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At least 721 records · Page 40Linked to original sources
PubMed1982

Nucleotide sequence analysis of avian retroviruses: structural similarities with transposable elements.

Integrated retroviral genomes are flanked by direct repeats of sequences derived from the termini of the viral RNA genome. These sequences are designated long terminal repeats (LTRs). We have determined and analyzed the nucleotide sequence of the LTRs from several exogenous and endogenous avian retroviruses. These LTRs possess several structural similarities with eukaryotic and prokaryotic transposable elements: 1) inverted complementary repeats at the termini, 2) deletions of sequences adjacent to the LTR, 3) small duplications of host sequences flanking the integrated provirus, and 4) sequence homologies with transposable and other genetic elements. These observations suggest that LTRs function in the integration and perhaps transposition of retrovirus genomes. Evidence exists for the presence of a strong promoter sequence within the LTR. The retroviral LTR also contains a "Hogness box" up-stream of the capping site and a poly(A) signal. These features suggest an additional role for the LTR in the regulation of gene expression.

Animals↗
PubMed2004

Mosquito transposable elements.

The completion of the genome assembly for the African malaria mosquito, Anopheles gambiae, and continuing genomic efforts for the yellow fever mosquito, Aedes aegypti, have allowed the use of bioinformatics tools to identify and characterize a diverse array of transposable elements (TEs) in these and other mosquito genomes. An overview of the types and number of both RNA-mediated and DNA-mediated TEs that are found in mosquito genomes is presented. A number of novel and interesting TEs from these species are discussed in more detail. These findings have significant implications for our understanding of mosquito genome evolution and for future modifications of natural mosquito populations through the use of TE-mediated genetic transformation.

Aedes↗
PubMedDate not supplied

Speculation on the role of transposable elements in human genetic disease with particular attention to achondroplasia and the fragile X syndrome.

We suggest that mutations for fragile X-positive Martin-Bell syndrome, and perhaps also for achondroplasia, may result from the insertion of transposable elements (TE's). Loss of genetic function could result from either the insertion of TE's within or adjacent to a normal chromosomal gene or, in the case of fragile X, from the loss of genes distal to the site of TE insertion following subsequent TE excision without ligation of the resulting discontinuity. The phenotypically and often cytogenetically normal transmitting males in fragile X pedigrees are interpreted not as "nonpenetrant" transmitters of a fully formed fragile X but rather as transmitters of some or all of the factors necessary for TE insertion at Xq27. We consider it likely that such insertion frequently first occurs, both in soma and especially in the germline, in their daughters. Our models predict that father to son transmission of causative factors would be a common occurrence in fragile X pedigrees. The absence of documented father to son transmission either points to a flaw in the models or reflects systematic bias in the collection of pedigree information.

Achondroplasia↗
PubMed1989

The putative transposase of transposable element Ac from Zea mays L. interacts with subterminal sequences of Ac.

The Ac-specific ORFa protein, overexpressed in a baculovirus system, specifically binds to several subterminal fragments of Ac. The 11 bp long inverted repeats of the transposable element are not bound by the ORFa protein. Major ORFa protein-binding sites were delineated on 60 and 70 bp long sequence segments that lie 100 bp inside of the 5' Ac terminus and 40 bp inside of the 3' terminus respectively. Within all strongly bound fragments, and particularly in these 60 or 70 bp long segments, the hexamer motif AAACGG is repeated several times in direct or inverted orientation. The ORFa protein binds to synthetic concatemers of this motif, whereas the mutant motif AAAGGG is not complexed. Methylation of the cytosine residues in the AAACGG motif and/or its complementary strand has pronounced effects: whereas one of the two hemimethylated sequences has a higher affinity to the ORFa protein than both unmethylated and holomethylated DNAs, the other hemimethylated DNA is virtually not complexed at all. The native ORFa protein binding sites are more complex than the AAACGG sequence: certain Ac and Ds1 fragments devoid of AAACGG motifs (but containing several similar sequences) are weakly bound by the ORFa protein.

Base Sequence↗
PubMed1981

A copy of the copia transposable element is very tightly linked to the Wa allele at the white locus of D. melanogaster.

Results are described demonstrating that several X chromosomes of Drosophila melanogaster carrying the Wa (white-apricot) mutant allele also carry homology to the copia transposable element in distal 3C of the polytene chromosome map as assessed by situ hybridization. The locus of the Wa mutation, white, resides in distal 3C. We further show, using fine scale genetic mapping techniques, that the copia homology in distal 3C in Wa-bearing chromosomes is very tightly linked to the Wa mutation. Both the Wa mutation and the copia homology associated with it map to the central portion of the white locus.

Animals↗
PubMed1986

Interactions among the gypsy transposable element and the yellow and the suppressor of hairy-wing loci in Drosophila melanogaster.

We cloned and characterized the yellow locus of Drosophila melanogaster. We also studied its transcription pattern in the suppressible allele y2, which is caused by the insertion of the transposable element gypsy, and the effect of mutations at the unlinked suppressor of Hairy-wing locus on the transcription of yellow RNAs. The gypsy element is transcribed in a temporal fashion that correlates with the pattern of expression of the yellow locus. We propose that the mutational effect of the gypsy element is due to developmentally specific transcriptional interference on yellow transcription. Mutations at the su(Hw) locus reverse this effect by altering the quantitative expression of gypsy.

Animals↗
PubMed2002

Excision of transposable elements from the chalcone isomerase and dihydroflavonol 4-reductase genes may contribute to the variegation of the yellow-flowered carnation (Dianthus caryophyllus).

In the "Rhapsody" cultivar of the carnation, which bears white flowers variegated with red flecks and sectors, a transposable element, dTdic1, belonging to the Ac/Ds superfamily, was found within the dihydroflavonol 4-reductase (DFR) gene. The red flecks and sectors of "Rhapsody" may be attributable to a reversion to DFR activity after the excision of dTdic1. The yellow color of the carnation petals is attributed to the synthesis and accumulation of chalcone 2'-glucoside. In several of the carnation cultivars that bear yellow flowers variegated with white flecks and sectors, both the chalcone isomerase (CHI) and DFR genes are disrupted by dTdic1.

Alcohol Oxidoreductases↗
PubMed1999

Nonmethylated transposable elements and methylated genes in a chordate genome.

The genome of the invertebrate chordate Ciona intestinalis was found to be a stable mosaic of methylated and nonmethylated domains. Multiple copies of an apparently active long terminal repeat retrotransposon and a long interspersed element are nonmethylated and a large fraction of abundant short interspersed elements are also methylation free. Genes, by contrast, are predominantly methylated. These data are incompatible with the genome defense model, which proposes that DNA methylation in animals is primarily targeted to endogenous transposable elements. Cytosine methylation in this urochordate may be preferentially directed to genes.

Animals↗
PubMed1986

Tx1: a transposable element from Xenopus laevis with some unusual properties.

A family of transposable genetic elements in the genome of the frog, Xenopus laevis, is described. They are designated Tx1. Transposability of the elements was deduced by characterization of a chromosomal locus which is polymorphic for the presence or absence of a Tx1 element. Nucleotide sequence analysis suggested that Tx1 elements show target site specificity, as they are inserted at the pentanucleotide TTTAA in all four cases that were examined. The elements appear to have 19-base-pair (bp) inverted terminal repeats, and they are flanked by 4-bp target duplications (TTAA), although the possibility that they do not create target site duplications is discussed. Tx1 elements have several unusual characteristics: the central portion of each element is comprised of a variable number of two types of 393-bp repeating units; the rightmost 1,000 bp of the element contains separate regions potentially capable of forming bends, left-handed Z-form DNA, and alternative stem-loop structures. Comparisons among single frogs suggest that germ line transposition is relatively infrequent and that variations in numbers of internal repeats accumulate quite slowly at any locus.

Animals↗
PubMed1996

Mrs, a new subfamily of Tourist transposable elements.

We have characterised a new family of repetitive sequences that we have named Mrs (maize repetitive sequences). Mrs elements are associated with different maize genes and seem to be specific for the genome of Zea species. Mrs elements are short, AT-rich and contain terminal inverted repeats (TIRs). The sequence of their TIRs, as well as the fact that they are flanked by short repetitions that tend to be TAA, allows us to propose Mrs as a new subfamily of Tourist transposable elements.

Base Sequence↗
PubMed1995

Gene disruptions using P transposable elements: an integral component of the Drosophila genome project.

Biologists require genetic as well as molecular tools to decipher genomic information and ultimately to understand gene function. The Berkeley Drosophila Genome Project is addressing these needs with a massive gene disruption project that uses individual, genetically engineered P transposable elements to target open reading frames throughout the Drosophila genome. DNA flanking the insertions is sequenced, thereby placing an extensive series of genetic markers on the physical genomic map and associating insertions with specific open reading frames and genes. Insertions from the collection now lie within or near most Drosophila genes, greatly reducing the time required to identify new mutations and analyze gene functions. Information revealed from these studies about P element site specificity is being used to target the remaining open reading frames.

Animals↗
PubMed1993

Noninvolvement of the long terminal repeat of transposable element 17.6 in insecticide resistance in Drosophila.

Waters and colleagues recently suggested [Waters, L. C., Zelhof, A. C., Shaw, B. J. & Ch'ang, L.-Y. (1992) Proc. Natl. Acad. Sci. USA 89, 4855-4859] that an insertion of a long terminal repeat of transposable element 17.6 into the 3' untranslated region of a P450 gene leads to susceptibility to the insecticide DDT in Drosophila melanogaster. We tested this hypothesis by screening lines from around the world and found that the presence or absence of a long terminal repeat was uncorrelated with resistance in 31 strains of D. melanogaster and Drosophila simulans. Thus we must reject the hypothesis that the insertion of a long terminal repeat leads to DDT susceptibility in Drosophila.

Animals↗
PubMed1985

A chlorophyll a/b-protein encoded by a gene containing an intron with characteristics of a transposable element.

We have sequenced a genomic subclone (pLg AB19/H5c) of Lemna gibba nuclear DNA containing a complete chlorophyll a/b protein coding region and 5' and 3' flanking nucleotides. The coding region contains an intron of 84 nucleotides that has features characteristic of a transposable element. Evidence from S1 nuclease mapping experiments is consistent with correct transcription and splicing of the AB19 or another closely related intron-containing gene. The encoded precursor polypeptide of 264 amino acid residues has a predicted Mr of 28,327. Approximately 35 N-terminal residues are cleaved from this protein to form the mature apoprotein. We have used theoretical considerations of protein structure to propose an experimentally testable model of the structure of this protein in thylakoid membranes.

Amino Acid Sequence↗
PubMedDate not supplied

Malazy, a degenerate, species-specific transposable element in Cercospora zeae-maydis.

Two fungal pathogens, Cercospora zeae-maydis Groups I and II, cause gray leaf spot of maize. During the sequencing of a cosmid library from C. zeae-maydis Group I, we discovered a sequence with high similarity to Maggy, a transposable element from Magnaporthe grisea. The element from C. zeae-maydis, named Malazy, contained 194-base-pair terminal repeats and sequences with high similarity to reverse transcriptase and integrase, components of the POL gene in the gypsy-like retrotransposons in fungi. Sequences with similarity to other POL gene components, protease and ribonuclease, were not detected in Malazy. A single copy of the element was detected by PCR and Southern analyses in all six North American isolates of C. zeae-maydis Group I but was not detected in the four isolates of C. zeae-maydis Group II from three continents or in phylogenetically related species. Fragments of the core domains of reverse transcriptase and integrase contained a high frequency of stop codons that were conserved in all six isolates of Group I. Additional C:G to T:A transitions in occasional isolates usually were silent mutations, while two resulted in isolate-specific stop codons. The absence of Malazy from related species suggests that it was acquired after the divergence of C. zeae-maydis Groups I and II. The high frequency of stop codons and the presence of a single copy of the element suggest that it was inactivated soon after it was acquired. Because the element is inactive and because reading frames for other genes were not found in sequences flanking the element, Malazy does not appear to be the cause of differences leading to speciation or genetic diversity between C. zeae-maydis Groups I and II.

Ascomycota↗
PubMed2003

Application of Minos, one of the Tc1/mariner superfamily transposable elements, to ascidian embryos as a tool for insertional mutagenesis.

As it has a simple genome structure, Ciona intestinalis is a good chordate species for studying the function of genes. To this end, it is a key requirement to introduce insertional mutagenesis using a transposable element to the ascidian system. The present study focuses on Minos, one of the Tc1/mariner superfamily transposons that is already used in a human cell line. By extrachromosomal excision and transposition assays, we found that Minos activity is very high in C. intestinalis. We also demonstrated the nuclear localization activity of Minos transposase in Ciona embryos. From these tests, we concluded that Minos transposase has complete activity when it is expressed in C. intestinalis, suggesting that Minos has the potential to be used for genome-wide insertional mutagenesis of C. intestinalis.

Animals↗
PubMed1990

Excision of the En/Spm transposable element of Zea mays requires two element-encoded proteins.

An excision assay system for En/Spm was developed in transgenic tobacco. The characteristics of excision and integration are similar to the natural system of Zea mays. In this transgenic model system two En/Spm encoded trans-acting functions, TNPA and TNPD, are required for excision. A biochemical model for transposition is proposed that might also be applicable to other transposable elements.

Cloning, Molecular↗
PubMed1995

Patterns of gene action in plant development revealed by enhancer trap and gene trap transposable elements.

The crucifer Arabidopsis thaliana has been used widely as a model organism for the study of plant development. We describe here the development of an efficient insertional mutagenesis system in Arabidopsis that permits identification of genes by their patterns of expression during development. Transposable elements of the Ac/Ds system carrying the GUS reporter gene have been designed to act as enhancer traps or gene traps. A novel selection scheme maximizes recovery of unlinked transposition events. In this study 491 plants carrying independent transposon insertions were generated and screened for expression patterns. One-half of the enhancer trap insertions and one-quarter of the gene trap insertions displayed GUS expression in seedlings or flowers, including expression patterns specific to organs, tissues, cell types, or developmental stages. The patterns identify genes that act during organogenesis, pattern formation, or cell differentiation. Transposon insertion lines with specific GUS expression patterns provide valuable markers for studies of Arabidopsis development and identify new cell types or subtypes in plants. The diversity of gene expression patterns generated suggests that the identification and cloning of Arabidopsis genes expressed in any developmental process is feasible using this system.

Arabidopsis↗
PubMed1994

Utilization of a mini-Dlac transposable element to create an alpha-complementation and regulated expression system for cloning in Pseudomonas aeruginosa.

A lac-based alpha-complementation and expression system was developed for use in molecular cloning in Pseudomonas aeruginosa. A bacteriophage D3112-based mini-Dlac transposable element, containing the lacIq-regulated lacZ delta M15 gene next to a selectable marker, was constructed. Mixed D3112 lysates were used to transduce P. aeruginosa PAO1, and derivatives containing randomly inserted chromosomal copies of the mini-Dlac element were obtained. Transformation of the PAO1::mini-Dlac transductants with the broad-host-range vector, pUCP19, led to the formation of blue colonies on indicator medium in the presence of inducer. In contrast, transformants harboring the pUCP19 derivative pCDO, containing the catechol-2,3-dioxygenase (C23O)-encoding xylE gene under lac promoter control, were white on the same medium. Expression of xylE was tightly controlled by single-copy mini-Dlac-encoded lac repressor and in induced cultures was increased more than 100-fold over that observed in uninduced cultures. The usefulness of the system for molecular cloning in P. aeruginosa was demonstrated by ligating size-fractionated PAO1 chromosomal fragments into pUCP19, followed by transformation of the newly isolated PAO1::mini-Dlac host. All randomly chosen white colonies contained recombinant plasmids, with inserts of the correct size range, while blue colonies contained pUCP19 alone. The functionality of the system was also shown in another frequently studied strain, PA103.

Cloning, Molecular↗