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     

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     

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.     

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.     

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.     

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.     

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.     

Analysis of secondary, integration sites for IS117 in Streptomyces lividans and their role in the generation of chromosomal deletions

IS117, the 2.6 kb mini-circle of Streptomyces coelicolor A3(2), is a transposable element previously shown to be integrated into two distant sites in the chromosome. When introduced into S. lividans, IS117 integrates into one preferred chromosomal site, but when this site was artificially deleted, IS117 integrated into many secondary sites. Nucleotide sequence analysis of several secondary integration sites revealed varying degrees of similarity with the preferred site, but no consensus sequence. Nevertheless, sites more similar to the preferred site tended to be occupied more often than those that are less similar. Insertion of IS117 into secondary sites in the chromosome of S. lividans sometimes mediated chromosomal rearrangements. It was shown that some strains containing IS117 integrated into secondary sites had suffered deletions of chromosomal DNA. Deletions were adjacent to the inserted element and were at least several kilobases long. The proposed model implicates homologous recombination between IS117 copies integrated into two different secondary sites in the same chromosome as a cause of the deletions.     

Excision and transposition of two Ds transposons from the bronze mutable 4 derivative 6856 allele of Zea mays L

Summary The regulatory mutation bronze mutable 4 Derivative 6856 (bz-m4 D6856) contains a complex 6.7 kb Dissociation (Ds) element tagged with a duplication of low copy bz 3 flanking sequences (Klein et al. 1988). This creates a unique opportunity to study the transposition of a single member of the repetitive family of Ds elements. Eighteen full purple revertants (Bz alleles) of bz-m4 were characterized enzymatically and by genomic mapping. For 17 of the Bz alleles, reversion to a wild-type phenotype was caused by excision of the 6.7 kb Ds transposon. Nine of these Bz alleles retained the transposon somewhere in their genome. In this study we show that like Ac (Schwartz 1989; Dooner and Belachew 1989), the 6.7 kb Ds element can transpose within a short physical distance, both proximal and distal to its original position. Additional bz sequences have been mapped immediately distal to the mutant locus in bz-m4 D6856; genetic evidence suggests these are flanked by two additional Ds elements. The remaining Bz revertant, Bz :107, arose from excision of a more complex 13 kb Ds element.     

Embryos in evolution: evo-devo at the Naples Zoological Station in 1874

Eighteen seventy-four was a high point in evolutionary embryology. Thanks to Charles Darwin, the theory of evolution by natural selection provided a revolutionary new way of viewing the relationships and origins of organisms on Earth. Thanks to Ernst Haeckel, embryos were the way to study evolution (Haeckel in Generelle morphologie der organismen, vols 1, 2. Verlag Georg Reimer, Berlin, 1866)—it really was embryos in evolution—and recapitulation was in the air. Thanks to Anton Dohrn, a new research facility was on the ground, designed, located and structured to facilitate the study of embryos in evolution. Anton Dohrn devised, designed, financed, supervised the construction and then administered the Naples Zoological Station specifically so that researchers from all nations would have a facility where Darwin’s theory of evolution by natural selection could be tested. The zoologists who took advantage of the brand new facility within weeks of its opening late in 1873 established lines of research into evolutionary embryology, the field we now know as evolutionary developmental biology (evo-devo), the study of embryos in evolution. I examine the approach taken by Ambrosius Hubrecht, the first Dutch embryologist to undertake research at the station, and then evaluate the research of three British zoologists—E. Ray Lankester, Albert Dew-Smith, and Francis Maitland (Frank) Balfour. All four sought insights into origins, especially vertebrate origins that rested on comparative embryology, homology, germ layers, and a Darwinian approach to origins.

Repeated big bangs and the expanding universe: Directionality in plant genome size evolution

The lack of correlation between genome size and organismal complexity has long been a topic of great interest. Over the last decade it has become clear that transposable elements play a dominant role in genome size growth, and that most of the observed genome size variation in plants can be ascribed to differential accumulation of transposable elements, particularly long terminal repeat retrotransposons, which often massively proliferate over exceptionally short evolutionary time-scales. In the absence of one or more counterbalancing forces, Bennetzen and Kellogg previously suggested that growth via transposable element accumulation would create a “one-way ticket to genomic obesity”. Phylogenetic evidence, however, indicates that lineages may experience genomic downsizing, notwithstanding the relative paucity of experimental evidence on mechanisms capable of eliminating massive amounts of DNA. Thus, genome size evolution in plants may involve both feast and famine. Here we review recent insights into the molecular mechanisms and evolutionary dynamics of genome size evolution in plants. These include mechanisms that contribute to genome size expansion, i.e. polyploidy and transposable element proliferation, in addition to the counteracting forces that act to remove DNA, particularly intra-strand homologous recombination and illegitimate recombination. We argue that extant genome sizes reflect myriad competing forces of genomic expansion and contraction, but that current evidence pertaining to rates and amounts of DNA loss prove insufficient to overcome transposable element proliferation in most lineages. Accordingly, the directionality of plant genome size evolution in most cases is biased toward growth, with mechanisms of DNA loss acting to attenuate (but not reverse) the march toward obesity.