Detection of de novo insertion of the medaka fish transposable element Tol2

Repetitive DNA in the Catfish Genome: rDNA, Microsatellites, and Tc1-Mariner Transposon Sequences in Imparfinis Species (Siluriformes, Heptapteridae)

Physical mapping of repetitive DNA families in the karyotypes of fish is important to understand the organization and evolution of different orders, families, genera, or species. Fish in the genus Imparfinis show diverse karyotypes with various diploid numbers and ribosomal DNA (rDNA) locations. Here we isolated and characterized Tc1-mariner nucleotide sequences from Imparfinis schubarti, and mapped their locations together with 18S rDNA, 5S rDNA, and microsatellite probes in Imparfinis borodini and I. schubarti chromosomes. The physical mapping of Tc1/Mariner on chromosomes revealed dispersed signals in heterochromatin blocks with small accumulations in the terminal and interstitial regions of I. borodini and I. schubarti. Tc1/Mariner was coincident with rDNA chromosomes sites in both species, suggesting that this transposable element may have participated in the dispersion and evolution of these sequences in the fish genome. Our analysis suggests that different transposons and microsatellites have accumulated in the I. borodini and I. schubarti genomes and that the distribution patterns of these elements may be related to karyotype evolution within Imparfinis.

Tc1-like Transposase Thm3 of Silver Carp (Hypophthalmichthys molitrix) Can Mediate Gene Transposition in the Genome of Blunt Snout Bream (Megalobrama amblycephala)

Tc1-like transposons consist of an inverted repeat sequence flanking a transposase gene that exhibits similarity to the mobile DNA element, Tc1, of the nematode, Caenorhabditis elegans. They are widely distributed within vertebrate genomes including teleost fish; however, few active Tc1-like transposases have been discovered. In this study, 17 Tc1-like transposon sequences were isolated from 10 freshwater fish species belonging to the families Cyprinidae, Adrianichthyidae, Cichlidae, and Salmonidae. We conducted phylogenetic analyses of these sequences using previously isolated Tc1-like transposases and report that 16 of these elements comprise a new subfamily of Tc1-like transposons. In particular, we show that one transposon, Thm3 from silver carp (Hypophthalmichthys molitrix; Cyprinidae), can encode a 335-aa transposase with apparently intact domains, containing three to five copies in its genome. We then coinjected donor plasmids harboring 367 bp of the left end and 230 bp of the right end of the nonautonomous silver carp Thm1 cis-element along with capped Thm3 transposase RNA into the embryos of blunt snout bream (Megalobrama amblycephala; one- to two-cell embryos). This experiment revealed that the average integration rate could reach 50.6% in adult fish. Within the blunt snout bream genome, the TA dinucleotide direct repeat, which is the signature of Tc1-like family of transposons, was created adjacent to both ends of Thm1 at the integration sites. Our results indicate that the silver carp Thm3 transposase can mediate gene insertion by transposition within the genome of blunt snout bream genome, and that this occurs with a TA position preference.

Goldfish transposase Tgf2 presumably from recent horizontal transfer is active

Hobo/Activator/Tam3 (hAT) superfamily transposons occur in plants and animals and play a role in genomic evolution. Certain hAT transposons are active and have been developed as incisive genetic tools. Active vertebrate elements are rarely discovered; however, Tgf2 transposon was recently discovered in goldfish (Carassius auratus). Here, we found that the endogenous Tgf2 element can transpose in goldfish genome. Seven different goldfish mRNA transcripts, encoding three lengths of Tgf2 transposase, were identified. Tgf2 transposase mRNA was detected in goldfish embryos, mainly in epithelial cells; levels were high in ovaries and mature eggs and in all adult tissues tested. Endogenous Tgf2 transposase mRNA is active in mature eggs and can mediate high rates of transposition (>30%) when injected with donor plasmids harboring a Tgf2 cis-element. When donor plasmid was coinjected with capped Tgf2 transposase mRNA, the insertion rate reached >90% at 1 yr. Nonautonomous copies of the Tgf2 transposon with large-fragment deletions and low levels of point mutations were also detected in common goldfish. Phylogenetic analysis indicates the taxonomic distribution of Tgf2 in goldfish is not due to vertical inheritance. We propose that the goldfish Tgf2 transposon originated by recent horizontal transfer and maintains a highly native activity.

Endogenous transposases affect differently Sleeping Beauty and Frog Prince transposons in fish cells

Fish cells stably expressing exogenous genes have potential applications in the production of fish recombinant proteins, gene-function studies, gene-trapping, and the production of transgenic fish. However, expression of a gene of interest after random integration may be difficult to predict or control. In the past decade, major contributions have been made in vertebrate-gene transfer, by using tools derived from DNA transposons. Among them, the Sleeping Beauty (SB) and Frog Prince (FP) transposons, derived, respectively, from fish and frog genomes, mediate transposition in a large variety of cells, although with different efficiency. This study was aimed at assessing the activities of the SB and the FP transposases in fish cell lines from genetically distant species (CHSE-214, RTG-2, BF-2, EPC, and SAF-1). Their transpositional ability was evaluated by the plasmid-based excision assay, the colony formation assay, and the footprint patterns. The results reveal that while both transposases are active in all cell lines, the transposition rates and the precision of the transposition are overall higher with FP than SB. Our results also indicated a key role of cell-specific host factors in transposition, which was associated with the presence of Tc1-like endogenous transposases; this effect was more accentuated in the two salmonid cell lines transfected with SB. This result agrees with previous studies supporting the use of transposons in heterologous organisms to prevent from genomic instability and from impeding the precise activity of the exogenous transposase.

Repeat structure of the catfish genome: a genomic and transcriptomic assessment of Tc1-like transposon elements in channel catfish (Ictalurus punctatus)

We have assessed the distribution and diversity of members of the Tc1/mariner superfamily of transposable elements in the channel catfish (Ictalurus punctatus) genome as well as evaluating the extent of transcription of Tc1 transposases in the species. Through use of PCR amplification and sequencing, assessment of random BAC end sequences (BES) equivalent to 1.2% genome coverage, and screening of over 45,000 catfish ESTs, a significant proportion of Tc1-like elements and their associated transcripts were captured. Up to 4.2% of the catfish genome in base pairs appears to be composed of Tc1-like transposon-related sequences and a significant fraction of the catfish cellular mRNA, approximately 0.6%, was transcribed from transposon-related sequences in both sense and antisense orientations. Based on results of repeat-masking, as much as 10% of BAC end sequences from catfish, which is a random survey of the genome, contain some remnant of Tc1 elements, suggesting that these elements are present in the catfish genome as numerous, small remnants of the transposons. Phylogenetic analysis allowed comparison of catfish Tc1 transposase types with those found in other vertebrate and invertebrate species. In spite of the existence of many types of Tc1-like sequences that are not yet able to be placed in clades with strong statistical support, it is clear that multiple families of Tc1-like elements exist in channel catfish.

Fish transposons and their potential use in aquaculture

A large part of repetitive DNA of vertebrate genomes have been identified as transposon elements (TEs) or mobile sequences. Although TEs detected to date in most vertebrates are inactivated, active TEs have been found in fish and a salmonid TE has been successfully reactivated by molecular genetic manipulation from inactive genomic copies (Sleeping Beauty, SB). Progress in the understanding of the dynamics, control and evolution of fish TEs will allow the insertion of selected sequences into the fish genomes of germ cells to obtain transgenics or to identify genes important for growth and/or of somatic cells to improve DNA vaccination. Expectations are high for new possible applications to fish of this well developed technology for mammals. Here, we review the present state of knowledge of inactive and active fish TEs and briefly discuss how their possible future applications might be used to improve fish production in aquaculture.

Reversion mutation of ib oculocutaneous albinism to wild-type pigmentation in medaka fish

We have previously identified three naturally occurring mutations in the medaka fish tyrosinase gene caused by transposable element insertions. Tyr-i(b) is one of these, containing the Tol2 element in the promoter region. Its homozygous carriers exhibit a weak oculocutaneous albino phenotype. We report here spontaneous reversion of the albino phenotype to the wild-type pigmentation, associated with excision of the Tol2 element. The newly arising mutant gene is inherited in the Mendelian fashion. Thus, oculocutaneous albinism is not strictly irreversible, at least in this organism and the results also indicate that the insertion of the Tol2 element is the main, and possibly the only, cause of the i(b) albinism. Importantly our data also suggest that medaka fish possess an active transposase.

The tyrosinase gene of the i(b) albino mutant of the medaka fish carries a transposable element insertion in the promoter region

The i locus of the medaka fish contains the tyrosinase gene whose product is the key enzyme required for melanin biosynthesis. The i(b) allele at this locus, also denoted as i( 5), causes oculocutaneous albinism in homozygous carriers. Its albino phenotype is very weak, characterized mainly by small and varying sized melanophores in juveniles. Cloning and sequencing analyses of the tyrosinase gene for the i (b) allele revealed the presence of a 4.7-kb extra DNA fragment in the 5' untranslated region, this being Tol2, a DNA-based transposable element of the hobo Activator Tam3 (hAT) family which had previously been identified as a cause of another mutant allele i(4). Its insertion point was 85 bp upstream of the main transcription initiation site and 50 bp downstream of the CATGTG motif that has been suggested to be essential for the promoter function of the tyrosinase gene. The transcription level of the tyrosinase gene was decreased in i(b)/i(b) fish, compared with wild-type fish. The insertion is thus a likely cause of the weak albino phenotype. The Tol2 element transposes in a cut-and-paste fashion, and its excision is mostly imprecise, leaving some nucleotides and/or removing excess nucleotides. The i (b) mutant strain can thus be expected to serve as a source from which various other mutations in the promoter region can be derived.

Generating and manipulating transgenic animals using transposable elements

Transposable elements, or transposons, have played a significant role in the history of biological research. They have had a major influence on the structure of genomes during evolution, they can cause mutations, and their study led to the concept of so-called "selfish DNA". In addition, transposons have been manipulated as useful gene transfer vectors. While primarily restricted to use in invertebrates, prokaryotes, and plants, it is now clear that transposon technology and biology are just as relevant to the study of vertebrate species. Multiple transposons now have been shown to be active in vertebrates and they can be used for germline transgenesis, somatic cell transgenesis/gene therapy, and random germline insertional mutagenesis. The sophistication of these applications and the number of active elements are likely to increase over the next several years. This review covers the vertebrate-active retrotransposons and transposons that have been well studied and adapted for use as gene transfer agents. General considerations and predictions about the future utility of transposon technology are discussed.

The medaka fish Tol2 transposable element can undergo excision in human and mouse cells

Tol2 is an active DNA-based transposable element identified in the medaka fish, Oryzias latipes. Originating from a vertebrate and belonging to the hAT ( hobo/ Activator/ Tam3) transposable element family, featuring a wide distribution among organisms, Tol2 would be expected to be active if introduced into mammals. We, therefore, examined if excision, one part of the transposition reaction, can occur in human and mouse culture cells. A Tol2 clone was introduced into cells and, after incubation, recovered. PCR and sequencing analysis provided evidence for precise and near precise excision in these cells. Tol2 can thus be expected to serve as a material for developing a gene transfer vector and other genetic tools applicable to mammals. It was also suggested that an intact Tol2 element could retain autonomy as a transposable element in mammalian cells.

Gamera, a family of LINE-like repetitive sequences widely distributed in medaka and related fishes

A family of repetitive sequences, designated Gamera, has been identified in the genome of the Hainan medaka fish Oryzias curvinotus, a closely related species to the common medaka fish O. latipes. Sequencing and Southern blot analyses of this family revealed: (1) amino acid sequence similarity to reverse transcriptase domains of long interspersed nuclear elements (LINEs); (2) 5' truncation of dispersed copies; and (3) the disruption of another genetic element, indicating a past transposition event. These results suggest that Gamera belongs to the LINE superfamily. Gamera is widely distributed in the genus Oryzias, and the phylogenetic relationship might indicate its presence in the common ancestor of the genus.

Transposable elements in medaka fish

DNA-based transposable elements appear to have been nearly or completely inactivated in vertebrates. Therefore the elements of the medaka fish Oryzias latipes that still have transposition activity provide precious materials for studying transposition mechanisms, as well as the evolution, of transposable elements in vertebrates. Fortunately, the medaka fish has a strong background for genetic and evolutionary studies. The advantages of this host species and their elements, together with results so far obtained, are here described.

The Tol2 transposable element of the medaka fish: an active DNA-based element naturally occurring in a vertebrate genome

Several DNA-based transposable elements are known to be present in vertebrate genomes, but few of them have been demonstrated to be active. The Tol2 element of the medaka fish is one such element and, therefore, is potentially useful for developing a gene tagging system and other molecular biological tools applicable to vertebrates. Towards this goal, analyses of the element at the molecular, cellular and population levels are in progress. Results so far obtained are described here.