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At least 433 records · Page 24Linked to original sources
PubMed2001

Micron, a microsatellite-targeting transposable element in the rice genome.

We have isolated a new family of mobile elements, Micron, which occur within microsatellites dispersed throughout the rice (Oryza sativa) genome. The first of these segments, Micron 001, was found in a microsatellite consisting of a (TA)n sequence upstream of the rice phytochrome A (phyA) gene. PCR analysis of related rice species suggests that Micron 001 integrated into this microsatellite locus prior to the divergence of the two wild species O. rufipogon and O. barthii from a common ancestor. Micron elements are short (393-bp), possess subterminal inverted repeats and the single strands have the potential to form stable secondary structures via several internal repeats. Aside from the absence of terminal inverted repeats, these characteristics resemble those of MITEs (Miniature Inverted-Repeat Transposable Elements). We estimate that 100-200 copies of Micron-related sequences are present in the rice nuclear genome, while the chloroplast and mitochondrial genomes lack this sequence. Nineteen homologs of Micron 001 exhibited extremely high nucleotide sequence conservation (greater than 90%), suggesting a recent spread of Micron elements within the genus Oryza. Surprisingly, nucleotide sequence alignments showed that all of the Micron elements are flanked on both sides by microsatellite sequence consisting mainly of (TA)n. Twenty-three elements were mapped to seven separate chromosomes. Therefore Micron elements form a family of dispersed, highly conserved repeats. This is the first report of a transposable element that targets microsatellite loci.

Amino Acid Sequence↗
PubMed1987

Identification of transposable elements which activate gene expression in Pseudomonas cepacia.

This study demonstrated that transposable elements in Pseudomonas cepacia could be inserted upstream of a poorly expressed gene and increase its expression more than 30-fold. Five elements, TnPc1, IS402, IS403, IS404, and IS405, were isolated by their ability to increase expression of the beta-lactamase gene of the broad-host-range plasmid pRP1. Increased expression resulted only from insertion of these elements, suggesting that insertional activation is an important means of elevating gene expression in this organism. Four of the elements inserted between a PstI site within the beta-lactamase gene and a BamHI site located 375 base pairs upstream of its promoter. The element IS403 inserted distal to the BamHI site within the coding region for the gene tnpR, suggesting that insertional activation can act over greater than expected distances. In addition, the element IS402 activated the beta-lactamase genes carried on plasmids pRP1 and pMR5 (temperature-sensitive pRP1) equally well in opposite orientations, demonstrating that insertional activation by this element occurs independent of its orientation.

DNA Restriction Enzymes↗
PubMed2006

Master: a novel family of PIF/Harbinger-like transposable elements identified in carrot (Daucus carota L.).

Members of a novel Master family of class II transposons were identified in the carrot genome. Two elements, 2.5 kb long DcMaster1 and 4.4 kb long DcMaster-a, are characterized by 22 bp imperfect terminal inverted repeats and by 3 bp target site duplications. GenBank search revealed that related elements are also present in Medicago truncatula, including a 5.1 kb element MtMaster-a. Both DcMaster-a and MtMaster-a contain open reading frames encoding for putative transposases with the complete DDE domain typical for plant class II transposable elements belonging to PIF/Harbinger superfamily, where the Master elements form a distinct group. Less than 10 copies of the DcMaster element containing the DDE domain are present in genomes of carrot and other Apiaceae, but more copies with internal deletions or insertions may occur. DcMaster elements were associated with putative coding regions in 8 of 14 identified insertion sites. PCR amplification of carrot genomic DNA using a primer complementary to TIRs of DcMaster gave products < 400 bp in size. We speculate that these may all represent a MITE-like family of transposable elements that we named Krak, present in the carrot genome in at least 3,600 copies.

Amino Acid Sequence↗
PubMed2001

Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome.

To test whether regions undergoing genomic imprinting have unique genomic characteristics, imprinted and nonimprinted human loci were compared for nucleotide and retroelement composition. Maternally and paternally expressed subgroups of imprinted genes were found to differ in terms of guanine and cytosine, CpG, and retroelement content, indicating a segregation into distinct genomic compartments. Imprinted regions have been normally permissive to L1 long interspersed transposable element retroposition during mammalian evolution but universally and significantly lack short interspersed transposable elements (SINEs). The primate-specific Alu SINEs, as well as the more ancient mammalian-wide interspersed repeat SINEs, are found at significantly low densities in imprinted regions. The latter paleogenomic signature indicates that the sequence characteristics of currently imprinted regions existed before the mammalian radiation. Transitions from imprinted to nonimprinted genomic regions in cis are characterized by a sharp inflection in SINE content, demonstrating that this genomic characteristic can help predict the presence and extent of regions undergoing imprinting. During primate evolution, SINE accumulation in imprinted regions occurred at a decreased rate compared with control loci. The constraint on SINE accumulation in imprinted regions may be mediated by an active selection process. This selection could be because of SINEs attracting and spreading methylation, as has been found at other loci. Methylation-induced silencing could lead to deleterious consequences at imprinted loci, where inactivation of one allele is already established, and expression is often essential for embryonic growth and survival.

CpG Islands↗
PubMed1986

Transposable elements generate novel spatial patterns of gene expression in Antirrhinum majus.

The pallida gene of A. majus encodes a product required for the synthesis of red flower pigment. We have shown that the unstable pallida(recurrens) mutation is due to the insertion of the Tam3 transposable element near the promoter of the gene. Imprecise excision of Tam3 alters pallida gene expression and generates new spatial patterns or different intensities of flower pigmentation. Distinct spatial patterns may also result from rearrangements induced by Tam3 that alter the relative position of the pallida gene. Changes in Tam3 structure or position result in new unstable phenotypes. These findings suggest that genes may be rendered genetically hypervariable as a consequence of transposable element insertion and excision.

Alleles↗
PubMed2003

Zaba: a novel miniature transposable element present in genomes of legume plants.

A novel family of miniature transposable elements, named Zaba, was identified in pea (Pisum sativum) and subsequently also in other legume species using computer analysis of their DNA sequences. Zaba elements are 141-190 bp long, generate 10-bp target site duplications, and their terminal inverted repeats make up most of the sequence. Zaba elements thus resemble class 3 foldback transposons. The elements are only moderately repetitive in pea (tens to hundreds copies per haploid genome), but they are present in up to thousands of copies in the genomes of several Medicago and Vicia species. More detailed analysis of the elements from pea, including isolation of new sequences from a genomic library, revealed that a fraction of these elements are truncated, and that their last transposition probably did not occur recently. A search for Zaba sequences in EST databases showed that at least some elements are transcribed, most probably due to their association with genic regions.

Base Sequence↗
PubMed1990

Rare de novo methylation within the transposable element activator (Ac) in transgenic tobacco plants.

Transgenic SR1 tobacco plants that contained the maize transposable element Ac or deletion derivatives thereof were isolated. The DNA methylation patterns of the foreign DNA sequences were analysed with methylation-sensitive restriction enzymes. By this method we tested 87 cytosine residues whose methylation is known to inhibit restriction by the corresponding enzyme. Most of the restriction sites were cleavable and hence unmethylated in transgenic tobacco plants. There were only three restriction sites at which a fraction of the Ac sequences was methylated. A similar result was obtained with two inactive, internally or terminally deleted Ac sequences. In one of the deletion derivatives a single restriction site was completely methylated. All other sites were unmethylated. The complete Ac elements described in this report were present as single copies in the transgenic plants. Their activity was demonstrated by the presence of the element-specific transcript. The deletion derivatives did not transpose in the transgenic tobacco plants and were thus still linked to the sequences of the plasmid that was used for transformation. These adjacent sequences represent part of a chimaeric NPTII gene inactivated by the insertion of the Ac deletion derivative. All 16 restriction sites examined in this sequence were unmethylated.

Blotting, Southern↗
PubMed1997

Penelope, a new family of transposable elements and its possible role in hybrid dysgenesis in Drosophila virilis.

A hybrid dysgenesis syndrome occurs in Drosophila virilis when males from an established laboratory strain are crossed to females obtained from the wild, causing the simultaneous mobilization of several different transposable elements. The insertion sequence responsible for the mutant phenotype of a dysgenic yellow allele has been characterized and named Penelope. In situ hybridization and Southern analyses reveal the presence of more than 30 copies of this element in the P-like parental strain, whereas Penelope is absent in all M-like strains tested. Penelope contains one 2.5-kb-long ORF that could encode products with homology to integrase and reverse transcriptase. Northern analysis and whole-mount in situ hybridization show strong induction of a 2.6-kb RNA in the ovaries of dysgenic females that is expressed at very low levels in the parental strains or in the progeny from the reciprocal cross. Injection of Penelope-containing plasmids into preblastoderm embryos of an M-like strain results in mutant progeny caused by insertion of Ulysses and perhaps other transposons, suggesting that Penelope expression might be responsible for the observed dysgenesis syndrome and the simultaneous mobilization of other transposable elements.

Amino Acid Sequence↗
PubMed2003

Colonization of heterochromatic genes by transposable elements in Drosophila.

As a further step toward understanding transposable element-host genome interactions, we investigated the molecular anatomy of introns from five heterochromatic and 22 euchromatic protein-coding genes of Drosophila melanogaster. A total of 79 kb of intronic sequences from heterochromatic genes and 355 kb of intronic sequences from euchromatic genes have been used in Blast searches against Drosophila transposable elements (TEs). The results show that TE-homologous sequences belonging to 19 different families represent about 50% of intronic DNA from heterochromatic genes. In contrast, only 0.1% of the euchromatic intron DNA exhibits homology to known TEs. Intraspecific and interspecific size polymorphisms of introns were found, which are likely to be associated with changes in TE-related sequences. Together, the enrichment in TEs and the apparent dynamic state of heterochromatic introns suggest that TEs contribute significantly to the evolution of genes located in heterochromatin.

Animals↗
PubMed2004

Identification of two subfamilies of micropia transposable element in species of the repleta group of Drosophila.

The occurrence, number of insertion sites and antisense RNA expression of micropia transposable element were studied in 26 species that belong to three subgroups (mercatorum, mulleri and hydei) of repleta group of Drosophila. Under high specific PCR, micropia sequences were detected in 11 species, but under less stringent condition, this retrotransposon was detected in all species. The widespread distribution of micropia suggests that this element was already present at the common ancestor of the repleta group of Drosophila. Southern blot analysis showed a variation from 0 to 17 different insertion sites and the occurrence of male-specific sequences. We found that the expression of the 1.0 kb micropia antisense RNA is variable among the species and tissues (soma and testis), which suggests that more than one mechanism regulates transposition in these species. Variation of amplification by PCR and of antisense RNA expression, as well as divergence of nucleotide sequences among the species allow us to suggest that at least two subfamilies of micropia transposable element are harbored by the genome of this species group.

Animals↗
PubMed1999

Floricultural traits and transposable elements in the Japanese and common morning glories.

The Japanese morning glory has an extensive history of genetic studies and over 200 different spontaneous mutant lines have been described. Of these, we identified that two mutable alleles, flecked and speckled, for flower variegations are caused by integration of transposable elements, belonging to the En/Spm family, into the DFR-B and CHI genes for flower pigmentation, respectively. The mutable flaked allele of the common morning glory bearing variegated flowers is caused by insertion of a new transposable element, Tip100, into one of the CHS genes for pigmentation and that Tip100 belongs to the Ac/Ds family. These results are discussed with regard to spontaneous transposon mutagenesis and generation of floricultural traits of morning glories.

Alleles↗
PubMed1995

Structural analysis of Tpn1, a transposable element isolated from Japanese morning glory bearing variegated flowers.

The 6.4 kb transposable element Tpn1 belonging to the En/Spm family was found within one of the DFR (dihydroflavonol-4-reductase) genes for anthocyanin biosynthesis in a line of Japanese morning glory (Pharbitis nil) bearing variegated flowers. Sequencing of the Tpn1 element revealed that it is 6412 bp long and carries 28-bp perfect terminal inverted repeats. Its subterminal repetitive regions, believed to be the cis-acting sequences for transposition, show striking structural features. Twenty-two copies of the 10-bp sequence motif GACAACGGTT can be found as direct or inverted repeats within 650 bp of the 5' end of the element, and 33 copies of the sequence motif lie within 800 bp of the 3' terminus. All these 22 copies of the sequence motif near the 5' terminus and 30 copies in the 3' terminal region are arranged as inverted repeats and 3-8 bp AT-rich sequences are detected between these inverted repeats. In addition, four copies of 122-bp tandem repeats and six copies of 104-bp tandem repeats are present in the 5' and 3' subterminal repetitive regions, respectively. No large open reading frame characteristic of autonomous elements of the En/Spm family can be detected within the element. The results are discussed with respect to heritable changes in flower variegation in this line of Japanese morning glory.

Alcohol Oxidoreductases↗
PubMed2000

Distribution of the transposable element mariner in anopheline mosquitoes.

We have surveyed the distribution of the transposable element mariner using PCR in 23 species of Anopheles mosquitoes, including all of the most important vectors of malaria in South-east Asia. Sequencing of the nine positive species revealed elements from the irritans, mauritiana and mellifera subfamilies. These are the first data showing the presence of three subfamilies of mariners in anophelines. The elements we encountered are likely to be inactive, based on the presence of multiple stop codons and/or frameshifts.

Animals↗
PubMed1983

Association of a Drosophila transposable element of the roo family with chromosomal deletion breakpoints.

A 9.3 kb transposable element of the roo family has been found inserted 3' to the Sgs-4 glue protein gene of Drosophila. The X chromosome which carries this insert also carries wDZL, a dominant, unstable allele of the white locus caused by the insertion of the 13 kb wDZL element. Three deletions isolated from the wDZL strain have molecular breakpoints 3' to Sgs-4 that are associated with the roo element. Though the deletions eliminate much of the DNA between white and Sgs-4, none of the distal breakpoints fall at or near the wDZL element. The results suggest that this copia-like element, which is structurally similar to an integrated retrovirus, is capable of promoting chromosomal deletions.

Alleles↗
PubMed1998

The Arabidopsis transposable element Tag1 is widely distributed among Arabidopsis ecotypes.

Tag1 is an autonomous transposable element (3.3 kb in length) first identified as an insertion in the CHL1 (NRT1) gene of Arabidopsis thaliana. Tag1 has been found in the Landsberg erecta ecotype of A. thaliana but not in Columbia or WS. In this paper, 41 additional ecotypes were examined for the presence of Tag1. Using an internal Tag1 fragment as probe, we found that DNA form 19 of the 41 ecotypes strongly hybridized to Tag1. Almost all of the Tag1-containing ecotypes had only one or two copies of Tag1 per haploid genome, as determined by Southern blot analysis. The only exception, Bf-1 from Bretagny-sur-Orge, France, had four copies. Two ecotypes, Di-G and S96, gave identical Southern blot patterns to that of Landsberg erecta and were subsequently shown to contain Tag1 at the same two positions found in Landsberg erecta (loci designated as Tag1-2 and Tag1-3). Two other ecotypes, Ag-0 and Lo-1, had a Tag1 element located at Tag1-2 but not at Tag1-3. The distance between these two loci was determined to be 0.37 cM. Analysis of DNA from two related species, A. griffithiana and A. pumila, showed that both species contain sequences that hybridize to Tag1 and that could be amplified with an oligonucleotide specific to the terminal inverted repeats of Tag1. These results show that Tag1 and related elements are present, and may be useful for insertional mutagenesis, in many A. thaliana ecotypes and several Arabidopsis species.

Arabidopsis↗
PubMed1989

Structural and functional analysis of the mini-circle, a transposable element of Streptomyces coelicolor A3(2).

The mini-circle is a transposable element which is present in Streptomyces coelicolor A3(2) in both free circular and chromosomally integrated linear forms. The nucleotide sequences of the mini-circle and its preferred site of integration in the Streptomyces lividans TK64 chromosome were determined. Three putative open reading frames were identified in the mini-circle sequence. The mini-circle does not appear to cause a target site duplication on transposition and does not have perfect terminal inverted repeats. The observed site-specificity of the mini-circle is not mediated by extensive homology between the element and the chromosomal integration site. Transposition of the mini-circle into the S. lividans chromosome was demonstrated and found to be some two orders of magnitude less efficient than integration of the circular form of the element, suggesting that the circular form of the mini-circle might be a normal intermediate in the transposition process.

Amino Acid Sequence↗
PubMed1999

Transposable elements as activators of cryptic genes in E. coli.

The concept of transposable elements (TEs) as purely selfish elements is being challenged as we have begun to appreciate the extent to which TEs contribute to allelic diversity, genome building, etc. Despite these long-term evolutionary contributions, there are few examples of TEs that make a direct, positive contribution to adaptive fitness. In E. coli cryptic (silent) catabolic operons can be activated by small TEs called insertion sequences (IS elements). Not only do IS elements make a direct contribution to fitness by activating cryptic operons, they do so in a regulated manner, transposing at a higher rate in starving cells than in growing cells. In at least one case, IS elements activate an operon during starvation only if the substrate for that operon is present in the environment. It appears that E. coli has managed to take advantage of IS elements for its own benefit.

DNA Transposable Elements↗
PubMed1989

Composite transposable elements in the Xenopus laevis genome.

Members of two related families of transposable elements, Tx1 and Tx2, were isolated from the genome of Xenopus laevis and characterized. In both families, two versions of the elements were found. The smaller version in each family (Tx1d and Tx2d) consisted largely of two types of 400-base-pair tandem internal repeats. These elements had discrete ends and short inverted terminal repeats characteristic of mobile DNAs that are presumed to move via DNA intermediates, e.g., Drosophila P and maize Ac elements. The longer versions (Tx1c and Tx2c) differed from Tx1d and Tx2d by the presence of a 6.9-kilobase-pair internal segment that included two long open reading frames (ORFs). ORF1 had one cysteine-plus-histidine-rich sequence of the type found in retroviral gag proteins. ORF2 showed more substantial homology to retroviral pol genes and particularly to the analogs of pol found in a subclass of mobile DNAs that are supposed retrotransposons, such as mammalian long interspersed repetitive sequences, Drosophila I factors, silkworm R1 elements, and trypanosome Ingi elements. Thus, the Tx1 elements present a paradox by exhibiting features of two classes of mobile DNAs that are thought to have very different modes of transposition. Two possible resolutions are considered: (i) the composite versions are actually made up of two independent elements, one of the retrotransposon class, which has a high degree of specificity for insertion into a target within the other, P-like element; and (ii) the composite elements are intact, autonomous mobile DNAs, in which the pol-like gene product collaborates with the terminal inverted repeats to cause transposition of the entire unit.

Amino Acid Sequence↗