46. http://dx.doi.org/10.1093/nar/gkab623.

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Abstract Most coding genes in the human genome are annotated with multiple alternative transcripts. However, clear evidence for the functional relevance of the protein isoforms produced by these alternative transcripts is often hard to find. Alternative isoforms generated from tandem exon duplication-derived substitutions are an exception. These splice events are rare, but have important functional consequences. Here, we have catalogued the 236 tandem exon duplication-derived substitutions annotated in the GENCODE human reference set. We find that more than 90% of the events have a last common ancestor in teleost fish, so are at least 425 million years old, and twenty-one can be traced back to the Bilateria clade. Alternative isoforms generated from tandem exon duplication-derived substitutions also have significantly more clinical impact than other alternative isoforms. Tandem exon duplication-derived substitutions have >25 times as many pathogenic and likely pathogenic mutations as other alternative events. Tandem exon duplication-derived substitutions appear to have vital functional roles in the cell and may have played a prominent part in metazoan evolution.

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Veit, B., E. Vollbrecht, J. Mathern, and S. Hake. "A tandem duplication causes the Kn1-O allele of Knotted, a dominant morphological mutant of maize." Genetics 125, no. 3 (July 1, 1990): 623–31. http://dx.doi.org/10.1093/genetics/125.3.623.

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Abstract Molecular and genetic techniques are used to define Kn1-O, a mutation which interferes with the normal differentiation of vascular tissue in leaves. Sequences associated with a previously cloned allele, Kn1-2F11, were used as hybridization probes in a Southern analysis of Kn1-O. By this analysis, Kn1-O lacks the Ds2 transposable element that causes Kn1-2F11 but instead is associated with a sequence duplication. Sequence and restriction analysis of genomic clones show that the duplication consists of a tandem array of two 17-kb repeats. Analysis of Kn1-O derivatives indicates that the duplication itself conditions the mutant phenotype; a severely knotted line, Kn1-Ox, has gained a repeat unit to form a triplication, whereas normal derivatives have either lost a repeat unit or sustained insertions that disrupt the tandem duplication. These insertions map near the central junction of the tandem duplication, suggesting that the mutant phenotype results from the novel juxtaposition of sequences. We discuss models that relate the tandem duplication of sequences to altered gene expression.

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Das, G., S. Consaul, and F. Sherman. "A highly revertible cyc1 mutant of yeast contains a small tandem duplication." Genetics 120, no. 1 (September 1, 1988): 57–62. http://dx.doi.org/10.1093/genetics/120.1.57.

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Abstract A mutant, cyc1-96, that reverts spontaneously at an extremely high rate, was uncovered after examining approximately 500 cyc1 mutants which lack or have defective iso-1-cytochrome c in the yeast Saccharomyces cerevisiae. Cloning and DNA sequencing of appropriate fragments revealed that the cyc1-96 mutation contained a 19 bp duplication whereas the spontaneously arising revertants contained the normal wild-type sequence. Because the 19 bp segment in the wild-type sequence is flanked by a 5 bp repeat and because the cyc1-96 mutation arose spontaneously, the 19 bp duplication may have arisen by slippage and misalignment during DNA synthesis. The high reversion rate was not diminished in strains containing the rad52 mutation, which generally reduces mitotic recombination, including recombination associated with the elimination of a segment of a long direct repeat. Thus the loss of segments from short and long duplications occur by different mechanisms. We suggest that the high reversion rates of cyc1-96 and other short duplications are due to misalignment errors during replication.

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Ghosal, Debabrota, and In-Soon You. "Gene duplication in haloaromatic degradative plasmids pJP4 and pJP2." Canadian Journal of Microbiology 34, no. 6 (June 1, 1988): 709–15. http://dx.doi.org/10.1139/m88-121.

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pJP2 and pJP4 are 2,4-dichlorophenoxyacetic acid catabolic plasmids, and they show DNA sequence homology. Most of the pJP2 molecules (80% or more) isolated from 2,4-dichlorophenoxyacetic acid grown cells of Alcaligenes eutrophus harbor a tandem duplication of a 25-kilobase (kb) segment encoding the catabolic functions. Unlike plasmid pJP4, pJP2 in A. eutrophus gives rise to a 3-chlorobenzoate phenotype without further genetic rearrangement. pJP4 under 3-chlorobenzoate selection contains an inverted duplication of 24.5 kb. Absence of selective pressure results in the prompt loss of one copy of the duplication in pJP4, but not of the tandem duplication in pJP2. In both pJP4 and pJP2, mutation of the duplicated copy, rather than gene dosage, is likely to be the basis of phenotypic change of catabolic functions. Experiments using the cloned DNA suggest that a tandem duplication is more stable than an inverted duplication.

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Wyandt, Herman E. "Reported tandem duplication/deletion of 9q is actually an inverted duplication." American Journal of Medical Genetics 100, no. 1 (2001): 82–83. http://dx.doi.org/10.1002/ajmg.1172.

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Steudel, Christine, Martin Wermke, Markus Schaich, Ulrike Schäkel, Thomas Illmer, Gerhard Ehninger, and Christian Thiede. "Comparative analysis ofMLLpartial tandem duplication andFLT3internal tandem duplication mutations in 956 adult patients with acute myeloid leukemia." Genes, Chromosomes and Cancer 37, no. 3 (April 16, 2003): 237–51. http://dx.doi.org/10.1002/gcc.10219.

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Zhang, Shuai, Lang Xie, Shuqing Zheng, Baoyue Lu, Wenjing Tao, Xiaoshuang Wang, Thomas D. Kocher, Linyan Zhou, and Deshou Wang. "Identification, Expression and Evolution of Short-Chain Dehydrogenases/Reductases in Nile Tilapia (Oreochromis niloticus)." International Journal of Molecular Sciences 22, no. 8 (April 18, 2021): 4201. http://dx.doi.org/10.3390/ijms22084201.

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The short-chain dehydrogenases/reductases (SDR) superfamily is involved in multiple physiological processes. In this study, genome-wide identification and comprehensive analysis of SDR superfamily were carried out in 29 animal species based on the latest genome databases. Overall, the number of SDR genes in animals increased with whole genome duplication (WGD), suggesting the expansion of SDRs during evolution, especially in 3R-WGD and polyploidization of teleosts. Phylogenetic analysis indicated that vertebrates SDRs were clustered into five categories: classical, extended, undefined, atypical, and complex. Moreover, tandem duplication of hpgd-a, rdh8b and dhrs13 was observed in teleosts analyzed. Additionally, tandem duplications of dhrs11-a, dhrs7a, hsd11b1b, and cbr1-a were observed in all cichlids analyzed, and tandem duplication of rdh10-b was observed in tilapiines. Transcriptome analysis of adult fish revealed that 93 SDRs were expressed in more than one tissue and 5 in one tissue only. Transcriptome analysis of gonads from different developmental stages showed that expression of 17 SDRs were sexually dimorphic with 11 higher in ovary and 6 higher in testis. The sexually dimorphic expressions of these SDRs were confirmed by in situ hybridization (ISH) and qPCR, indicating their possible roles in steroidogenesis and gonadal differentiation. Taken together, the identification and the expression data obtained in this study contribute to a better understanding of SDR superfamily evolution and functions in teleosts.

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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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Badano, Jose L., Ken Inoue, Nicholas Katsanis, and James R. Lupski. "New Polymorphic Short Tandem Repeats for PCR-based Charcot-Marie-Tooth Disease Type 1A Duplication Diagnosis." Clinical Chemistry 47, no. 5 (May 1, 2001): 838–43. http://dx.doi.org/10.1093/clinchem/47.5.838.

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Abstract Background: Charcot-Marie-Tooth disease type 1A (CMT1A) accounts for 70–90% of cases of CMT1 and is most frequently caused by the tandem duplication of a 1.4-Mb genomic fragment on chromosome 17p12. Molecular diagnosis of CMT1A has been based primarily on pulsed-field electrophoresis, fluorescence in situ hybridization, polymorphic allele dosage analysis, and quantitative PCR. We sought to improve the fidelity and applicability of PCR-based diagnosis by developing a panel of novel, highly polymorphic short tandem repeats (STRs) from within the CMT1A duplicated region. Methods: We used a recently available genomic sequence to identify potentially polymorphic simple repeats. We then amplified these sequences in a multiethnic cohort of unaffected individuals and assessed the heterozygosity and number of alleles for each STR. Highly informative markers were then tested in a set of previously diagnosed CMT1A duplication patients, and the ability to identify the genomic duplication through the presence of three bands was assessed. Results: We identified 34 polymorphic markers, 15 of which were suitable for CMT1A diagnosis on the basis of high heterozygosity in different ethnic groups, peak uniformity, and a large number of alleles. On the basis of the fluorescent dye and allele range of each marker, we developed two panels, each of which could be analyzed concurrently. Panel 1, which comprised 10 markers, detected 37 of 39 duplications, whereas panel 2, which comprised the remaining 5 markers, identified 21 of 39 duplications. Through the combination of both panels, we identified 39 of 39 duplications in previously diagnosed CMT1A patients. Conclusions: The newly developed 15-marker set has the capability of detecting >99% of duplications and thus is a powerful and versatile diagnostic tool.

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Kumagai, M., T. Yamashita, M. Honda, and H. Ikeda. "Effects of uvsX, uvsY and DNA topoisomerase on the formation of tandem duplications of the rII gene in bacteriophage T4." Genetics 135, no. 2 (October 1, 1993): 255–64. http://dx.doi.org/10.1093/genetics/135.2.255.

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Abstract We have characterized tandem duplications in the rII regions of phage T4. The rII deletion r1589 blocks only the function of the rIIA cistron, although it extends into the B cistron. Another rII deletion, r1236, blocks the function of the rIIB cistron and overlaps r1589. When a cross is made between r1589 and r1236, true rII+ progeny cannot form. Instead, anomalous phenotypically rII+ phages are detected carrying an rII region from each parent. Analyses of nucleotide sequences of the recombination junctions indicate that recombination takes place between short regions of homology (from 2 to 10 bp). Open reading frames of the recombinants deduced from the nucleotide sequences reveal that they contain a normal rIIA cistron and one of a variety of fused, duplicated rIIB cistrons. The T4 uvsX and uvsY genes, which participate in homologous recombination, are involved in this duplication formation. T4 DNA topoisomerase is encoded by genes 39, 52 and 60. Mutations in 52 and 60 reduced the frequency of such duplications, but mutations in gene 39 and some in gene 52 did not. Hence, the effects of topoisomerase mutations are allele-specific. Models are proposed in which these proteins are involved in tandem duplication.

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Jain, Siddharth, Farzad Farnoud Hassanzadeh, and Jehoshua Bruck. "Capacity and Expressiveness of Genomic Tandem Duplication." IEEE Transactions on Information Theory 63, no. 10 (October 2017): 6129–38. http://dx.doi.org/10.1109/tit.2017.2728079.

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Reams, Andrew B., and Ellen L. Neidle. "Selection for Gene Clustering by Tandem Duplication." Annual Review of Microbiology 58, no. 1 (October 2004): 119–42. http://dx.doi.org/10.1146/annurev.micro.58.030603.123806.

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Flatz, Sibylle, Christa Fonatsch, and Christa Fonatsch. "Partial trisomy 1q due to tandem duplication." Clinical Genetics 15, no. 6 (April 23, 2008): 541–42. http://dx.doi.org/10.1111/j.1399-0004.1979.tb00839.x.

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33

Zhang, L., B. Ma, L. Wang, and Y. Xu. "Greedy method for inferring tandem duplication history." Bioinformatics 19, no. 12 (August 11, 2003): 1497–504. http://dx.doi.org/10.1093/bioinformatics/btg191.

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O'Neil, Jennifer, Joelle Tchinda, Alejandro Gutierrez, Lisa Moreau, Richard S. Maser, Kwok-Kin Wong, Wei Li, et al. "Alu elements mediate MYB gene tandem duplication in human T-ALL." Journal of Experimental Medicine 204, no. 13 (December 10, 2007): 3059–66. http://dx.doi.org/10.1084/jem.20071637.

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Recent studies have demonstrated that the MYB oncogene is frequently duplicated in human T cell acute lymphoblastic leukemia (T-ALL). We find that the human MYB locus is flanked by 257-bp Alu repeats and that the duplication is mediated somatically by homologous recombination between the flanking Alu elements on sister chromatids. Nested long-range PCR analysis indicated a low frequency of homologous recombination leading to MYB tandem duplication in the peripheral blood mononuclear cells of ∼50% of healthy individuals, none of whom had a MYB duplication in the germline. We conclude that Alu-mediated MYB tandem duplication occurs at low frequency during normal thymocyte development and is clonally selected during the molecular pathogenesis of human T-ALL.

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35

Brosch, Roland, Stephen V. Gordon, Carmen Buchrieser, Alexander S. Pym, Thierry Garnier, and Stewart T. Cole. "Comparative Genomics Uncovers Large Tandem Chromosomal Duplications inMycobacterium bovisBCG Pasteur." Yeast 1, no. 2 (2000): 111–23. http://dx.doi.org/10.1002/1097-0061(20000630)17:2<111::aid-yea17>3.0.co;2-g.

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On direct comparison of minimal sets of ordered clones from bacterial artificial chromosome (BAC) libraries representing the complete genomes ofMycobacterium tuberculosisH37Rv and the vaccine strain,Mycobacterium bovisBCG Pasteur, two major rearrangements were identified in the genome ofM. bovisBCG Pasteur. These were shown to correspond to two tandem duplications, DU1 and DU2, of 29 668 bp and 36 161 bp, respectively. While DU1 resulted from a single duplication event, DU2 apparently arose from duplication of a 100 kb genomic segment that subsequently incurred an internal deletion of 64 kb. Several lines of evidence suggest that DU2 may continue to expand, since two copies were detected in a subpopulation of BCG Pasteur cells. BCG strains harbouring DU1 and DU2 are diploid for at least 58 genes and contain two copies oforiC, the chromosomal origin of replication. These findings indicate that these genomic regions of the BCG genome are still dynamic. Although the role of DU1 and DU2 in the attenuation and/or altered immunogenicity of BCG is yet unknown, knowledge of their existence will facilitate quality control of BCG vaccine lots and may help in monitoring the efficacy of the world's most widely used vaccine.

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36

Campregher, Paulo Vidal, Vinicius Renan Pinto de Mattos, Marco Aurélio Salvino, Fabio Pires de Souza Santos, and Nelson Hamerschlak. "Successful treatment of post-transplant relapsed acute myeloid leukemia with FLT3 internal tandem duplication using the combination of induction chemotherapy, donor lymphocyte infusion, sorafenib and azacitidine. Report of three cases." Einstein (São Paulo) 15, no. 3 (July 24, 2017): 355–58. http://dx.doi.org/10.1590/s1679-45082017rc3784.

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ABSTRACT Acute myeloid leukemia is a hematopoietic stem cell neoplastic disease associated with high morbidity and mortality. The presence of FLT3 internal tandem duplication mutations leads to high rates of relapse and decreased overall survival. Patients with FLT3 internal tandem duplication are normally treated with hematopoietic stem cell transplantation in first complete remission. Nevertheless, the incidence of post-transplant relapse is considerable in this group of patients, and the management of this clinical condition is challenging. The report describes the outcomes of patients with FLT3 internal tandem duplication positive acute myeloid leukemia who relapsed after allogeneic hematopoietic stem cell transplantation and were treated with the combination of re-induction chemotherapy, donor lymphocyte infusion, sorafenib and azacitidine. Three cases are described and all patients achieved prolonged complete remission with the combined therapy. The combination of induction chemotherapy followed by donor lymphocyte infusion, and the maintenance with azacitidine and sorafenib can be effective approaches in the treatment of post-hematopoietic stem cell transplant and relapsed FLT3 internal tandem duplication positive acute myeloid leukemia patients. This strategy should be further explored in the context of clinical trials.

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O’Neil, Jennifer, Joelle Tchinda, Alejandro Gutierrez, Lisa Moreau, Keith McKenna, Richard Maser, Kwok-Kin Wong, et al. "Large Scale Copy Number Variation Upregulates the Expression of MYB in Human T-ALL." Blood 108, no. 11 (November 16, 2006): 1408. http://dx.doi.org/10.1182/blood.v108.11.1408.1408.

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Abstract Using comparative genome hybridization (array CGH), we have discovered a small area of increased copy number on the long arm of chromosome 6 in 8 out of 20 (40%) T-ALL cell lines. The region of increased copy number is very small, containing only one gene, MYB, the cellular homolog of the avian oncogene v-myb. By performing fiber-FISH on these cell lines, we have shown that the increased copy number results from a discrete tandem duplication of the MYB gene on one allele. Although myb is a frequent target of retroviral insertional activation in screens for oncogenes whose overexpression accelerates the onset of murine T-ALL, its overexpression and increased copy number has not previously been implicated in human T-ALL. Using gene expression profiling and Western blotting, we have demonstrated that the duplication in human T-ALL results in increased levels of MYB expression. Furthermore, using quantitative PCR we have confirmed that this tandem duplication occurs in primary human T-ALL samples. In our studies to date, MYB tandem duplication and overexpression appears to occur as part of the major multistep molecular pathway in T-ALL that affects a majority of cases, in which the leukemic cells also have TAL1/SCL and LMO1/2 overexpression, and NOTCH1 gene activating mutations, together with homozygous deletion of the INK4A/ARF locus. We are currently determining the mechanism through which MYB overexpression contributes to the pathogenesis of T-ALL by siRNA knockdown in T-ALL cell lines. Our finding of MYB tandem gene duplication differs from classic forms of oncogene amplification involving double minutes or homogenously staining regions. It is possible that MYB copy number is increased through a novel somatic mechanism of allele-specific, tandem duplication of a small genomic region during the process of malignant transformation. Another possibility is suggested by recent studies documenting that inherited large-scale copy number variation (CNV) accounts for much of the phenotypic diversity within human populations. Further studies will be needed to determine whether MYB tandem duplication is present in the germline DNA of T-ALL patients, which if identified, would provide the first example of an inherited CNV functioning as a mechanism of cancer susceptibility.

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Greenwell, T. J., S. Kumar, and C. Hysell. "High-Grade Uterine Sarcoma with BCOR Internal Tandem Duplication Presenting With Total Uterine Inversion." American Journal of Clinical Pathology 154, Supplement_1 (October 2020): S78—S79. http://dx.doi.org/10.1093/ajcp/aqaa161.172.

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Abstract Casestudy: High-grade uterine sarcomas are rare mesenchymal tumors in which the underlying genetics of many have been recently elucidated. BCOR internal tandem duplications are present in a subset of high-grade uterine sarcomas. We report a diagnostically challenging case of a high-grade uterine sarcoma with a BCOR internal tandem duplication presenting with total uterine inversion. The case is that of a 24 year old G0P0 female with a four month history of intermittent diffuse abdominal pain and abnormal uterine bleeding. Pelvic examination revealed a mass protruding to the hymenal ring. The patient was suspected of having a prolapsed fibroid through the cervix, and a myomectomy was planned. During the procedure, total uterine inversion was noted as a result of a submucosal mass emanating from the uterine apex. The mass was removed off a broad base using sharp dissection, and the uterus was reverted in a subsequent procedure. Grossly, the mass was polypoid, rubbery, and measured 7 cm in greatest dimension. It was grey-white to red-brown, variegated, and fibrotic with focal hemorrhagic areas. Histologically, the neoplasm had variable cellularity with spindle cells and a myxoid background. There was diffuse mild to moderate cytologic atypia and areas of increased mitotic activity. Tongue-like growth was present at the interface of the tumor with the normal myometrium. The neoplastic cells showed strong immunoreactivity for cyclin D1, BCOR, and TRK. There was focal immunoreactivity for CD10, and ALK was negative. Next-generation sequencing was performed and demonstrated an insertion into the BCOR gene, consistent with a diagnosis of high- grade uterine sarcoma with BCOR internal tandem duplication. In conclusion, we report an interesting presentation of a high-grade uterine sarcoma with BCOR internal tandem duplication causing total uterine inversion. The morphologic features and immunohistochemical profile suggested the possibility of the entity, and next generation sequencing confirmed the diagnosis.

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Suzuki, Erina, Ryosuke Bo, Kaori Sue, Hiroyuki Awano, Tsutomu Ogata, Satoshi Narumi, Masayo Kagami, Shinichiro Sano, and Maki Fukami. "A de novo 50-bp GNAS Intragenic Duplication in a Patient with Pseudohypoparathyroidism Type 1a." Cytogenetic and Genome Research 153, no. 3 (2017): 125–30. http://dx.doi.org/10.1159/000485644.

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Germline intragenic mutations in the GNAS locus result in pseudohypoparathyroidism type 1a (PHP1a) and related conditions. Nearly half of the previously reported GNAS intragenic mutations were structural variants, including 3 tandem duplications of 12-25 bp. However, the precise mutation spectrum and the genomic basis of GNAS structural variants remain to be clarified. Here, we report a de novo 50-bp tandem duplication in GNAS (c.723_772dup50, p.Glu259Leufs*29) identified in a patient with typical clinical features of PHP1a. The mutant transcript was predicted to undergo mRNA decay or encode a nonfunctional protein. The 2 breakpoints of the duplication shared a 1-bp microhomology but were not associated with long homology or nucleotide stretches. We also examined the breakpoint structures of 3 previously reported GNAS duplications and found that 1 had a structure similar to that of our case, while the remaining 2 had blunt-ended breakpoints without microhomologies. In silico analyses revealed that the GNAS-flanking region was not enriched with repeats, palindromes, noncanonical DNA motifs, or GC content. This study expands the mutation spectrum of GNAS and provides the first indication that GNAS intragenic structural variants are induced by multiple processes, including nonhomologous end-joining and/or microhomology-mediated break-induced replication, independently of known rearrangement-inducing DNA features.

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40

Katju, Vaishali, and Michael Lynch. "The Structure and Early Evolution of Recently Arisen Gene Duplicates in theCaenorhabditis elegansGenome." Genetics 165, no. 4 (December 1, 2003): 1793–803. http://dx.doi.org/10.1093/genetics/165.4.1793.

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AbstractThe significance of gene duplication in provisioning raw materials for the evolution of genomic diversity is widely recognized, but the early evolutionary dynamics of duplicate genes remain obscure. To elucidate the structural characteristics of newly arisen gene duplicates at infancy and their subsequent evolutionary properties, we analyzed gene pairs with ≤10% divergence at synonymous sites within the genome of Caenorhabditis elegans. Structural heterogeneity between duplicate copies is present very early in their evolutionary history and is maintained over longer evolutionary timescales, suggesting that duplications across gene boundaries in conjunction with shuffling events have at least as much potential to contribute to long-term evolution as do fully redundant (complete) duplicates. The median duplication span of 1.4 kb falls short of the average gene length in C. elegans (2.5 kb), suggesting that partial gene duplications are frequent. Most gene duplicates reside close to the parent copy at inception, often as tandem inverted loci, and appear to disperse in the genome as they age, as a result of reduced survivorship of duplicates located in proximity to the ancestral copy. We propose that illegitimate recombination events leading to inverted duplications play a disproportionately large role in gene duplication within this genome in comparison with other mechanisms.

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Li, Wanlong, and Bikram S. Gill. "The Colinearity of the Sh2/A1 Orthologous Region in Rice, Sorghum and Maize Is Interrupted and Accompanied by Genome Expansion in the Triticeae." Genetics 160, no. 3 (March 1, 2002): 1153–62. http://dx.doi.org/10.1093/genetics/160.3.1153.

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Abstract The Sh2/A1 orthologous region of maize, rice, and sorghum contains five genes in the order Sh2, X1, X2, and two A1 homologs in tandem duplication. The Sh2 and A1 homologs are separated by ~20 kb in rice and sorghum and by ~140 kb in maize. We analyzed the fate of the Sh2/A1 region in large-genome species of the Triticeae (wheat, barley, and rye). In the Triticeae, synteny in the Sh2/A1 region was interrupted by a break between the X1 and X2 genes. The A1 and X2 genes remained colinear in homeologous chromosomes as in other grasses. The Sh2 and X1 orthologs also remained colinear but were translocated to a nonhomeologous chromosome. Gene X1 was duplicated on two nonhomeologous chromosomes, and surprisingly, a paralog shared homology much higher than that of the orthologous copy to the X1 gene of other grasses. No tandem duplication of A1 homologs was detected but duplication of A1 on a nonhomeologous barley chromosome 6H was observed. Intergenic distances expanded greatly in wheat compared to rice. Wheat and barley diverged from each other 12 million years ago and both show similar changes in the Sh2/A1 region, suggesting that the break in colinearity as well as X1 duplications and genome expansion occurred in a common ancestor of the Triticeae species.

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42

Brosch, Roland, Stephen V. Gordon, Carmen Buchrieser, Alexander S. Pym, Thierry Garnier, and Stewart T. Cole. "Comparative Genomics Uncovers Large Tandem Chromosomal Duplications in Mycobacterium bovis BCG Pasteur." Yeast 1, no. 2 (January 1, 2000): 111–23. http://dx.doi.org/10.1155/2000/217049.

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On direct comparison of minimal sets of ordered clones from bacterial artificial chromosome (BAC) libraries representing the complete genomes of Mycobacterium tuberculosis H37Rv and the vaccine strain, Mycobacterium bovis BCG Pasteur, two major rearrangements were identified in the genome of M. bovis BCG Pasteur. These were shown to correspond to two tandem duplications, DU1 and DU2, of 29 668 bp and 36 161 bp, respectively. While DU1 resulted from a single duplication event, DU2 apparently arose from duplication of a 100 kb genomic segment that subsequently incurred an internal deletion of 64 kb. Several lines of evidence suggest that DU2 may continue to expand, since two copies were detected in a subpopulation of BCG Pasteur cells. BCG strains harbouring DU1 and DU2 are diploid for at least 58 genes and contain two copies of oriC, the chromosomal origin of replication. These findings indicate that these genomic regions of the BCG genome are still dynamic. Although the role of DU1 and DU2 in the attenuation and/or altered immunogenicity of BCG is yet unknown, knowledge of their existence will facilitate quality control of BCG vaccine lots and may help in monitoring the efficacy of the world's most widely used vaccine.

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43

Li, Ran, Zhiming Lei, Wenjuan Li, Wei Zhang, and Changfa Zhou. "Comparative Mitogenomic Analysis of Heptageniid Mayflies (Insecta: Ephemeroptera): Conserved Intergenic Spacer and tRNA Gene Duplication." Insects 12, no. 2 (February 16, 2021): 170. http://dx.doi.org/10.3390/insects12020170.

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Large intergenic spacers and tRNA gene duplications have been reported in several insect groups, although little is known about mitogenomes of mayflies. Here, we determined complete mitogenomes of ten heptageniid species and systemically analyzed their mitogenomic features. Both a conserved intergenic spacer (IGS) and trnM duplication were detected in those mitogenomes. The IGS, which was observed in heptageniids, could be further folded into a stable stem–loop structure. The tRNA gene duplication was found in almost all analyzed mitogenomes, and a unique gene block trnI-trnM-trnQ-trnM-ND2 was also discovered. Our analysis demonstrates that the heptageniid gene arrangement pattern can be explained by the tandem duplication-random loss (TDRL) model. Phylogenetic analyses using both Bayesian inference (BI) and maximum likelihood (ML) methods based on the nucleotide and amino acid sequence data recovered the genus Epeorus as monophyletic with strong support. Our results provide a better understanding of mitogenomic evolution in Heptageniidae, as well as novel molecular markers for species identification of mayflies.

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Schmidt, T., I. Bartels, T. Liehr, P. Burfeind, B. Zoll, and M. Shoukier. "A Family with an Inverted Tandem Duplication 5q22.1q23.2." Cytogenetic and Genome Research 139, no. 1 (2013): 65–70. http://dx.doi.org/10.1159/000342914.

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Clark, R. D., T. Mohandas, and M. Fenner-Gonzales. "TANDEM DUPLICATION OF CHROMOSOME 1q IN FRYNS SYNDROME." Pediatric Research 21, no. 4 (April 1987): 226A. http://dx.doi.org/10.1203/00006450-198704010-00358.

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Kondrashov, F. A. "Origin of alternative splicing by tandem exon duplication." Human Molecular Genetics 10, no. 23 (November 1, 2001): 2661–69. http://dx.doi.org/10.1093/hmg/10.23.2661.

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de Ravel, T. J. L., J. R. Vermeesch, and J. P. Fryns. "De novo interstitial tandem duplication of chromosome 20p12.1p13." American Journal of Medical Genetics 117A, no. 1 (January 24, 2003): 76–79. http://dx.doi.org/10.1002/ajmg.a.10825.

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Schneider, Michael C., Christopher R. Hughes, Shawnia Forrester, and Virginia Kimonis. "Mild phenotype due to tandem duplication of l7p11.2." American Journal of Medical Genetics 94, no. 4 (2000): 296–99. http://dx.doi.org/10.1002/1096-8628(20001002)94:4<296::aid-ajmg6>3.0.co;2-b.

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49

Tang, Mengxiang, Michael Waterman, and Shibu Yooseph. "Zinc Finger Gene Clusters and Tandem Gene Duplication." Journal of Computational Biology 9, no. 2 (April 2002): 429–46. http://dx.doi.org/10.1089/10665270252935557.

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Malik, Faizan, Riyam T. Zreik, Dale J. Hedges, Joy Nakitandwe, Seungjae Lee, Russell A. Ward, M. Beth McCarville, Alberto Pappo, and Armita Bahrami. "Primary bone sarcoma with BCOR internal tandem duplication." Virchows Archiv 476, no. 6 (January 3, 2020): 915–20. http://dx.doi.org/10.1007/s00428-019-02729-z.

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Journal articles on the topic 'Tandem duplication'

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