DNA transposons: nature and applications in genomics

Repeated DNA makes up a large fraction of a typical mammalian genome, and some repetitive elements are able to move within the genome (transposons and retrotransposons). DNA transposons move from one genomic location to another by a cut-and-paste mechanism. They are powerful forces of genetic change and have played a significant role in the evolution of many genomes. As genetic tools, DNA transposons can be used to introduce a piece of foreign DNA into a genome. Indeed, they have been used for transgenesis and insertional mutagenesis in different organisms, since these elements are not generally dependent on host factors to mediate their mobility. Thus, DNA transposons are useful tools to analyze the regulatory genome, study embryonic development, identify genes and pathways implicated in disease or pathogenesis of pathogens, and even contribute to gene therapy. In this review, we will describe the nature of these elements and discuss recent advances in this field of research, as well as our evolving knowledge of the DNA transposons most widely used in these studies.     

Merlin, a new superfamily of DNA transposons identified in diverse animal genomes and related to bacterial IS1016 insertion sequences

Several new families of DNA transposons were identified by computer-assisted searches in a wide range of animal species that includes nematodes, flat worms, mosquitoes, sea squirt, zebrafish, and humans. Many of these elements have coding capacity for transposases, which are related to each other and to those encoded by the IS1016 group of bacterial insertion sequences. Although these transposases display a motif similar to the DDE motif found in many transposases and integrases, they cannot be directly allied to any of the previously described eukaryotic transposases. Other common features of the new eukaryotic and bacterial transposons include similarities in their terminal inverted repeats and 8-bp or 9-bp target-site duplications. Together, these data indicate that these elements belong to a new superfamily of DNA transposons, called Merlin/IS1016, which is common in many eubacterial and animal genomes. We also present evidence that these transposons have been recently active in several animal species. This evidence is particularly strong in the parasitic blood fluke Schistosoma mansoni, in which Merlin is also the first described DNA transposon family.     

A new family of the poly-deoxyadenylated class of Drosophila transposable elements identified by a representative member at the dunce locus

Summary Two transposable elements have been identified at the dunce locus in chromosomes recovered after a premeiotic and interchromosomal conversion event occurred at this gene. One is approximately 8.2 kb and is inserted near the 5 end of the gene. This element was identified by sequence analysis as a member of the B104 (roo) family of copia-like transposable elements. The second resides near the 3 end of the gene and represents a new family of the class of poly-deoxyadenylated [poly(dA)] transposable elements. It is 0.38 kb in length and has one terminus consisting of a stretch of 29 deoxyadenosine residues with a polyadenylation site like those found in mRNA molecules, located about 20 pb away from the poly(dA) stretch. Fourteen base pairs of genome DNA is duplicated at the target site of this element.     

A nuclear protein that binds specifically to several maize transposons is not essential for Ds1 excision

Specific binding of plant nuclear proteins to GGTAAA-like motifs in the terminal regions of the transposable elements Ac and Mu1 has been detected in several laboratories. However, the role of these proteins in transposition remains unknown. To test the hypothesis that this binding activity is necessary for transposition, we identified and mutagenized all the binding motifs within the Ds1 element. This analysis enabled us to define more precisely the requirements for binding of the host protein. We then tested the ability of the mutated elements to excise from the maize streak virus (MSV) genome. We found that mutated Ds1 elements that do not bind the host proteins, as determined by gel-shift competition assay, are still capable of undergoing excision in maize, although for one of the maize lines the rate of excision was reduced. Excision of mutated Ds1 elements generated typical excision footprints. These data indicate that binding of host protein(s) to the GGTAAA-like motifs is not essential for Ds1 excision; however, it may contribute to the efficiency of the process. Received: 30 September 1999 / Accepted: 17 January 2000     

Anton Dohrn and the problems of 19th century phylogenetic morphology

According to Anton Dohrn, evolutionary development was performed in a single progressive lineage where some proto-annelid initiated an evolutionary development that went straight on via annelids and lower vertebrates to man. From that line, a kind of metamorphosing nature, certain branches were derived, like protists or worms or even tunicates, which Dohrn thought off as degenerating groups. With that concept Dohrn came close to typological ideas of his time. Nevertheless, recent evo-devo literature seems to be influenced by Dohrn's outline of evolution.     

A novel simple satellite DNA is colocalized with the Stalker retrotransposon in Drosophila melanogaster heterochromatin

In the T(1;2)dor ^var7 multibreak rearrangement the distal 1A-2B segment of the X chromosome of Drosophila melanogaster is juxtaposed to an inverted portion of the heterochromatin of chromosome 2. Analysis of mitotic chromosomes by a series of banding techniques has permitted us precisely to locate the heterochromatic breakpoint of this translocation in the h42 region of 2R. Cloning and sequencing of the eu-heterochromatic junction revealed that the translocated 1A-2B fragment is joined to (AACAC)_n repeats, which represent a previously undescribed satellite DNA in D. melanogaster. These repeated sequences have been estimated to account for about 1 Mb of the D. melanogaster genome. The repeats are located mainly in the Y chromosome and in the heterochromatin of the right arm of chromosome 2 (2Rh), where they are colocalized with the Stalker retrotransposon. Received: 3 October 1998 / Accepted: 3 December 1998     

The splicing of transposable elements and its role in intron evolution

Recent studies have demonstrated that transposable elements in maize and Drosophila are spliced from pre-mRNA. These transposable element introns represent the first examples of recent addition of introns into nuclear genes. The eight reported examples of transposable element splicing include members of the maize Ac/Ds and Spm/dSpm and the Drosophila P and 412 element families. The details of the splicing of these transposable elements and their relevance to models of intron origin are discussed.     

Covalent DNA modification and the regulation of Mutator element transposition in maize

Summary Analyses of the multiple genomic Mu transposable elements in active Mutator lines with several C-methylation sensitive restriction enzymes indicate that Mu elements are undermodified compared with total maize nuclear DNA. Intercrossing of diverse Mutator lines leads to a discrete hypermodification of the Mu elements in a particular plant concurrent with a loss of mutagenic and transpositional potential. The modification events observed appear to be methylation of cytosine at the 5 position in the sequences 5-CG-3 and 5-CNG-3. Some potential C-methylation sites in Mu elements show a higher degree of methylation than others. Once established, the modified Mu state, like the loss of Mutator activity, is stable on outcrossing. Crosses between active Mutator lines with unmodified Mu elements and Mutator-loss lines with modified Mu elements show partial maternal dominance for the modification event. Mutator activity may also be lost thorugh outcrossing in a mechanism not associated with any detected modification events.     

Conserved motifs and dynamic aspects of the terminal inverted repeat organization within <Emphasis Type="Italic">Bari</Emphasis>-like transposons

In this work the structural variations of Terminal Inverted Repeats (TIR) of Bari like transposons in Drosophila species has been studied. The aim is to try and assess the relevance of different variants in the evolutionary distribution of Bari elements. Bari is a member of the widespread Tc1 superfamily of transposable elements that has colonized most species of the Drosophila genus. We previously reported the structure of two related elements that differ in their TIR organization: Bari1 harbouring 26-bp TIR (short TIRs) and Bari2 with about 250-bp TIR (long TIR). While elements with short TIRs are complete and potentially autonomous, long ones are invariably composed of defective copies. The results show that in D. pseudobscura, D. persimilis and D. mojavensis, there is a third class of Bari elements, Bari3, that exhibit a long TIR structure and are not defective. Phylogenetic relationships among reconstructed transposases are consistent with the three subfamilies sharing a common origin. However, the final TIR organization into long or short structure is not related by descent but appears to be lineage-specific. Furthermore, we show that, independently of origin and organization, within the 250-bp terminal sequences there are three regions that are conserved in both sequence and position suggesting they are under functional constraint. Nucleotide sequence data from this article have been deposited in the EMBL/GenBank databases with the accession numbers: AM493769, AM493770, AM493771, AM493772.     

Keeping the soma free of transposons: programmed DNA elimination in ciliates

Many transposon-related sequences are removed from the somatic macronucleus of ciliates during sexual reproduction. In the ciliate Tetrahymena, an RNAi-related mechanism produces small noncoding RNAs that induce heterochromatin formation, which is followed by DNA elimination. Because RNAi-related mechanisms repress transposon activities in a variety of eukaryotes, the DNA elimination mechanism of ciliates might have evolved from these types of transposon-silencing mechanisms. Nuclear dimorphism allows ciliates to identify any DNA that has invaded the germ-line micronucleus using small RNAs and a whole genome comparison of the micronucleus and the somatic macronucleus.     

Widespread occurence of mariner transposons in coastal crabs

Mariner-like elements (MLEs) are ubiquitous DNA mobile elements found in almost all eukaryote genomes. Nevertheless most of the known copies are inactive and the question of the genome invasion by MLEs remains largely hypothetical. We have previously reported the presence of highly homologous copies of MLEs in the genome of phylogenetically distant crustacea living in the same hydrothermal environment suggesting the possibility of horizontal transfer. In order to further support the hypothesis that horizontal transmission of MLEs might occur between crustacean sympatric species, we described here 85 MLE sequences found in the genome of a large spectrum of coastal crab species. The number of the MLEs copies in genomes was variable. Half of these MLEs fit with the irritans subfamily of MLEs whereas the second half grouped in a new subfamily called marmoratus. In addition, a molecular phylogeny of crabs was established by using the 16S information. The comparison between 16S and MLEs based trees reveals their incongruence, and suggests either the existence of horizontal transfer events between phylogenetically distant species, or an ancestral MLE polymorphism followed by different evolution and stochastic loss.     

Spontaneous transposition of HzSINE1 into CYP321A2 is undetectable in the field populations of Helicoverpa zea

The enrichment of transposable elements (TEs) within allelochemical- and insecticide-metabolizing P450 alleles in Helicoverpa zea enables these P450s to gain TE-introduced adaptive variations otherwise not readily available to cope with the ever-changing and diverse xenobiotic stress factors in varying cropping systems. The critical role of each TE-inserted P450 allele depends on whether the inserted P450 allele is more adaptive than its TE-free counterpart or not. Previous study has reported a HzSINE1-inserted CYP321A2 allele in a laboratory strain of H. zea reared with xenobiotic-free artificial diets. Here we show that the HzSINE1-inserted CYP321A2 allele transcribes into two HzSINE1 sequence-containing mutant mRNA isoforms of different length that encode an identical C terminus-truncated and heme-binding region deleted non-functional P450. Nonetheless, HzSINE1 insertion does not disrupt the regulatory functional aspect of CYP321A2 since this allele is constitutively expressed and highly inducible by the allelochemicals xanthotoxin, quercetin and chlorogenic acid. Furthermore, while the HzSINE1-inserted CYP321A2 allele is fixed in the laboratory strain, the insertion is purged in the bifenthrin-resistant strain and the Georgia field population of H. zea. To sum up, the HzSINE1-inserted CYP321A2 allele represents an allelochemical-inducible non-functional P450 allele that is selected against in the field populations frequently encountering toxic plant allelochemicals and synthetic insecticides. However, such an insertion can reach fixation under the xenobiotic-free laboratory rearing conditions most likely due to random genetic drift across multiple generations.     

苏云金芽孢杆菌转座因子研究进展

近年来的研究发现苏云金芽孢杆菌转座因子和许多毒力因子可能是紧密联系的。由于转座因子的特殊性质,使它们在现代农业生物技术中有着广泛的应用前景,科学家对苏云金芽孢杆菌转座因子的研究也在不断深入。本文主要针对苏云金芽孢杆菌转座因子的研究进展进行综述,并对发展前景进行展望。     

An interchromosomal gene conversion of the Drosophila dunce locus identified with restriction site polymorphisms: a potential involvement of transposable elements in gene conversion

Summary Females heterozygous for the two alleles dnc ² and dnc ^M14 of the X-linked gene dunce (dnc), and carrying a copy of dnc ⁺ progeny X-chromosomes from recombination experiments. Restriction site polymorphisms have been used as genetic markers to follow the parentage of dnc locus segments in these chromosomes. All six chromosomes are identical with respect to the spectrum of restriction site markers they carry in the dnc ⁺ chromosomal region. In the progeny chromosomes, this region is comprised of sequences like the dnc ^M14 X-chromosome and the translocation copy of dnc ⁺. Sequences flanking the dnc gene in the progeny chromosomes are like the dnc ^M14 chromosome. Internal to the gene but near the 5 end, is a segment from the dnc ⁺ translocation which has apparently originated from an interchromosomal and premeiotic gene conversion event. In addition, two transposable elements have inserted into the progeny chromosomes, one towards the 5 end of dnc and the other near the 3 end. The insertion of these elements occurred premeiotically since all six chromosomes are structurally identical. The data are interpreted with respect to a potential role of transposable element transposition in the process of gene conversion.     

A branching process model for the evolution of transposable elements

A discrete-time multitype branching process model is presented for the evolution of transposable elements in haploid populations. An individual is classified as type i if it possesses i copies of the TE, i0. The general model incorporates copy-dependent selection and transposition, and recursion relations are derived for the distribution of the number of individuals of the various types. The asymptotic relative proportions of individuals of the different types is studied in the neutral case. The behavior of this equilibrium distribution is examined for various patterns of regulated transposition and deletion.     

The generation of Mutator transposable element subfamilies in maize

The mobile DNAs of the Mutator system of maize (Zea mays) are exceptional both in structure and diversity. So far, six subfamilies of Mu elements have been discovered; all Mu elements share highly conserved terminal inverted repeats (TIRs), but each sub-family is defined by internal sequences that are apparently unrelated to the internal sequences of any other Mu subfamily. The Mu1/Mu2 subfamily of elements was created by the acquisition of a portion of a standard maize gene (termed MRS-A) within two Mu TIRs. Beside the unusually long (185–359 bp) and diverse TIRs found on all of these elements, other direct and inverted repeats are often found either within the central portion of a Mu element or within a TIR.Our computer analyses have shown that sequence duplications (mostly short direct repeats interrupted by a few base pairs) are common in non-autonomous members of the Mutator, Ac/Ds, and Spm(En) systems. These duplications are often tightly associated with the element-internal end of the TIRs. Comparisons of Mu element sequences have indicated that they share more terminal components than previously reported; all subfamilies have at least the most terminal 215 bp, at one end or the other, of the 359-bp Mu5 TIR. These data suggest that many Mu element subfamilies were generated from a parental element that had termini like those of Mu5. With the Mu5 TIRs as a standard, it was possible to determine that elements like Mu4 could have had their unusual TIRs created through a three-step process involving (1) addition of sequences to interrupt one TIR, (2) formation of a stem-loop structure by one strand of the element, and (3) a subsequent DNA repair/gene conversion event that duplicated the insertion(s) within the other TIR. A similar repair/conversion extending from a TIR stem into loop DNA could explain the additional inverted repeat sequences added to the internal ends of the Mu4 and Mu7 TIRs. This same basic mechanism was found to be capable of generating new Mu element subfamilies. After endonucleolytic attack of the loop within the stem-loop structure, repair/conversion of the gap could occur as an intermolecular event to generate novel internal sequences and, therefore, a new Mu element subfamily. Evidence supporting and expanding this model of new Mu element subfamily creation was identified in the sequence of MRS-A.     

Widespread occurrence of the Tc1 transposon family: Tc1-like transposons from teleost fish

We characterized five transposable elements from fish: one from zebrafish (Brachydanio rerio), one from rainbow trout (Salmo gairdneri), and three from Atlantic salmon (Salmo salar). All are closely similar in structure to the Tel transposon of the nematode Caenorhabditis elegans. A comparison of 17 Tc1-like transposons from species representing three phyla (nematodes, arthropods, and chordates) showed that these elements make up a highly conserved transposon family. Most are close to 1.7 kb in length, have inverted terminal repeats, have conserved terminal nucleotides, and each contains a single gene encoding similar poly peptides. The phylogenetic relationships of the transposons were reconstructed from the amino acid sequences of the conceptual proteins and from DNA sequences. The elements are highly diverged and have evidently inhabited the genomes of these diverse species for a long time. To account for the data, it is not necessary to invoke recent horizontal transmission.