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1
Ros, Francesca, and Reinhard Kunze. "Regulation of Activator/Dissociation Transposition by Replication and DNA Methylation." Genetics 157, no. 4 (April 1, 2001): 1723–33. http://dx.doi.org/10.1093/genetics/157.4.1723.
Повний текст джерелаАнотація:
Abstract In maize the transposable elements Activator/Dissociation (Ac/Ds) transpose shortly after replication from one of the two resulting chromatids (“chromatid selectivity”). A model has been suggested that explains this phenomenon as a consequence of different affinity for Ac transposase binding to holo-, hemi-, and unmethylated transposon ends. Here we demonstrate that in petunia cells a holomethylated Ds is unable to excise from a nonreplicating vector and that replication restores excision. A Ds element hemi-methylated on one DNA strand transposes in the absence of replication, whereas hemi-methylation of the complementary strand causes a >6.3-fold inhibition of Ds excision. Consistently in the active hemi-methylated state, the Ds ends have a high binding affinity for the transposase, whereas binding to inactive ends is strongly reduced. These results provide strong evidence for the above-mentioned model. Moreover, in the absence of DNA methylation, replication enhances Ds transposition in petunia protoplasts >8-fold and promotes formation of a predominant excision footprint. Accordingly, replication also has a methylation-independent regulatory effect on transposition.
2
Sota, Masahiro, Masahiro Endo, Keiji Nitta, Haruhiko Kawasaki, and Masataka Tsuda. "Characterization of a Class II Defective Transposon Carrying Two Haloacetate Dehalogenase Genes from Delftia acidovorans Plasmid pUO1." Applied and Environmental Microbiology 68, no. 5 (May 2002): 2307–15. http://dx.doi.org/10.1128/aem.68.5.2307-2315.2002.
Повний текст джерелаАнотація:
ABSTRACT The two haloacetate dehalogenase genes, dehH1 and dehH2, on the 65-kb plasmid pUO1 from Delftia acidovorans strain B were found to be located on transposable elements. The dehH2 gene was carried on an 8.9-kb class I composite transposon (TnHad1) that was flanked by two directly repeated copies of IS1071, IS1071L and IS1071R. The dehH1 gene was also flanked by IS1071L and a truncated version of IS1071 (IS1071N). TnHad1, dehH1, and IS1071N were located on a 15.6-kb class II transposon (TnHad2) whose terminal inverted repeats and res site showed high homology with those of the Tn21-related transposons. TnHad2 was defective in transposition because of its lacking the transposase and resolvase genes. TnHad2 could transpose when the Tn21-encoded transposase and resolvase were supplied in trans. These results demonstrated that Tn Had2 is a defective Tn21-related transposon carrying another class I catabolic transposon.
3
Gorbunova, Vera, and Avraham A. Levy. "Circularized Ac/Ds Transposons: Formation, Structure and Fate." Genetics 145, no. 4 (April 1, 1997): 1161–69. http://dx.doi.org/10.1093/genetics/145.4.1161.
Повний текст джерелаАнотація:
The maize Ac/Ds transposable elements are thought to transpose via a cut-and-paste mechanism, but the intermediates formed during transposition are still unknown. In this work we present evidence that circular Ac molecules are formed in plants containing actively transposing elements. In these circles, transposon ends are joined head-to-head. The sequence at the ends' junction is variable, containing small deletions or insertions. Circles containing deleted Ac ends are probably unable to successfully reintegrate. To test the ability of circles with intact transposon ends to integrate into the genome, an artificial Ds circle was constructed by cloning the joined ends of Ac into a plasmid carrying a plant selectable marker. When such a circular Ds was introduced into tobacco protoplasts in the presence of Ac-transposase, no efficient transposase-mediated integration was observed. Although a circular transposition intermediate cannot be ruled out, the findings of circles with deleted transposon ends and the absence of transposase-mediated integration of the circular Ds suggest that some of the joined-ends-carrying elements are not transposition intermediates, but rather abortive excision products. The formation of Ac circles might account for the previously described phenomenon of Ac-loss. The origin of Ac circles and the implications for models of Ac transposition are discussed.
4
Gay, N. J., V. L. Tybulewicz, and J. E. Walker. "Insertion of transposon Tn7 into the Escherichia coli glmS transcriptional terminator." Biochemical Journal 234, no. 1 (February 15, 1986): 111–17. http://dx.doi.org/10.1042/bj2340111.
Повний текст джерелаАнотація:
The transposon Tn7 is unusual as it transposes at high frequencies from episomal elements to a unique site in the Escherichia coli chromosome. This unique site is within a region of dyad symmetry that we have demonstrated to be the transcriptional terminator of the glmS gene which encodes the glutamine amidotransferase, glucosamine synthetase. Transposition of Tn7 abolishes termination of glmS transcription at this site; the transcripts now extend into the left end of Tn7 and terminate at a new site, tm, 127 base pairs from the left end of Tn7. This region of the transposon contains a long open reading frame which encodes a protein sequence that is significantly related to the transposase proteins of the transposable elements IS1 and Tn3. A weak transcript has been identified that emanates from a promoter on the 5′ side of this reading frame. This promoter is over-run by glmS transcripts and so it appears that expression of the Tn7 transposase may be regulated by promoter occlusion.
5
Kawakami, Koichi, and Tetsuo Noda. "Transposition of the Tol2 Element, an Ac-Like Element From the Japanese Medaka Fish Oryzias latipes, in Mouse Embryonic Stem Cells." Genetics 166, no. 2 (February 1, 2004): 895–99. http://dx.doi.org/10.1093/genetics/166.2.895.
Повний текст джерелаАнотація:
Abstract The Tol2 transposable element of the Japanese medaka fish belongs to the hAT family of transposons including hobo of Drosophila, Ac of maize, and Tam3 of snapdragon. To date, Tol2 is the only natural transposon in vertebrates that has ever been shown to encode a fully functional transposase. It has not been known, however, whether Tol2 can transpose in vertebrates other than fish. We report here transposition of Tol2 in mouse embryonic stem (ES) cells. We constructed a transposon donor plasmid containing a nonautonomous Tol2 element with the neomycin resistance gene and a helper plasmid capable of expressing the transposase and introduced the donor plasmid with various amounts of the helper plasmid by electroporation into mouse ES cells. The number of G418-resistant ES colonies increased as the amount of helper plasmid was increased, in a dose-dependent manner, indicating that the transposase activity elevated the integration efficiency. These G418-resistant ES colonies were cloned and the structure of the junction of the integrated Tol2 element and the genomic DNA was analyzed by inverse PCR. In those clones, Tol2 was surrounded by mouse genomic sequences and an 8-bp direct repeat was created adjacent to both ends of Tol2, indicating that Tol2 was integrated in the genome through transposition. The Tol2 transposon system is thus active in mouse as well as in fish. We propose that it should be used as a genetic tool to develop novel gene transfer, transgenesis, and mutagenesis methods in mammals.
6
Migheli, Quirico, Richard Laugé, Jean-Michel Davière, Catherine Gerlinger, Fiona Kaper, Thierry Langin, and Marie-Josée Daboussi. "Transposition of the Autonomous Fot1 Element in the Filamentous Fungus Fusarium oxysporum." Genetics 151, no. 3 (March 1, 1999): 1005–13. http://dx.doi.org/10.1093/genetics/151.3.1005.
Повний текст джерелаАнотація:
Abstract Autonomous mobility of different copies of the Fot1 element was determined for several strains of the fungal plant pathogen Fusarium oxysporum to develop a transposon tagging system. Two Fot1 copies inserted into the third intron of the nitrate reductase structural gene (niaD) were separately introduced into two genetic backgrounds devoid of endogenous Fot1 elements. Mobility of these copies was observed through a phenotypic assay for excision based on the restoration of nitrate reductase activity. Inactivation of the Fot1 transposase open reading frame (frameshift, deletion, or disruption) prevented excision in strains free of Fot1 elements. Molecular analysis of the Nia+ revertant strains showed that the Fot1 element reintegrated frequently into new genomic sites after excision and that it can transpose from the introduced niaD gene into a different chromosome. Sequence analysis of several Fot1 excision sites revealed the socalled footprint left by this transposable element. Three reinserted Fot1 elements were cloned and the DNA sequences flanking the transposon were determined using inverse polymerase chain reaction. In all cases, the transposon was inserted into a TA dinucleotide and created the characteristic TA target site duplication. The availability of autonomous Fot1 copies will now permit the development of an efficient two-component transposon tagging system comprising a trans-activator element supplying transposase and a cis-responsive marked element.
7
Hughes, K. T., and J. R. Roth. "Transitory cis complementation: a method for providing transposition functions to defective transposons." Genetics 119, no. 1 (May 1, 1988): 9–12. http://dx.doi.org/10.1093/genetics/119.1.9.
Повний текст джерелаАнотація:
Abstract A genetic complementation system is described in which the complementing components are close together in a single linear DNA fragment; the complementation situation is temporary. This system is useful for providing transposition functions to transposition-defective transposons, since transposition functions act preferentially in cis. The basic procedure involves placing a transposition-defective transposon near the gene(s) for its transposition functions on a single DNA fragment. This fragment is introduced, here by general transduction, into a new host. The transposase acts in cis to permit the defective element to transpose from the introduced fragment into the recipient chromosome. The helper genes do not transpose and are lost by degradation and segregation. The method yields single insertion mutants that lack transposase and are not subject to further transposition or chromosome rearrangement. The general procedure is applicable to other sorts of transposable elements and could be modified for use in other genetic systems.
8
Urasaki, Akihiro, Yasuhiko Sekine, and Eiichi Ohtsubo. "Transposition of Cyanobacterium Insertion Element ISY100 in Escherichia coli." Journal of Bacteriology 184, no. 18 (September 15, 2002): 5104–12. http://dx.doi.org/10.1128/jb.184.18.5104-5112.2002.
Повний текст джерелаАнотація:
ABSTRACT The genome of the cyanobacterium Synechocystis sp. strain PCC6803 has nine kinds of insertion sequence (IS) elements, of which ISY100 in 22 copies is the most abundant. A typical ISY100 member is 947 bp long and has imperfect terminal inverted repeat sequences. It has an open reading frame encoding a 282-amino-acid protein that appears to have partial homology with the transposase encoded by a bacterial IS, IS630, indicating that ISY100 belongs to the IS630 family. To determine whether ISY100 has transposition ability, we constructed a plasmid carrying the IPTG (isopropyl-β-d-thiogalactopyranoside)-inducible transposase gene at one site and mini-ISY100 with the chloramphenicol resistance gene, substituted for the transposase gene of ISY100, at another site and introduced the plasmid into an Escherichia coli strain already harboring a target plasmid. Mini-ISY100 transposed to the target plasmid in the presence of IPTG at a very high frequency. Mini-ISY100 was inserted into the TA sequence and duplicated it upon transposition, as do IS630 family elements. Moreover, the mini-ISY100-carrying plasmid produced linear molecules of mini-ISY100 with the exact 3′ ends of ISY100 and 5′ ends lacking two nucleotides of the ISY100 sequence. No bacterial insertion elements have been shown to generate such molecules, whereas the eukaryotic Tc1/mariner family elements, Tc1 and Tc3, which transpose to the TA sequence, have. These findings suggest that ISY100 transposes to a new site through the formation of linear molecules, such as Tc1 and Tc3, by excision. Some Tc1/mariner family elements leave a footprint with an extra sequence at the site of excision. No footprints, however, were detected in the case of ISY100, suggesting that eukaryotes have a system that repairs a double strand break at the site of excision by an end-joining reaction, in which the gap is filled with a sequence of several base pairs, whereas prokaryotes do not have such a system. ISY100 transposes in E. coli, indicating that it transposes without any host factor other than the transposase encoded by itself. Therefore, it may be able to transpose in other biological systems.
9
Barret, P., M. Brinkman, and M. Beckert. "A sequence related to rice Pong transposable element displays transcriptional activation by in vitro culture and reveals somaclonal variations in maize." Genome 49, no. 11 (November 2006): 1399–407. http://dx.doi.org/10.1139/g06-109.
Повний текст джерелаАнотація:
Miniature inverted-repeat transposable elements (MITEs) are nonautonomous elements that are abundant in plant genomes. The rice MITE mPing was shown to be mobilized by anther culture, and the associated transposon Pong was shown to transpose actively in an Oryza sativa ‘indica’ rice cell-culture line. We have identified 3 sequences in maize named ZmTPAPong-like 1, 2, and 3 that displayed homology with the transposase of Pong. Here, we show that these sequences are differentially expressed during the in vitro androgenetic process in maize. We also demonstrate that the ZmTPAPong-like 1 and 3 sequences reveal somaclonal variations among plants regenerated from the calli of a doubled haploid line. These data suggest that the ZmTPAPong-like sequences could form part of a Zea mays element related to the rice Pong element. The possible activation of this newly discovered element under stress conditions is discussed.
10
Beckermann, Thomas M., Wentian Luo, Catherine M. Wilson, Ruth Ann Veach, and Matthew H. Wilson. "Cognate restriction of transposition by piggyBac-like proteins." Nucleic Acids Research 49, no. 14 (July 7, 2021): 8135–44. http://dx.doi.org/10.1093/nar/gkab578.
Повний текст джерелаАнотація:
Abstract Mobile genetic elements have been harnessed for gene transfer for a wide variety of applications including generation of stable cell lines, recombinant protein production, creation of transgenic animals, and engineering cell and gene therapy products. The piggyBac transposon family includes transposase or transposase-like proteins from a variety of species including insect, bat and human. Recently, human piggyBac transposable element derived 5 (PGBD5) protein was reported to be able to transpose piggyBac transposons in human cells raising possible safety concerns for piggyBac-mediated gene transfer applications. We evaluated three piggyBac-like proteins across species including piggyBac (insect), piggyBat (bat) and PGBD5 (human) for their ability to mobilize piggyBac transposons in human cells. We observed a lack of cross-species transposition activity. piggyBac and piggyBat activity was restricted to their cognate transposons. PGBD5 was unable to mobilize piggyBac transposons based on excision, colony count and plasmid rescue analysis, and it was unable to bind piggyBac terminal repeats. Within the piggyBac family, we observed a lack of cross-species activity and found that PGBD5 was unable to bind, excise or integrate piggyBac transposons in human cells. Transposition activity appears restricted within species within the piggyBac family of mobile genetic elements.
11
Movafagh, Abolfazl. "The Role of Transposable Element or Jumping Genes in Cancers." Asian Pacific Journal of Cancer Biology 1, no. 4 (December 25, 2016): 75–76. http://dx.doi.org/10.31557/apjcb.2016.1.4.75-76.
Повний текст джерелаАнотація:
Genomic, proteomic, transcriptomic, and epigenomic analyses of human tumors indicate that there are thousands of anomalies within each cancer genome compared to matched normal tissue. Based on these analyses it is evident that there are many undiscovered genetic drivers of cancer. Performing an unbiased forward genetic screen in human provides the tools to generate tumors and analyze their genetic composition, while reducing the background of passenger mutations. The transposon system is one such method that can be inserted throughout the genome by the transposable element. A transposable element or jumping genes (TE or transposon) is a DNA sequence that can change its position within a genome, sometimes creating or reversing mutations and altering the cell’s genome size. Transposable elements make up a large fraction of the genome and are responsible for much of the mass of DNA in a eukaryotic cell. There are at least two classes of TEs: Class I TEs or retrotransposons generally function via reverse transcr ption, while Class II TEs or DNA transposons encode the protein transposase, which they require for insertion and excision, and some of these TEs also encode other proteins. The most common transposable element in humans is the Alu sequence. It is approximately 300 bases long and can be found between 300,000 and one million times in the human genome. Alu alone is estimated to make up 15–17% of the human genome. Transposon s are mutagens and their movements are often the causes of genetic disease. They can damage the genome of their host cell in different ways. A transposon or a retrotransposon that inserts itself into a functional gene will most likely disable that gene causing cancers. After a DNA transposon leaves a gene, the resulting gap will probably not repaired correctly.
12
Healy, J., C. Corr, J. DeYoung, and B. Baker. "Linked and unlinked transposition of a genetically marked Dissociation element in transgenic tomato." Genetics 134, no. 2 (June 1, 1993): 571–84. http://dx.doi.org/10.1093/genetics/134.2.571.
Повний текст джерелаАнотація:
Abstract We have introduced a genetically marked Dissociation transposable element (Dsneo) into tomato. In the presence of Ac transposase, Dsneo excised from an integrated T-DNA and reinserted at numerous new sites in the tomato genome. The marker genes of Dsneo (NPTII) and the T-DNA (HPT) facilitated identification of plants bearing transposon excisions and insertions. To explore the feasibility of gene tagging strategies in tomato using Dsneo, we examined the genomic distribution of Dsneo receptor sites, relative to the location of the donor T-DNA locus. Restriction fragment length polymorphism mapping of transposed Dsneo elements was conducted in two tomato families, derived from independent primary transformants each bearing Dsneo within a T-DNA at a unique position in the genome. Transposition of Dsneo generated clusters of insertions that were positioned on several different tomato chromosomes. Dsneo insertions were often located on the same chromosome as the T-DNA donor site. However, no insertion showed tight linkage to the T-DNA. We consider the frequency and distance of Dsneo transposition observed in tomato to be well suited for transposon mutagenesis. Our study made use of a novel, stable allele of Ac (Ac3) that we discovered in transgenic tomato. We determined that the Ac3 element bears a deletion of the outermost 5 base pairs of the 5'-terminal inverted repeat. Though incapable of transposition itself, Ac3 retained the ability to mobilize Dsneo. We conclude that a dual element system, composed of the stable Ac3 trans-activator in combination with Dsneo, is an effective tool for transposon tagging experiments in tomato.
13
Miskey, Csaba, Balázs Papp, Lajos Mátés, Ludivine Sinzelle, Heiko Keller, Zsuzsanna Izsvák, and Zoltán Ivics. "The Ancient mariner Sails Again: Transposition of the Human Hsmar1 Element by a Reconstructed Transposase and Activities of the SETMAR Protein on Transposon Ends." Molecular and Cellular Biology 27, no. 12 (April 2, 2007): 4589–600. http://dx.doi.org/10.1128/mcb.02027-06.
Повний текст джерелаАнотація:
ABSTRACT Hsmar1, one of the two subfamilies of mariner transposons in humans, is an ancient element that entered the primate genome lineage ∼50 million years ago. Although Hsmar1 elements are inactive due to mutational damage, one particular copy of the transposase gene has apparently been under selection. This transposase coding region is part of the SETMAR gene, in which a histone methylatransferase SET domain is fused to an Hsmar1 transposase domain. A phylogenetic approach was taken to reconstruct the ancestral Hsmar1 transposase gene, which we named Hsmar1-Ra. The Hsmar1-Ra transposase efficiently mobilizes Hsmar1 transposons by a cut-and-paste mechanism in human cells and zebra fish embryos. Hsmar1-Ra can also mobilize short inverted-repeat transposable elements (MITEs) related to Hsmar1 (MiHsmar1), thereby establishing a functional relationship between an Hsmar1 transposase source and these MITEs. MiHsmar1 excision is 2 orders of magnitude more efficient than that of long elements, thus providing an explanation for their high copy numbers. We show that the SETMAR protein binds and introduces single-strand nicks into Hsmar1 inverted-repeat sequences in vitro. Pathway choices for DNA break repair were found to be characteristically different in response to transposon cleavage mediated by Hsmar1-Ra and SETMAR in vivo. Whereas nonhomologous end joining plays a dominant role in repairing excision sites generated by the Hsmar1-Ra transposase, DNA repair following cleavage by SETMAR predominantly follows a homology-dependent pathway. The novel transposon system can be a useful tool for genome manipulations in vertebrates and for investigations into the transpositional dynamics and the contributions of these elements to primate genome evolution.
14
Cerbin, Stefan, Ching Man Wai, Robert VanBuren, and Ning Jiang. "GingerRoot: A Novel DNA Transposon Encoding Integrase-Related Transposase in Plants and Animals." Genome Biology and Evolution 11, no. 11 (October 21, 2019): 3181–93. http://dx.doi.org/10.1093/gbe/evz230.
Повний текст джерелаАнотація:
Abstract Transposable elements represent the largest components of many eukaryotic genomes and different genomes harbor different combinations of elements. Here, we discovered a novel DNA transposon in the genome of the clubmoss Selaginella lepidophylla. Further searching for related sequences to the conserved DDE region uncovered the presence of this superfamily of elements in fish, coral, sea anemone, and other animal species. However, this element appears restricted to Bryophytes and Lycophytes in plants. This transposon, named GingerRoot, is associated with a 6 bp (base pair) target site duplication, and 100–150 bp terminal inverted repeats. Analysis of transposase sequences identified the DDE motif, a catalytic domain, which shows similarity to the integrase of Gypsy-like long terminal repeat retrotransposons, the most abundant component in plant genomes. A total of 77 intact and several hundred truncated copies of GingerRoot elements were identified in S. lepidophylla. Like Gypsy retrotransposons, GingerRoots show a lack of insertion preference near genes, which contrasts to the compact genome size of about 100 Mb. Nevertheless, a considerable portion of GingerRoot elements was found to carry gene fragments, suggesting the capacity of duplicating gene sequences is unlikely attributed to the proximity to genes. Elements carrying gene fragments appear to be less methylated, more diverged, and more distal to genes than those without gene fragments, indicating they are preferentially retained in gene-poor regions. This study has identified a broadly dispersed, novel DNA transposon, and the first plant DNA transposon with an integrase-related transposase, suggesting the possibility of de novo formation of Gypsy-like elements in plants.
15
Slotkin, R. Keith, Michael Freeling, and Damon Lisch. "Mu killer Causes the Heritable Inactivation of the Mutator Family of Transposable Elements in Zea mays." Genetics 165, no. 2 (October 1, 2003): 781–97. http://dx.doi.org/10.1093/genetics/165.2.781.
Повний текст джерелаАнотація:
Abstract Mutations in a number of genes responsible for the maintenance of transposon silencing have been reported. However, the initiation of epigenetic silencing of transposable elements is poorly characterized. Here, we report the identification of a single dominant locus, Mu killer (Muk), that acts to silence MuDR, the autonomous regulatory transposon of the Mutator family of transposable elements in maize. Muk results in the methylation of MuDR TIRs and is competent to silence one or several active MuDR elements. Silencing by Muk is not dependent on the position of the MuDR element and occurs gradually during plant development. Transcript levels of the MuDR transposase, mudrA, decrease substantially when Muk is present. The other transcript encoded by MuDR, mudrB, also fails to accumulate in the poly(A) RNA fraction when MuDR and Muk are combined. Additionally, plants undergoing MuDR silencing produce small, mudrA-homologous ∼26-nt RNAs, suggesting a role for RNA-directed DNA methylation in MuDR silencing. MuDR elements silenced by Muk remain silenced even in plants that do not inherit Muk, suggesting that Muk is required for the initiation of MuDR silencing but not for its maintenance.
16
Ipek, Ahmet, and Philipp W. Simon. "070 Non-autonomous Maize Transposable Element, Dissociation (Ds) Transposed in Carrot (Daucus carota L.)." HortScience 34, no. 3 (June 1999): 453C—453. http://dx.doi.org/10.21273/hortsci.34.3.453c.
Повний текст джерелаАнотація:
Maize transposable elements, Activator (Ac) and Ds transformed into several heterologous plant species for transposon tagging of genes. Several genes in Arabidopsis, flax, petunia, tobacco, and tomato have been tagged and cloned by using Ac and Ds. We have double transformed carrot lines, B493 and B7262 with stabilized autonomous Ac and non-autonomous Ds element to develop a two-element based transposon tagging system. PCR and Southern hybridization indicated that Ds element transposed from T-DNA in calli, somatic embryos and transgenic plants. The insertion of Ds element into new sites in carrot genome after excision verified by GUS assay, Southern hybridization and inverse-PCR. Currently, the behavior of non-autonomous Ds element is being studied. Ds induced mutation will be screened in transgenic plants. These initial results demonstrate that the Ac/Ds-based transposon tagging system may work in carrot.
17
Belzile, François, and John I. Yoder. "Unstable transmission and frequent rearrangement of two closely linked transposed Ac elements in transgenic tomato." Genome 37, no. 5 (October 1, 1994): 832–39. http://dx.doi.org/10.1139/g94-118.
Повний текст джерелаАнотація:
We are examining the behavior of the maize transposable element Ac in transgenic tomato with the goal of developing an efficient insertional mutagenesis system. Among the self progeny of a transgenic tomato plant containing an active Ac element, we identified six plants that contained the same germinally transposed Ac. In one of these plants, we found a second Ac element inserted in the same orientation and approximately 2 kb to the 5′ side of the original Ac insertion. Transmission of this composite structure was significantly reduced with less than one-quarter of the self progeny inheriting Ac either in the form of the intact parental allele (two neighboring Ac's) or derivatives of it. The derivative alleles that arose were complex in structure and could not be explained solely on the basis of the excision of one or the other Ac element. These results illustrate the potential of transposable elements to cause genetic instabilities and complex chromosomal rearrangements.Key words: Ac element, rearrangements, tomato, transposable element, transposon tagging.
18
Yant, Stephen R., and Mark A. Kay. "Nonhomologous-End-Joining Factors Regulate DNA Repair Fidelity during Sleeping Beauty Element Transposition in Mammalian Cells." Molecular and Cellular Biology 23, no. 23 (December 1, 2003): 8505–18. http://dx.doi.org/10.1128/mcb.23.23.8505-8518.2003.
Повний текст джерелаАнотація:
ABSTRACT Herein, we report that the DNA-dependent protein kinase (DNA-PK) regulates the DNA damage introduced during Sleeping Beauty (SB) element excision and reinsertion in mammalian cells. Using both plasmid- and chromosome-based mobility assays, we analyzed the repair of transposase-induced double-stranded DNA breaks in cells deficient in either the DNA-binding subunit of DNA-PK (Ku) or its catalytic subunit (DNA-PKcs). We found that the free 3′ overhangs left after SB element excision were efficiently and accurately processed by the major Ku-dependent nonhomologous-end-joining pathway. Rejoining of broken DNA molecules in the absence of Ku resulted in extensive end degradation at the donor site and greatly increased the frequency of recombination with ectopic templates. Therefore, the major DNA-PK-dependent DNA damage response predominates over more-error-prone repair pathways and thereby facilitates high-fidelity DNA repair during transposon mobilization in mammalian cells. Although transposable elements were not found to be efficiently circularized after transposase-mediated excision, DNA-PK deficiency supported more-frequent transposase-mediated element insertion than was found in wild-type controls. We conclude that, based on its ability to regulate excision site junctional diversity and transposon insertion frequency, DNA-PK serves an important protective role during transpositional recombination in mammals.
19
Lipkow, Karen, Nicolas Buisine, David J. Lampe, and Ronald Chalmers. "Early Intermediates of mariner Transposition: Catalysis without Synapsis of the Transposon Ends Suggests a Novel Architecture of the Synaptic Complex." Molecular and Cellular Biology 24, no. 18 (September 15, 2004): 8301–11. http://dx.doi.org/10.1128/mcb.24.18.8301-8311.2004.
Повний текст джерелаАнотація:
ABSTRACT The mariner family is probably the most widely distributed family of transposons in nature. Although these transposons are related to the well-studied bacterial insertion elements, there is evidence for major differences in their reaction mechanisms. We report the identification and characterization of complexes that contain the Himar1 transposase bound to a single transposon end. Titrations and mixing experiments with the native transposase and transposase fusions suggested that they contain different numbers of transposase monomers. However, the DNA protection footprints of the two most abundant single-end complexes are identical. This indicates that some transposase monomers may be bound to the transposon end solely by protein-protein interactions. This would mean that the Himar1 transposase can dimerize independently of the second transposon end and that the architecture of the synaptic complex has more in common with V(D)J recombination than with bacterial insertion elements. Like V(D)J recombination and in contrast to the case for bacterial elements, Himar1 catalysis does not appear to depend on synapsis of the transposon ends, and the single-end complexes are active for nicking and probably for cleavage. We discuss the role of this single-end activity in generating the mutations that inactivate the vast majority of mariner elements in eukaryotes.
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Petrovski, Steve, та Vilma A. Stanisich. "Embedded elements in the IncPβ plasmids R772 and R906 can be mobilized and can serve as a source of diverse and novel elements". Microbiology 157, № 6 (1 червня 2011): 1714–25. http://dx.doi.org/10.1099/mic.0.047761-0.
Повний текст джерелаАнотація:
IncP plasmids are important contributors to bacterial adaptation. Their phenotypic diversity is due largely to accessory regions located in one or two specific parts of the plasmid. The accessory regions are themselves diverse, as judged from sequenced plasmids mostly isolated from non-clinical sources. To further understand the diversity, evolutionary history and functional attributes of the accessory regions, we compared R906 and R772, focusing on the oriV–trfA accessory region. These IncPβ plasmids were from porcine and clinical sources, respectively. We found that the accessory regions formed potentially mobile elements, Tn510 (from R906) and Tn511 (from R772), that differed internally but had identical borders. Both elements appeared to have evolved from a TnAO22-like mer transposon that had inserted into an ancestral IncPβ plasmid and then accrued additional transposable elements and genes from various proteobacteria. Structural comparisons suggested that Tn510 (and a descendent in pB10), Tn511 and the mer element in pJP4 represent three lineages that evolved from the same widely dispersed IncPβ carrier. Functional studies on Tn511 revealed that its mer module is inactive due to a merT mutation, and that its aphAI region is prone to deletion. More significantly, we showed that by providing a suitable transposase gene in trans, the defective Tn510 and Tn511 could transpose intact or in part, and could also generate new elements (stable cointegrates and novel transposons). The ingredients for assisted transposition events similar to those observed here occur in natural microcosms, providing non-self-mobile elements with avenues for dispersal to new replicons and for structural diversification. This work provides an experimental demonstration of how the complex embedded elements uncovered in IncP plasmids and in other plasmid families may have been generated.
21
Collins, J. J., and P. Anderson. "The Tc5 family of transposable elements in Caenorhabditis elegans." Genetics 137, no. 3 (July 1, 1994): 771–81. http://dx.doi.org/10.1093/genetics/137.3.771.
Повний текст джерелаАнотація:
Abstract We have identified Tc5, a new family of transposable genetic elements in the nematode Caenorhabditis elegans. All wild-type varieties of C. elegans that we examined contain 4-6 copies of Tc5 per haploid genome, but we did not observe transposition or excision of Tc5 in these strains. Tc5 is active, however, in the mut-2 mutant strain TR679. Of 60 spontaneous unc-22 mutations isolated from strain TR679, three were caused by insertion of Tc5. All three Tc5-induced mutations are unstable; revertants results from precise or nearly precise excision of Tc5. Individual Tc5 elements are similar to each other in size and structure. The 3.2-kb element is bounded by inverted terminal repeats of nearly 500 bp. Eight of the ten terminal nucleotides of Tc5 are identical to the corresponding nucleotides of Tc4. Further, both elements recognize the same target site for insertion (CTNAG) and both cause duplication of the central TNA trinucleotide upon insertion. Other than these similarities to Tc4, Tc5 is unrelated to the three other transposon families (Tc1, Tc3 and Tc4) that transpose and excise at high frequency in mut-2 mutant strains. Mechanisms are discussed by which four apparently unrelated transposon families are all affected by the same mut-2 mutation.
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Handler, Alfred M., and Sheilachu P. Gomez. "The hobo Transposable Element Excises and Has Related Elements in Tephritid Species." Genetics 143, no. 3 (July 1, 1996): 1339–47. http://dx.doi.org/10.1093/genetics/143.3.1339.
Повний текст джерелаАнотація:
Abstract Function of the Drosophila melanogaster hobo transposon in tephritid species was tested in transient embryonic excision assays. Wild-type and mutant strains of Anastrepha suspensa, Bactrocera dorsalis, B. cucurbitae, Ceratitis capitata, and Toxotrypana curvicauda all supported hobo excision or deletion both in the presence and absence of co-injected hobo transposase, indicating a permissive state for hobo mobility and the existence of endogenous systems capable of mobilizing hobo. In several strains hobo helper reduced excision. Excision depended on hobo sequences in the indicator plasmid, though almost all excisions were imprecise and the mobilizing systems appear mechanistically different from hobo. hobe-related sequences were identified in all species except T. curvicauda. Parsimony analysis yielded a subgroup including the B. cucurbitae and C. capitata sequences along with hobo and Hermes, and a separate, more divergent subgroup including the A. suspensa and B. dorsalis sequences. All of the sequences exist as multiple genomic elements, and a deleted form of the B. cucurbitae element exists in B. dorsalis. The hobo-related sequences are probably members of the hAT transposon family with some evolving from distant ancestor elements, while others may have originated from more recent horizontal transfers.
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Lohe, Allan R., and Daniel L. Hartl. "Reduced Germline Mobility of a mariner Vector Containing Exogenous DNA: Effect of Size or Site?" Genetics 143, no. 3 (July 1, 1996): 1299–306. http://dx.doi.org/10.1093/genetics/143.3.1299.
Повний текст джерелаАнотація:
Abstract Germline mobilization of the transposable element mariner is severely inhibited by the insertion of a 4.5- to 11.9-kb fragment of exogenous DNA into a unique SacI site approximately in the middle of the 1286bp element. In the presence of transposase driven by the germline-specific hsp26-sgs3 promoter, mobilization of the MlwB construct (containing a 11.9-kb insertion) is detected at low frequency. Analysis of a mobilized MlwB element indicated that mobilization is mediated by the marinertransposase. However, transposed MlwB elements are also defective in germline mobilization. Rare, transposase-induced germline excision events were also recovered for such vectors. The estimated rate of excision is <0.1% per chromosome per generation. Excision appears to be accompanied by gap repair if a suitable template is available. The data imply that the reduced mobility of mariner vectors with exogenous DNA in the SacI site results from disruption of sequences necessary for efficient mobilization. The relative stability may be a valuable property in the uses of mariner-like elements in genetic engineering of insects of economic importance.
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Fablet, Marie, and Cristina Vieira. "Evolvability, epigenetics and transposable elements." BioMolecular Concepts 2, no. 5 (October 1, 2011): 333–41. http://dx.doi.org/10.1515/bmc.2011.035.
Повний текст джерелаАнотація:
AbstractEvolvability can be defined as the capacity of an individual to evolve and thus to capture adaptive mutations. Transposable elements (TE) are an important source of mutations in organisms. Their capacity to transpose within a genome, sometimes at a high rate, and their copy number regulation are environment-sensitive, as are the epigenetic pathways that mediate TE regulation in a genome. In this review we revisit the way we see evolvability with regard to transposable elements and epigenetics.
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Zhang, Xiaoyu, Ning Jiang, Cédric Feschotte, and Susan R. Wessler. "PIF- and Pong-Like Transposable Elements: Distribution, Evolution and Relationship With Tourist-Like Miniature Inverted-Repeat Transposable Elements." Genetics 166, no. 2 (February 1, 2004): 971–86. http://dx.doi.org/10.1093/genetics/166.2.971.
Повний текст джерелаАнотація:
Abstract Miniature inverted-repeat transposable elements (MITEs) are short, nonautonomous DNA elements that are widespread and abundant in plant genomes. Most of the hundreds of thousands of MITEs identified to date have been divided into two major groups on the basis of shared structural and sequence characteristics: Tourist-like and Stowaway-like. Since MITEs have no coding capacity, they must rely on transposases encoded by other elements. Two active transposons, the maize P Instability Factor (PIF) and the rice Pong element, have recently been implicated as sources of transposase for Tourist-like MITEs. Here we report that PIF- and Pong-like elements are widespread, diverse, and abundant in eukaryotes with hundreds of element-associated transposases found in a variety of plant, animal, and fungal genomes. The availability of virtually the entire rice genome sequence facilitated the identification of all the PIF/Pong-like elements in this organism and permitted a comprehensive analysis of their relationship with Tourist-like MITEs. Taken together, our results indicate that PIF and Pong are founding members of a large eukaryotic transposon superfamily and that members of this superfamily are responsible for the origin and amplification of Tourist-like MITEs.
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Bakoulis, Stylianos, Robert Krautz, Nicolas Alcaraz, Marco Salvatore, and Robin Andersson. "Endogenous retroviruses co-opted as divergently transcribed regulatory elements shape the regulatory landscape of embryonic stem cells." Nucleic Acids Research 50, no. 4 (February 15, 2022): 2111–27. http://dx.doi.org/10.1093/nar/gkac088.
Повний текст джерелаАнотація:
Abstract Transposable elements are an abundant source of transcription factor binding sites, and favorable genomic integration may lead to their recruitment by the host genome for gene regulatory functions. However, it is unclear how frequent co-option of transposable elements as regulatory elements is, to which regulatory programs they contribute and how they compare to regulatory elements devoid of transposable elements. Here, we report a transcription initiation-centric, in-depth characterization of the transposon-derived regulatory landscape of mouse embryonic stem cells. We demonstrate that a substantial number of transposable element insertions, in particular endogenous retroviral elements, are associated with open chromatin regions that are divergently transcribed into unstable RNAs in a cell-type specific manner, and that these elements contribute to a sizable proportion of active enhancers and gene promoters. We further show that transposon subfamilies contribute differently and distinctly to the pluripotency regulatory program through their repertoires of transcription factor binding site sequences, shedding light on the formation of regulatory programs and the origins of regulatory elements.
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Chakravarty, Leena, Joseph D. Kittle Jr., and Olli H. Tuovinen. "Insertion sequence IST3091 of Thiobacillus ferrooxidans." Canadian Journal of Microbiology 43, no. 6 (June 1, 1997): 503–8. http://dx.doi.org/10.1139/m97-072.
Повний текст джерелаАнотація:
An insertion sequence, designated as IST3091, was located adjacent to the putative origin of replication region of plasmid pTFI91 of Thiobacillus ferrooxidans TFI-91. The DNA sequence of the transposase gene of IST3091 revealed similarity with that of IS30, IS1086, IS4351, and the integrase gene of SpV1-R8A2 B (a bacteriophage of Spiroplasma citri). The sequence of IST3091 is 1063 bp long with partially matched 30-bp terminal inverted repeats. Several restriction fragments of plasmid pTFI91 of T. ferrooxidans containing the IST3091 element were cloned into the vector pHSG398. The hybrid plasmids (pBTL) were transformed into Escherichia coli NK7379 containing a miniF plasmid, which was devoid of transposable elements. The transposition function of the IST3091 element was confirmed by mobilizing hybrid plasmids via conjugation from transformed E. coli NK7379 (donor) to E. coli M8820 (recipient). The presence of the transposed element in transconjugants was detected by polymerase chain reaction amplification.Key words: insertion element, Thiobacillus ferrooxidans, transformation, transposase.
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Szekely, A. Alex, R. C. Woodruff, and R. Mahendran. "P element mediated germ line transformation of Drosophila melanogaster with the Tc1 transposable DNA element from Caenorhabditis elegans." Genome 37, no. 3 (June 1, 1994): 356–66. http://dx.doi.org/10.1139/g94-051.
Повний текст джерелаАнотація:
Questions relating to the origin and regulation of mobile genetic elements are currently of considerable interest. Since it is now possible to address more precisely issues concerning the entry, dispersion, and regulation of elements within a virgin genome, one approach that may afford a better understanding of transposable elements in general could be provided by interspecific DNA transformation. Therefore, the Tc1 transposable DNA element from Caenorhabditis elegans was chosen as a proposed invading element of the Drosophila melanogaster genome. The basis for this selection resided in the inherent structural and functional similarities, as well as sequence identities, between the Caenorhabditis element and elements innate to Drosophila (e.g., P, HB1, and Uhu). Initial investigations were carried out to define a clone carrying an intact Tc1 element. This Tc1 element was inserted into a P transposon vector and two P–Tc1–ry+ constructs, differing only in insert orientation, were identified. P element mediated germ line transfer was then used to generate a transformant that was genetically and molecularly identified as containing a single, structurally intact Tc1 element at cytological location 64C4-5 on the third chromosome. The single P[(Tc1, ry+)]SAS-B insertion was thereafter mobilized by using a P[ry+Δ2-3] element as a transposase source, and the genetic and molecular data suggested that the insertion had been successfully reintegrated to a variety of genomic locations. On the basis of genetic and molecular analyses, the Tc1 element in the P[(Tc1, ry+)] transformed stock is not highly unstable in germ line and somatic tissues.Key words: Tc1 transposable element, transformation, Drosophila melanogaster, Caenorhabditis elegans, P elements.
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Tanovic, Brankica, G. Delibasic, Jasminka Milivojevic, and M. Nikolic. "Characterization of Botrytis cinerea isolates from small fruits and grapevine in Serbia." Archives of Biological Sciences 61, no. 3 (2009): 419–29. http://dx.doi.org/10.2298/abs0903419t.
Повний текст джерелаАнотація:
Twenty-six single-spore isolates of Botrytis cinerea from blackberry, raspberry, strawberry, and grapevine were investigated using transposable elements, morphological characterization, and sensitivity to fungicides. Both transposable elements, Flipper and Boty, were detected among isolates from all the hosts. Six vacuma (without transposable elements) and seven transposa (containing both elements) isolates were found to be present in sympatry in Serbia. Isolates containing only the Boty element were detected. Eight morphological types of colonies on PDA and MA media were observed, confirming the great phenotypic variability of B. cinerea. Sensitivity to fungicides was various, depending on both the fungicide and the isolate.
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Takamatsu, Daisuke, Makoto Osaki, and Tsutomu Sekizaki. "Chloramphenicol resistance transposable element TnSs1 of Streptococcus suis, a transposon flanked by IS6-family elements." Plasmid 49, no. 2 (March 2003): 143–51. http://dx.doi.org/10.1016/s0147-619x(02)00149-x.
Повний текст джерела
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Samuel, Stylianos, Thomas Veloukas, Antonios Papavasileiou, and George S. Karaoglanidis. "Differences in Frequency of Transposable Elements Presence in Botrytis cinerea Populations from Several Hosts in Greece." Plant Disease 96, no. 9 (September 2012): 1286–90. http://dx.doi.org/10.1094/pdis-01-12-0103-re.
Повний текст джерелаАнотація:
This study was conducted primarily to investigate the presence and frequency distribution of the transposable elements Boty and Flipper in populations of the necrotroph plant pathogen Botrytis cinerea in Greece. In total, 334 isolates were collected from diseased grape, strawberry, tomato, cucumber, kiwifruit, and apple fruit during 2009. The presence of the two transposable elements was based on polymerase chain reaction detection. Results showed that all the sampled hosts occurred in sympatry, with four possible different genotypes (transposa type carrying both transposable elements, Boty type carrying only the Boty element, Flipper type carrying only the Flipper element, and vacuma type carrying neither transposable element). Marked differences in genotype frequencies among populations were observed. In tomato, cucumber, grape, and strawberry, transposa isolates carrying both elements were predominant in the populations whereas, in kiwifruit and apple fruit populations, the vacuma isolates were prevailing. Furthermore, in kiwi and apple fruit populations, high frequencies of Flipper-type isolates were observed. In an attempt to explain the observed predominance of vacuma isolates in kiwifruit populations, the mycelial growth rate of a set of vacuma isolates was compared with the mycelial growth rate of a set of transposa isolates at three different temperatures (0, 10, and 20°C). The same set of isolates was used to compare pathogenicity of isolates on wound-inoculated kiwifruit incubated at two different temperatures (0 and 20°C), in terms of disease incidence and disease severity. In addition, the selected isolates were used to compare their ability in causing latent infections on kiwifruit in the field. The results showed that vacuma and transposa isolates had similar mycelial growth rates at the limiting temperatures of 0 and 10°C, while vacuma isolates grew faster at the optimum temperature of 20°C. Similarly, there was no significant difference regarding pathogenicity on kiwifruit between transposa and vacuma isolates. However, artificial inoculations conducted on blossoms in the field showed that vacuma isolates caused significantly higher incidence of latent infections.
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Shiga, Yasuyuki, Yasuhiko Sekine, Yasunobu Kano, and Eiichi Ohtsubo. "Involvement of H-NS in Transpositional Recombination Mediated by IS1." Journal of Bacteriology 183, no. 8 (April 15, 2001): 2476–84. http://dx.doi.org/10.1128/jb.183.8.2476-2484.2001.
Повний текст джерелаАнотація:
ABSTRACT IS1, the smallest active transposable element in bacteria, encodes a transposase that promotes inter- and intramolecular transposition. Host-encoded factors, e.g., histone-like proteins HU and integration host factor (IHF), are involved in the transposition reactions of some bacterial transposable elements. Host factors involved in the IS1 transposition reaction, however, are not known. We show that a plasmid with an IS1 derivative that efficiently produces transposase did not generate miniplasmids, the products of intramolecular transposition, in mutants deficient in a nucleoid-associated DNA-binding protein, H-NS, but did generate them in mutants deficient in histone-like proteins HU, IHF, Fis, and StpA. Nor did IS1 transpose intermolecularly to the target plasmid in the H-NS-deficient mutant. The hns mutation did not affect transcription from the indigenous promoter of IS1 for the expression of the transposase gene. These findings show that transpositional recombination mediated by IS1 requires H-NS but does not require the HU, IHF, Fis, or StpA protein in vivo. Gel retardation assays of restriction fragments of IS1-carrying plasmid DNA showed that no sites were bound preferentially by H-NS within the IS1 sequence. The central domain of H-NS, which is involved in dimerization and/or oligomerization of the H-NS protein, was important for the intramolecular transposition of IS1, but the N- and C-terminal domains, which are involved in the repression of certain genes and DNA binding, respectively, were not. The SOS response induced by the IS1 transposase was absent in the H-NS-deficient mutant strain but was present in the wild-type strain. We discuss the possibility that H-NS promotes the formation of an active IS1 DNA-transposase complex in which the IS1 ends are cleaved to initiate transpositional recombination through interaction with IS1 transposase.
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Takumi, Shigeo. "Hygromycin-resistant calli generated by activation and excision of maize Ac/Ds transposable elements in diploid and hexaploid wheat cultured cell lines." Genome 39, no. 6 (December 1, 1996): 1169–75. http://dx.doi.org/10.1139/g96-147.
Повний текст джерелаАнотація:
To investigate the activation and transposition of maize transposable elements in wheat cultured cells, plasmid DNAs containing the maize Ac/Ds elements located between the CaMV 35S promoter and a hygromycin B resistance gene (hph) were introduced into two wheat (Triticum aestivum and Triticum monococcum) cultured cell lines by microprojectile bombardment. In the first experiment, hph was activated by excision of the Ac element, which encodes transposase, in the two wheat cell lines. In the second experiment, the Ds element was excised by a stabilized Ac element, lacking inverted repeats of the Ac element and located on another plasmid, and therefore leading to activation of hph. After selection of bombarded cells by hygromycin B, many resistant calli were recovered in both wheat cell lines. The integration of hph and the Ac transposase gene was confirmed by PCR and genomic Southern analysis. The stable expression of hph and the transposase gene was also assessed by Northern blot and reverse transcriptase PCR analysis, respectively. Moreover, characteristic sequence alterations were found at Ac/Ds excision sites. These findings indicate that the maize Ac/Ds transposable elements are activated and excised by expression of the Ac transposase gene in both diploid and hexaploid wheat cells. Key words : transposable elements, excision site, transgenic wheat callus, particle bombardment, Ac/Ds.
34
Peterson, Peter A. "A Modified Autonomous En Transposon in Maize (Zea mays L.) Elicits a Differential Response of Reporter Alleles." Genetics 147, no. 3 (November 1, 1997): 1329–38. http://dx.doi.org/10.1093/genetics/147.3.1329.
Повний текст джерелаАнотація:
Transposable elements in maize are composed of a defined molecular structure that includes coding sequences, determiners of functionality and ordered terminal motifs that provide binding sites for transposase proteins. Alterations in these components change the phenotypic expression of unstable genes with transposon inserts. The molecular basis for the altered timing and frequency of transposition as determined by the size and number of spots on kernels or stripes on leaves has generally been described for defective inserts in genes. Most differential patterns can be ascribed to alterations in the terminal motifs of the reporter allele structure that supplies a substrate (terminal inverted repeat motifs) for transposase activity. For autonomously functioning alleles, the explanations for changes in phenotype are not so clear. In this report, an En-related element identified as F-En is described that shares with En the recognition of a specific defective element c1(mr)888104 but differs from En in that this F-En element does not recognize the canonical c1(mr) elements that are recognized by En. Evidence is provided suggesting that F-En does not recognize other En/Spm-related defective elements, some of whose sequences are known. This modified En arose from a c1-m autonomously mutating En allele.
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Phadnis, Suhas H., Chihiro Sasakawa, and Douglas E. Berg. "LOCALIZATION OF ACTION OF THE IS50-ENCODED TRANSPOSASE PROTEIN." Genetics 112, no. 3 (March 1, 1986): 421–27. http://dx.doi.org/10.1093/genetics/112.3.421.
Повний текст джерелаАнотація:
ABSTRACT The movement of the bacterial insertion sequence IS50 and of composite elements containing direct terminal repeats of IS50 involves the two ends of IS50, designated O (outside) and I (inside), which are weakly matched in DNA sequence, and an IS50 encoded protein, transposase, which recognizes the O and I ends and acts preferentially in cis. Previous data had suggested that, initially, transposase interacts preferentially with the O end sequence and then, in a second step, with either an O or an I end. To better understand the cis action of transposase and how IS50 ends are selected, we generated a series of composite transposons which contain direct repeats of IS50 elements. In each transposon, one IS50 element encoded transposase (tnp +), and the other contained a null (tnp -) allele. In each of the five sets of composite transposons studied, the transposon for which the tnp + IS50 element contained its O end was more active than a complementary transposon for which the tnp - IS50 element contained its O end. This pattern of O end use suggests models in which the cis action of transposase and its choice of ends is determined by protein tracking along DNA molecules.
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Roberts, D. E., D. Ascherman, and N. Kleckner. "IS10 promotes adjacent deletions at low frequency." Genetics 128, no. 1 (May 1, 1991): 37–43. http://dx.doi.org/10.1093/genetics/128.1.37.
Повний текст джерелаАнотація:
Abstract Some transposable elements move by a replicative mechanism involving cointegrate formation. Intramolecular cointegration can generate a product called an "adjacent deletion" in which a contiguous chromosomal segment adjacent to the transposon is deleted while the element responsible remains intact. Insertion sequence IS10 is thought to transpose by a nonreplicative mechanism. In the simplest models, nonreplicative transposition cannot give rise to an adjacent deletion because an intrinsic feature of such transposition is excision of the IS element from the donor location. We report here that IS10 can generate adjacent deletions, but at a frequency which is approximately 1/30th the frequency of transposition for the same element. We suggest that these deletions might arise either by nonreplicative transposition events that involve two IS10 elements located on sister chromosomes or by aberrant nonreplicative events involving cleavage and ligation at only one end of the element.
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Strøman, Per, Christina C. Müller, and Kim I. Sørensen. "Heat Shock Treatment Increases the Frequency of Loss of an Erythromycin Resistance-Encoding Transposable Element from the Chromosome of Lactobacillus crispatus CHCC3692." Applied and Environmental Microbiology 69, no. 12 (December 2003): 7173–80. http://dx.doi.org/10.1128/aem.69.12.7173-7180.2003.
Повний текст джерелаАнотація:
ABSTRACT A 3,165-bp chromosomally integrated transposon, designatedTn3692, of the gram-positive strain Lactobacillus crispatus CHCC3692 contains an erm(B) gene conferring resistance to erythromycin at concentrations of up to 250μ g/ml. Loss of this resistance can occur spontaneously, but the rate is substantially increased by heat shock treatment. Heat shock treatment at 60°C resulted in an almost 40-fold increase in the frequency of erythromycin-sensitive cells (erythromycin MIC, 0.047μ g/ml). The phenotypic change was followed by a dramatic increase in transcription of the transposase gene and the concomitant loss of an approximately 2-kb DNA fragment carrying the erm(B) gene from the 3,165-bp erm transposon. In cells that were not subjected to heat shock, transcription of the transposase gene was not detectable. The upstream sequence of the transposase gene did not show any homology to known heat shock promoters in the gene data bank. Significant homology (>99%) was observed between the erythromycin resistance-encoding gene from L. crispatus CHCC3692 and the erm(B) genes from other gram-positive bacteria, such as Streptococcus agalactiae, Streptococcus pyogenes, Enterococcus faecium, and Lactobacillus reuteri, which strongly indicates a common origin of the erm(B) gene for these species. The transposed DNA element was not translocated to other parts of the genome of CHCC3692, as determining by Southern blotting, PCR analysis, and DNA sequencing. No other major aberrations were observed, as judged by colony morphology, growth performance of the strain, and pulsed-field gel electrophoresis. These observations suggest that heat shock treatment could be used as a tool for the removal of unwanted antibiotic resistance genes harbored in transposons flanked by insertion sequence elements or transposases in lactic acid bacteria used for animal and human food production.
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Ghanim, George E., Donald C. Rio, and Felipe Karam Teixeira. "Mechanism and regulation of P element transposition." Open Biology 10, no. 12 (December 2020): 200244. http://dx.doi.org/10.1098/rsob.200244.
Повний текст джерелаАнотація:
P elements were first discovered in the fruit fly Drosophila melanogaster as the causative agents of a syndrome of aberrant genetic traits called hybrid dysgenesis. This occurs when P element-carrying males mate with females that lack P elements and results in progeny displaying sterility, mutations and chromosomal rearrangements. Since then numerous genetic, developmental, biochemical and structural studies have culminated in a deep understanding of P element transposition: from the cellular regulation and repression of transposition to the mechanistic details of the transposase nucleoprotein complex. Recent studies have revealed how piwi-interacting small RNA pathways can act to control splicing of the P element pre-mRNA to modulate transposase production in the germline. A recent cryo-electron microscopy structure of the P element transpososome reveals an unusual DNA architecture at the transposon termini and shows that the bound GTP cofactor functions to position the transposon ends within the transposase active site. Genome sequencing efforts have shown that there are P element transposase-homologous genes (called THAP9) in other animal genomes, including humans. This review highlights recent and previous studies, which together have led to new insights, and surveys our current understanding of the biology, biochemistry, mechanism and regulation of P element transposition.
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Jansz, Natasha. "DNA methylation dynamics at transposable elements in mammals." Essays in Biochemistry 63, no. 6 (October 11, 2019): 677–89. http://dx.doi.org/10.1042/ebc20190039.
Повний текст джерелаАнотація:
Abstract Transposable elements dominate the mammalian genome, but their contribution to genetic and epigenetic regulation has been largely overlooked. This was in part due to technical limitations, which made the study of repetitive sequences at single copy resolution difficult. The advancement of next-generation sequencing assays in the last decade has greatly enhanced our understanding of transposable element function. In some instances, specific transposable elements are thought to have been co-opted into regulatory roles during both mouse and human development, while in disease such regulatory potential can contribute to malignancy. DNA methylation is arguably the best characterised regulator of transposable element activity. DNA methylation is associated with transposable element repression, and acts to limit their genotoxic potential. In specific developmental contexts, erasure of DNA methylation is associated with a burst of transposable element expression. Developmental regulation of DNA methylation enables transposon activation, ensuring their survival and propagation throughout the host genome, and also allows the host access to regulatory sequences encoded within the elements. Here I discuss DNA methylation at transposable elements, describing its function and dynamic regulation throughout murine and human development.
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Arcà, Bruno, Sophia Zabalou, Thanasis G. Loukeris, and Charalambos Savakis. "Mobilization of a Minos Transposon in Drosophila melanogaster Chromosomes and Chromatid Repair by Heteroduplex Formation." Genetics 145, no. 2 (February 1, 1997): 267–79. http://dx.doi.org/10.1093/genetics/145.2.267.
Повний текст джерелаАнотація:
Transposase-mediated mobilization of the element Minos has been studied in the Drosophila melanogaster genome. Excision and transposition of a nonautonomous Minos transposon in the presence of a Minos transposase gene was detected with a dominant eye color marker carried by the transposon. Frequencies of excision in somatic tissues and in the germ line were higher in flies heterozygous for the transposon than in homozygotes or hemizygotes. Transposition of a X chromosome-linked insertion of Minos into new autosomal sites occurred in 1-12% of males expressing transposase, suggesting that this system is usable for gene tagging and enhancer trapping in Drosophila. Sequence analysis of PCR-amplified donor sites after excision showed precise restoration of the original target sequence in ∼75% of events in heterozygotes and the presence of footprints or partially deleted elements in the remaining events. Most footprints consisted of the four terminal bases of the transposon, flanked by the TA target duplication. Sequencing of a chromosomal donor site that was directly cloned after excision showed a characteristic two-base mismatch heteroduplex in the center of the 6bp footprint. Circular extrachromosomal forms of the transposon, presumably representing excised Minos elements, could be detected only in the presence of transposase. A model for chromatid repair after Minosexcision is discussed in which staggered cuts are first produced at the ends of the inverted repeats, the broken chromatid ends are joined, and the resulting heteroduplex is subsequently repaired. The model also suggests a simple mechanism for the production of the target site duplication and for regeneration of the transposon ends during reintegration.
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Shin, Eunjung, Qianying Ye, and Sung-Jae Lee. "Active Transposition of Insertion Sequences in Prokaryotes: Insights from the Response of Deinococcus geothermalis to Oxidative Stress." Antioxidants 11, no. 3 (February 28, 2022): 481. http://dx.doi.org/10.3390/antiox11030481.
Повний текст джерелаАнотація:
Bacterial genomes contain numerous insertion sequences (ISs) as transposable elements involved in actions such as the sequestration, transmission, mutation and activation of genes that can influence the responsive capacity of the organism to environmental challenges. To date, at least 30 IS families have been identified. In this review, we describe how certain ISs are transposed to carotenoid biosynthesis genes, such as phytoene synthase and phytoene desaturase, when radiation-resistant Deinococcus geothermalis with a redox imbalance and a targeted gene disruption mutation is exposed to oxidative stressors, such as gamma-irradiation, dielectric bilayer discharge plasma and hydrogen peroxide. We also explain the genetic features of IS elements, spontaneous mutation and various stress responses, including nutrient limitation, and physicochemical and oxidative stress, associated with the active transposition of bacterial ISs. Based on the current knowledge, we posit that the redox signalling mechanism inducing IS transposition involves redox sensing and redox switching for the activation of transposase expression and its activity.
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Daniels, S. B., and A. Chovnick. "P element transposition in Drosophila melanogaster: an analysis of sister-chromatid pairs and the formation of intragenic secondary insertions during meiosis." Genetics 133, no. 3 (March 1, 1993): 623–36. http://dx.doi.org/10.1093/genetics/133.3.623.
Повний текст джерелаАнотація:
Abstract The gap-repair model proposes that P elements move via a conservative, "cut-and-paste" mechanism followed by double-strand gap repair, using either the sister chromatid or homolog as the repair template. We have tested this model by examining meiotic perturbations of an X-linked ry+ transposon during the meiotic cycle of males, employing the mei-S332 mutation, which induces high frequency equational nondisjunction. This system permits the capture of both sister-X chromatids in a single patroclinous daughter. In the presence of P-transposase, transpositions within the immediate proximity of the original site are quite frequent. These are readily detectable among the patroclinous daughters, thereby allowing the combined analysis of the transposed element, the donor site and the putative sister-strand template. Molecular analysis of 22 meiotic transposition events provide results that support the gap-repair model of P element transposition. Prior to this investigation, it was not known whether transposition events were exclusively or predominantly premeiotic. The results of our genetic analysis revealed that P elements mobilize at relatively high frequencies during meiosis. We estimated that approximately 4% of the dysgenic male gametes have transposon perturbations of meiotic origin; the proportion of gametes containing lesions of premeiotic origin was estimated at 32%.
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Han, Chang-Gyun, Mary Jean Frank, Hisako Ohtsubo, and Eiichi Ohtsubo. "New transposable elements identified as insertions in rice transposon Tnr1." Genes & Genetic Systems 75, no. 2 (2000): 69–77. http://dx.doi.org/10.1266/ggs.75.69.
Повний текст джерела
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Bancroft, I., and C. Dean. "Transposition pattern of the maize element Ds in Arabidopsis thaliana." Genetics 134, no. 4 (August 1, 1993): 1221–29. http://dx.doi.org/10.1093/genetics/134.4.1221.
Повний текст джерелаАнотація:
Abstract As part of establishing an efficient transposon tagging system in Arabidopsis using the maize elements Ac and Ds, we have analyzed the inheritance and pattern of Ds transposition in four independent Arabidopsis transformants. A low proportion (33%) of plants inheriting the marker used to monitor excision contained a transposed Ds. Selection for the transposed Ds increased this to at least 49%. Overall, 68% of Ds transpositions inherited with the excision marker were to genetically linked sites; however, the distribution of transposed elements varied around the different donor sites. Mapping of transposed Ds elements that were genetically unlinked to the donor site showed that a proportion (3 of 11 tested) integrated into sites which were still physically linked.
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Kuzmanovska, Biljana, Rade Rusevski, Ljupcho Jankuloski, Mirjana Jankulovska, Dario Ivic, and Katerina Bandzo. "Phenotypic and genetic characterization of Botrytis cinerea isolates from tomato." Genetika 44, no. 3 (2012): 633–47. http://dx.doi.org/10.2298/gensr1203663k.
Повний текст джерелаАнотація:
One hundred and twenty-three isolates of Botrytis cinerea were collected from 7 different areas in the Republic of Macedonia, where tomato is mostly grown in greenhouses and high tunnels. Based on the mycelial formation, intensity of sporulation and sclerotial production, 9 different phenotypes were detected: 4 mycelial and 5 sclerotial. One sclerotial morphological type has not been previously reported. The presence or absence of two transposable elements, boty and flipper, was detected by PCR. Out of 123 isolates, 20 had two transposable elements, boty and flipper (transposa genotype), 48 had neither of these elements (vacuma genotype) and 55 had only the flipper element (flipper genotype). Isolates that contain only boty element were not detected. No relationship between the phenotypes, origin of isolates and the presence/absence of transposable elements, boty and flipper, was found.
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Rubin, Eitan, Gila Lithwick, and Avraham A. Levy. "Structure and Evolution of the hAT Transposon Superfamily." Genetics 158, no. 3 (July 1, 2001): 949–57. http://dx.doi.org/10.1093/genetics/158.3.949.
Повний текст джерелаАнотація:
Abstract The maize transposon Activator (Ac) was the first mobile DNA element to be discovered. Since then, other elements were found that share similarity to Ac, suggesting that it belongs to a transposon superfamily named hAT after hobo from Drosophila, Ac from maize, and Tam3 from snapdragon. We addressed the structure and evolution of hAT elements by developing new tools for transposon mining and searching the public sequence databases for the hallmarks of hAT elements, namely the transposase and short terminal inverted repeats (TIRs) flanked by 8-bp host duplications. We found 147 hAT-related sequences in plants, animals, and fungi. Six conserved blocks could be identified in the transposase of most hAT elements. A total of 41 hAT sequences were flanked by TIRs and 8-bp host duplications and, out of these, 34 sequences had TIRs similar to the consensus determined in this work, suggesting that they are active or recently active transposons. Phylogenetic analysis and clustering of hAT sequences suggest that the hAT superfamily is very ancient, probably predating the plant-fungi-animal separation, and that, unlike previously proposed, there is no evidence that horizontal gene transfer was involved in the evolution of hAT elements.
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Daimon, Takaaki, Masao Mitsuhiro, Susumu Katsuma, Hiroaki Abe, Kazuei Mita, and Toru Shimada. "Recent transposition of yabusame, a novel piggyBac-like transposable element in the genome of the silkworm, Bombyx mori." Genome 53, no. 8 (August 2010): 585–93. http://dx.doi.org/10.1139/g10-035.
Повний текст джерелаАнотація:
On the W chromosome of the silkworm, Bombyx mori , we found a novel piggyBac-like DNA transposon that potentially encodes an intact transposase (610 amino acid residues), which is flanked by 16-bp perfect inverted terminal repeats and a duplicated TTAA target site. Interestingly, we also identified another intact copy of this transposon on an autosome (chromosome 21), which showed 99.6% identity in the DNA sequence of the transposase (99.3% amino acid identity). These features raised the possibility that this novel piggyBac-like DNA transposon, designated as yabusame, may retain transposition activity. Here we report the identification and characterization of yabusame transposons from the silkworm. We cloned the full length of the yabusame transposon on the W chromosome (yabusame-W) and its autosomal copy (yabusame-1). Southern blot analysis showed that there are interstrain polymorphisms in yabusame elements for their insertion sites and copy number. We also found strong evidence for the recent transposition of yabusame elements in the silkworm genome. Although our in vitro excision assays suggested that the transposition activity of yabusame-1 and yabusame-W has been lost almost entirely, our data will lead to a greater understanding of the characteristics of piggyBac superfamily elements.
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Fitzmaurice, Wayne P., Long V. Nguyen, Earl A. Wernsman, William F. Thompson, and Mark A. Conkling. "Transposon Tagging of the Sulfur Gene of Tobacco Using Engineered Maize Ac/Ds Elements." Genetics 153, no. 4 (December 1, 1999): 1919–28. http://dx.doi.org/10.1093/genetics/153.4.1919.
Повний текст джерелаАнотація:
Abstract The Sulfur gene of tobacco is nuclearly encoded. A Su allele at this locus acts as a dominant semilethal mutation and causes reduced accumulation of chlorophyll, resulting in a yellow color in the plant. An engineered transposon tagging system, based upon the maize element Ac/Ds, was used to mutate the gene. High frequency of transposon excision from the Su locus produced variegated sectors. Plants regenerated from the variegated sector exhibited a similar variegated phenotype. Genetic analyses showed that the variegation was always associated with the transposase construct and the transposon was linked to the Su locus. Sequences surrounding the transposon were isolated, and five revertant sectors possessed typical direct repeats following Ds excisions. These genetic and molecular data are consistent with the tagging of the Su allele by the transposon.
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Kim, Dae-Soo, Jae-Won Huh, Hong-Seok Ha, Tae-Hong Kim, Un-Jong Jo, and Heui-Soo Kim. "Bioinformatics Analysis of Gene Expression Regulation by Transposable Elements in Dementia Patients." Journal of Life Science 16, no. 7 (December 1, 2006): 1188–94. http://dx.doi.org/10.5352/jls.2006.16.7.1188.
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Kaplan, Norman, Tom Darden, and Charles H. Langley. "EVOLUTION AND EXTINCTION OF TRANSPOSABLE ELEMENTS IN MENDELIAN POPULATIONS." Genetics 109, no. 2 (February 1, 1985): 459–80. http://dx.doi.org/10.1093/genetics/109.2.459.
Повний текст джерелаАнотація:
ABSTRACT A model of the evolution of a transposable element family in a Mendelian host population is proposed that incorporates heritable phenotypic mutations in the elements. The temporal behavior of the numbers of mutant and wild-type elements is studied, and the expected extinction time of the transposable element family is examined. Our results indicate that, if the mutant can be transposed equally well in the presence of the wild type, then it can be expected to be found in preponderance, whereas elements, such as retroviruses, where the transposing genome and its phenotypic expression are coupled, may be characterized by a low mutant frequency.