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PubMed2000

Playing second fiddle: second-strand processing and liberation of transposable elements from donor DNA.

Retroviruses and many transposons of both prokaryotes and eukaryotes share similar chemical reactions in their transposition. Some elements remain attached to donor DNA during transposition and their translocation results in a fusion between target and donor replicons. However, many elements are separated from their flanking donor DNA prior to their insertion into a target site, which requires processing of both strands at both ends of the element. A variety of strategies have been adopted for cleavage of the second, complementary strand to liberate the transposon.

Animals↗
PubMed1992

The sequence of an 8 kb segment on the left arm of chromosome II from Saccharomyces cerevisiae identifies five new open reading frames of unknown functions, two tRNA genes and two transposable elements.

The DNA sequence of an 8079 bp ClaI fragment located at 40 kb from the centromere on the left arm of chromosome II from Saccharomyces cerevisiae has been determined. Sequence analysis reveals five new open reading frames, tRNA(Gly) and tRNA(Leu) genes as well as sigma and truncated delta elements. The disruption of the three larger open reading frames shows that they are not essential for mitotic growth.

Amino Acid Sequence↗
PubMed2001

Perspective: transposable elements, parasitic DNA, and genome evolution.

The nature of the role played by mobile elements in host genome evolution is reassessed considering numerous recent developments in many areas of biology. It is argued that easy popular appellations such as "selfish DNA" and "junk DNA" may be either inaccurate or misleading and that a more enlightened view of the transposable element-host relationship encompasses a continuum from extreme parasitism to mutualism. Transposable elements are potent, broad spectrum, endogenous mutators that are subject to the influence of chance as well as selection at several levels of biological organization. Of particular interest are transposable element traits that early evolve neutrally at the host level but at a later stage of evolution are co-opted for new host functions.

Animals↗
PubMed1988

Ribosomal DNA insertion elements R1Bm and R2Bm can transpose in a sequence specific manner to locations outside the 28S genes.

A fraction of the ribosomal 28S genes in some insects are interrupted at specific sites by insertion elements R1 and R2 (also called Type I and II). These elements contain long open-reading frames with homology to reverse transcriptase. We have identified in the silkmoth, Bombyx mori, copies of these elements which have inserted into sites outside the ribosomal DNA (rDNA) units. The 3' ends of all "non-rDNA" elements are identical to the elements within the 28S genes; however their 5' ends are often truncated. Each non-rDNA copy has inserted into sequences that exhibit similarity to their target sites in the 28S gene. We also demonstrate by genomic blot analysis of different strains of B. mori that insertions of R1 and R2 outside the rDNA units have been infrequent, while considerable turnover of elements has occurred within the rDNA locus. One race of B. mori has lost all copies of R1 from its rDNA units, while retaining normal levels of R2. The level of both R1 and R2 have significantly increased in a tissue culture line. These findings add considerable support to the model that R1 and R2 are retrotransposable elements that utilize sequence specific endonucleases in their integration into the genome.

Animals↗
PubMed2026

Aging and Reproductive Cancers: An Integrative View on Cell-Free DNA and Transposable Elements.

Aging is one of the strongest risk factors for cancer, and its impact is particularly evident in malignancies of the reproductive system. Ovarian, endometrial, cervical, vulvar, prostate, and penile cancers are mainly diagnosed in older adults and often show different clinical and biological features compared with the same tumors in younger patients. Aging is associated with hormonal changes, immune decline, epigenetic alterations, and accumulation of DNA damage, all of which contribute to cancer development and progression. At the same time, many older patients have frailty and multiple comorbidities, which can limit the use of screening programs and invasive diagnostic procedures. This often leads to delayed diagnosis and worse outcomes. Cell-free DNA (cfDNA) is a minimally invasive biomarker that can be obtained from blood samples and provides molecular information on both tumor and host tissues. Circulating DNA reflects tumor-specific alterations but is also influenced by aging-related changes in DNA release, fragmentation, and methylation. For this reason, aging must be considered when cfDNA-based biomarkers are applied in clinical practice. In this review, we describe how aging influences the biology of reproductive system cancers and how these processes are mirrored in cfDNA profiles. We focus on the clinical use of cfDNA for cancer detection and monitoring in older and fragile patients. Special attention is given to repetitive elements in cfDNA, which are strongly affected by aging and tumor-related epigenetic changes and can be detected with high sensitivity even when the tumor fraction is low. We propose an integrative mechanistic framework in which age-related epigenetic and genomic changes influence both tumor biology and cfDNA composition, with transposable elements acting as a central link between aging and cancer.

Humans↗
PubMed1993

The sex determining region of Chironomus thummi is associated with highly repetitive DNA and transposable elements.

The dominant male sex determiner in chromosome III of the midge Chironomus thummi thummi is closely linked to a large cluster of tandem-repetitive DNA elements, the Cla elements, which are otherwise highly repetitive and distributed over more than 200 sites on all chromosomes. Chromosome III displays a hemizygous cluster of Cla elements in males but not in females. The chromosomal location of this hemizygous Cla element cluster is in the region of the male determiner M as localized by cytogenetic analysis. With Cla elements as hybridization probe, it was possible to clone a large part of the sex determining region. Molecular analysis of the DNA of males and females in this region displayed a number of differences between the two sexes. One striking difference is an unusual transposable element associated with the male sex determining region. The sex determining region also contains several other tandem-repetitive DNA elements in addition to the Cla elements. They are interspersed with single copy DNA. The accumulation of repetitive elements in the sex determining region interpreted as the result of a lack of recombination between the male/female heteromorphic region, although recombination in the other sections of chromosome III occurs.

Animals↗
PubMed1989

Drosophila P element transposase recognizes internal P element DNA sequences.

Drosophila P transposable elements encode an 87 kd trans-acting protein, transposase, that is required to catalyze P element transposition and excision. We show here that purified transposase is a site-specific DNA binding protein. P element transposase does not interact with the terminal 31 bp inverted repeats but instead interacts specifically with an internal 10 bp consensus sequence present at both the 5' and 3' ends of P element DNA. These binding sites lie within sequences known to be important for transposition in vivo. Transposase also displays an unusually high nonspecific affinity for DNA. The transposase binding site at the 5' and overlaps sequences we show to be essential for transcription from the P element promoter in vitro, which raises the possibility that either transposase or the related 66 kd P element protein may affect P element transcription. From these and other observations, we suggest that the P element transposition reaction probably requires the binding of additional Drosophila protein factors to the terminal DNA sequences.

Animals↗
PubMed1986

Activation of oncogenes by transposable elements.

Mammalian DNA contains several families of highly repeated sequences, some of which have been suggested to be mobile elements. We have screened tumour tissue for the rearrangement of cellular oncogenes and found evidence for the behaviour of repetitive DNA sequences as transposable elements which may activate oncogenes. In the mouse myeloma NSI and XRPC24 we found that intracisternal A particle genome was inserted into the coding region of c-mos. In both cases the rearranged c-mos was transcriptionally activated and was also able to transform NIH 3T3 cells. In the canine transmissible venereal tumour we found that c-myc was rearranged due to the insertion of an 1.8 kilobase pair cellular DNA. Nucleotide sequence analysis demonstrated that the inserted piece is 60% homologous to the monkey KpnI element which is a representative of the LINE group.

Animals↗
PubMed1997

Segmented structure of separate and transposable DNA and RNA elements as suggested by their size distributions.

A collection of about 1000 different eukaryotic and prokaryotic DNA mobile and separate elements is compiled from literature-transposons, plasmids, extrachromosomal circular DNA, insertion sequences, as well as viral genomes and separate genome segments. Only small elements are collected, upto 2000 base pairs. Analysis of the sequence length distributions of the elements reveals that certain sizes are clearly preferred, namely those which correspond to multiples of about 345 bp in eukaryotes and multiples of about 210 bp in prokaryotes. This provides additional evidence in support of the theory (1) that segmented structure is characteristic of not only protein-coding sequences (2) but rather of genomes in general. In particular, it confirms the prediction (1) that mobile and separate elements would also be segmented.

Animals↗
PubMed1994

Transposition of Tnr1 in rice genomes to 5'-PuTAPy-3' sites, duplicating the TA sequence.

Tnr1 is a repetitive sequence in rice with several features characteristic of a transposable DNA element. Its copy number was estimated to be about 3500 per haploid genome by slot-blot hybridization. We have isolated six members of Tnr1 located at different loci by PCR (polymerase chain reaction) and determined their nucleotide sequences. The Tnr1 elements were similar in size and highly homologous (about 85%) to the Tnr1 sequence identified first in the Waxy gene in Oryza glaberrima. A consensus sequence of 235 bp could be derived from the nucleotide sequences of all the Tnr1 members. The consensus sequence showed that base substitutions occurred frequently in Tnr1 by transition, and that Tnr1 has terminal inverted repeat sequences of 75 bp. Almost all the chromosomal sequences that flank the Tnr1 members were 5'-PuTA-3' and 5'-TAPy-3', indicating that Tnr1 transposed to 5'-PuTAPy-3' sites, duplicating the TA sequence. PCR-amplified fragments from some rice species did not contain the Tnr1 members at corresponding loci. Comparison of nucleotide sequences of the fragments with or without a Tnr1 member confirmed preferential transposition of Tnr1 to 5'-PuTAPy-3' sites, duplicating the TA sequence. One amplified sequence suggested that imprecise excision had occurred to remove a DNA segment containing a Tnr1 member and its neighboring sequences at the Waxy locus of rice species with genome types other than AA. We also present data that may suggest that Tnr1 is a defective form of an autonomous transposable element.

Adenine Nucleotides↗
PubMed2002

Repetitive DNA elements in fungi (Mycota): impact on genomic architecture and evolution.

Repetitive DNA elements, microsatellites or simple repeats, minisatellites, mobile elements that transpose at the level of DNA, retrotransposons and various derivatives thereof are ubiquitous constituents of all fungal genomes. Many of these elements, especially the different types of transposon, have been cloned and characterised at the sequence level. Their biological role, however, has not yet been sufficiently elucidated. We are far from understanding the selection mechanisms that tend to conserve repeated DNA at defined loci. There is also little insight into the mechanisms that provide the balance between spreading repetitive elements within genomes and control of their copy number. Depending on the fungal group, this balance can be stabilised at different levels. Asco- and basidiomycetes rarely contain more than 5% repetitive DNA, whereas the phylogenetically older division Zygomycota is characterised by typically more than 30%. The effects of repetitive DNAs on the expression of adjacent genes are only rarely understood and their role for genomic plasticity on an evolutionary time scale is still especially enigmatic. This survey summarises the main characteristics of well studied experimental systems and intends to define important open questions for stimulating future research.

Base Sequence↗
PubMed1998

Transposase makes critical contacts with, and is stimulated by, single-stranded DNA at the P element termini in vitro.

P elements transpose by a cut-and-paste mechanism. Donor DNA cleavage mediated by transposase generates 17 nucleotide (nt) 3' single-strand extensions at the P element termini which, when present on oligonucleotide substrates, stimulate both the strand-transfer and disintegration reactions in vitro. A significant amount of the strand-transfer products are the result of double-ended integration. Chemical DNA modification-interference experiments indicate that during the strand-transfer reaction, P element transposase contacts regions of the substrate DNA that include the transposase binding site and the duplex portion of the 31 bp inverted repeat, as well as regions of the terminal 17 nt single-stranded DNA. Together these data suggest that the P element transposase protein contains two DNA-binding sites and that the active oligomeric form of the transposase protein is at least a dimer.

Animals↗
PubMed1994

DNA length, bending, and twisting constraints on IS50 transposition.

Transposition is a multistep process in which a transposable element DNA sequence moves from its original genetic location to a new site. Early steps in this process include the formation of a transposition complex in which the end sequences of the transposable element are brought together in a structurally precise fashion through the action of the element-encoded transposase protein and the cleavage of the element free from the adjoining DNA. If transposition complex formation must precede DNA cleavage (or nicking), then changing the length of the donor DNA between closely spaced ends should have dramatic effects on the frequency of the transposition. This question has been examined by studying the effects of altering donor DNA length on IS50 transposition. Donor DNA < or = 64 bp severely impaired transposition. Donor DNA > or = 200 bp demonstrated high transposition frequencies with only modest length dependencies. Constructs with donor DNA lengths between 66 and 174 bp demonstrated a dramatic periodic effect on transposition (periodicity approximately 10.5 bp).

Base Sequence↗
PubMed1987

Base substitutions in transposable element IS1 cause DNA duplication of variable length at the target site for plasmid co-integration.

We demonstrate that base substitutions in the IS1 sequence affect the length of the nucleotide sequence which is duplicated during IS1-mediated co-integration. IS1K, an IS1 variant present in the Escherichia coli chromosome, has seven base substitutions in its sequence as compared with that of IS1R derived from the plasmid R100. All substitutions are located in the internal region of IS1K. We have constructed plasmids containing IS1R, IS1K and hybrids between them: one contains four base substitutions causing an amino acid substitution in the insA gene and the other has three substitutions producing an amino acid substitution in the insB gene. We have isolated co-integrate plasmids formed by each IS1 and analysed nucleotide sequences of the target sites duplicated at the co-integration junctions. The results show that IS1K generates duplications of 8 or 14 bp as well as 9 bp, while IS1R exclusively generates the 9-bp duplications. Both hybrid IS1s also create 8- or 7-bp target duplications in addition to 9-bp duplications. These results indicate that the base substitutions in either insA or insB are sufficient for the occurrence of unusual target duplications, suggesting that both genes are involved in the target duplication.

Base Sequence↗
PubMed1988

The structure of the regulatory region of the rat L1 (L1Rn, long interspersed repeated) DNA family of transposable elements.

Here we report the DNA structure of the left 1.5 kb of two newly isolated full length members of the rat L1 DNA family (L1Rn, long interspersed repeated DNA). In contrast to earlier isolated rat L1 members, both of these contain promoter-like regions that are most likely full length. In addition, the promoter-like region of both members has undergone a partial tandem duplication. A second internal region of the left end of one of the reported members is also tandemly duplicated. The propensity of the left end of rat L1 elements to undergo this form of genetic rearrangement, as well as other structural features revealed by the present work, is discussed in light of the fact that during evolution the otherwise conserved mammalian L1 DNA families have each acquired completely different promoter-like regions. In an accompanying paper [Nur, I., Pascale, E., and Furano, A. V. (1988) Nucleic Acids Res. 16, submitted], we report that one of the rat promoter-like regions can function as a promoter in rat cells when fused to the Escherichia coli chloramphenicol acyltransferase gene.

Amino Acid Sequence↗
PubMed2001

A PCR-based assay to detect En/Spm-like transposon sequences in plants.

Degenerate primers deduced from the TPase region of plant En/Spm-like transposons allowed the amplification of similar sequences from various plant species including sugar beet, wheat and pea. These primers are efficient tools for the detection of this family of transposons in many plant genomes irrespective of sequence knowledge or phenotypic pecularities. An efficient PCR assay was therefore developed for these class II transposons, similar to assays already available for Ty1-copia-, Ty3-gypsy- or LINEs. This approach allowed us not only to show the widespread almost-ubiquitous presence of En/Spm-elements in plant genomes, but also to characterize their genomic organization and chromosomal distribution in the genome of chickpea (Cicer arietinum L.) and its abundance in related Cicer species. This approach can be used for the detection and characterization of endogenous DNA transposable elements in plant species, their complete isolation and evaluation of their use for genome analysis.

Amino Acid Sequence↗
PubMed2006

Vertebrate DNA transposon as a natural mutator: the medaka fish Tol2 element contributes to genetic variation without recognizable traces.

DNA-based transposable elements, or DNA transposons, transpose in a cut-and-paste fashion, involving excision from the chromosome. If this process affects the function of a host gene and the excision rate is high, any gene associated with such an element would clearly be in a genetically "unstable" state, and there are many examples of unstable genes in various organisms. However, none have hitherto been reported in vertebrates. We here document the finding of an unstable mutant gene in the medaka fish, Oryzias latipes, a useful model animal for vertebrate genetics and evolutionary studies. In an inbred strain, excision of the Tol2 element inserted in a pigmentation gene occurs spontaneously, giving rise to different heritable phenotypes and new mutant genes that carry different excision footprint sequences. The phenotypic mutation rate is as high as 2% per gamete, representing a 1000-fold increase from spontaneous mutation rates so far determined with the same organism. With mutations caused by insertion, and then excision, of transposons, one can no longer recognize participation of transposons in their generation. Thus, the impact of DNA transposons on vertebrate genomes may be, and may have been, larger than commonly supposed.

Alleles↗