SEVERAL transposable elements of the terminal- sion has been demonstrated (Kawakami and Shima

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1 Copyright 2000 by the Genetics Society of America Detection of de Novo Insertion of the Medaka Fish Transposable Element Tol2 Akihiko Koga and Hiroshi Hori Division of Biological Sciences, Graduate School of Science, Nagoya University, Nagoya , Japan Manuscript received April 24, 2000 Accepted for publication July 10, 2000 ABSTRACT Tol2 is a terminal-inverted-repeat transposable element of the medaka fish Oryzias latipes. It is a member of the hat (hobo/activator/tam3) transposable element family that is distributed in a wide range of organisms. We here document direct evidence for de novo insertion of this element. A Tol2 clone marked with the bacterial tetracycline-resistance gene was microinjected into fertilized eggs together with a target plasmid, and the plasmid was recovered from embryos. The screening of plasmid molecules after transformation into Escherichia coli demonstrated transposition of tet into the plasmid and, by inference, precise insertion of Tol2 in medaka fish cells. De novo excision of Tol2 has previously been demonstrated. The present study provides direct evidence that the Tol2 element has the entire activity necessary for cut-andpaste transposition. Some elements of the mariner/tc1 family, another widespread group, have already been applied to development of gene tagging systems in vertebrates. The Tol2 element of the hat family, having different features from mariner/tc1 family elements, also has potential as an alternative gene tagging tool in vertebrates. SEVERAL transposable elements of the terminal- sion has been demonstrated (Kawakami and Shima inverted-repeat class are known to exist in vertebrate 1999). The same enzyme would also be expected to genomes. However, only a few of them have been catalyze insertion, as is usually the case with terminal- demonstrated to be active. The first example for which inverted-repeat elements. The reason de novo insertion a transposition event was observed is the Tzf element has not been detected earlier is that it requires, in conof zebrafish (Lam et al. 1996). Other examples are the trast to the excision case, a suitable experimental system synthetic element Sleeping Beauty (Ivics et al. 1997) and to allow detection of the inserted element at what would exogenous elements such as Tc3 of Caenorhabditis elegans normally be random locations. One strategy to over- (Raz et al. 1997) and mariner of Drosophila (Fadool et come this difficulty is to trace a genetically marked eleal. 1998). All these elements are members of the mari- ment. In this study, we marked Tol2 with the bacterial ner/tc1 transposable element family. There is one other tetracycline-resistance (Tet R ) gene and screened target element for which part of the transposition reaction has DNA fragments in Escherichia coli transformants for been demonstrated. The element is Tol2, found in the transposition products conferring tetracycline resismedaka fish (Koga et al. 1996), and de novo excision tance. Precise insertion, with Tol2 flanked by 8-bp target has also been detected in zebrafish (Kawakami et al. site duplications, was detected. In addition, the transpo- 1998). However, de novo insertion has hitherto not been sition was proven to be catalyzed by the transposase that observed. This element is a member of the hoto/activa- is encoded by a sequence within Tol2. tor/tam3 (hat) element family found in various organisms, even across kingdoms (Calvi et al. 1991; Atkinson et al. 1993; Koga et al. 2000). Such widespread occur- MATERIALS AND METHODS rence is an important feature for developing a gene tagging system because it implies relative independence Fish: Oryzias latipes (medaka fish, also called Japanese me- daka fish) and O. melastigma (Indian medaka fish) were used. of transposition mechanisms from species-specific host O. latipes was purchased from a pet shop in Nagoya and the factors and, thus, applicability to a relatively wide range fish contained 20 Tol2 copies per diploid genome according of organisms. to genomic Southern blots (Koga and Hori 1999). O. melastigma The purpose of this study was to detect de novo insertion was obtained from the World Medaka Aquarium of the of Tol2. A putative transposase of Tol2 has already Nagoya City Higashiyama Zoological Garden. This species does not harbor Tol2 in its genome (Koga et al. 2000). been suggested (Koga et al. 1999) and catalysis of exci- Construction of plasmids: Tol2 was first identified as a 4.7- kb insertion sequence in the tyrosinase gene of an albino mutant fish (Koga et al. 1996). This particular Tol2 copy Corresponding author: Hiroshi Hori, Division of Biological Sciences, (Tol2-tyr, GenBank accession no. D84375) together with its Graduate School of Science, Nagoya University, Nagoya , 8-bp target site duplication sequences was amplified by PCR. Japan. hori@bio.nagoya-u.ac.jp The primers used were 5 -AAGGATCCTCAAGAACCAGAG Genetics 156: (November 2000)

2 1244 A. Koga and H. Hori Figure 1. Organization of plasmids. pdon01 is a donor plasmid. It contains the chloramphenicolresistance (Cam R ) gene and a Tol2 element carrying the tetracycline-resistance (Tet R ) gene. ptar01 is a target plasmid containing the kanamycin-resistance (Kan R ) gene. GTGTAAAGT-3 and 5 -CCTCTAGAGTTCTTGACAGAGG chosen and checked for their sizes by agarose gel elec- TGTAAAAA-3. The third to eighth nucleotides are restric- trophoresis (Figure 3). This test revealed the majority tion enzyme sites (BamHI and XbaI, respectively) for cloning, the next eight nucleotides are target site duplications (part of the plasmids to be of two sizes: 7.7 and 10 kb. Plasmids of the tyrosinase gene), and the remaining sequences to 3 are of 7.7 kb were observed only in experiments B and D, the ends of Tol2 (the left and right ends, respectively). The in which mrna was microinjected together with the amplified fragment was cloned into phsg399 (Takeshita et plasmid DNAs. If the Tol2 portion (4274 bp) of pdon01 al. 1987) at its BamHI and XbaI sites in the lacz gene. An (6517 bp) is integrated precisely into ptar01 (3446 bp), internal region of Tol2 between its two PstI sites (positions 2401 and 4272 on the Tol2-tyr sequence) was removed and the expected size of a resultant plasmid is 7.7 kb. Therereplaced with the Tet R gene of pbr322 amplified with PCR fore, these plasmids are likely to be products of precise (nucleotides , including nucleotide 1, of accession Tol2 insertion. The fact that all these plasmids were no. J01749). This Tol2-carrying donor plasmid was denoted found to carry single SacI cutting sites also supports this pdon01 (Figure 1). The target plasmid ptar01 (Figure 1) was inference because pdon01 and ptar01 both have single prepared by inserting a 0.8-kb DNA fragment (nucleotides , including nucleotide 1, of accession no. M12787 SacI sites in their vector portions (see Figure 1). for phsg664; Hashimoto-Gotoh et al. 1986) into phsg299 (Takeshita et al. 1987). The fragment contains the streptomycin-sensitive (Str S ) gene whose disruption, in association with a specific bacterial strain, confers the streptomycin-resistance phenotype. It was prepared with the long-range plan of screening for insertions in this gene. In the present study, the 0.8-kb fragment was employed simply to enlarge the target plasmid. Transposition assay: The scheme of the transposition assay is illustrated in Figure 2. The pdon01 and ptar01 plasmids, 150 ng/ l each in 10 mm Tris-HCl (ph 8.0), were microinjected into fertilized eggs at the one-cell stage, with or without mrna for the putative Tol2 transposase (Koga et al. 1999), prepared by in vitro transcription using the RiboMAX large scale RNA production system SP6 (Promega, Madison, WI). A mammalian-cap-like sequence was added to its 5 end and the mrna was included in the DNA solution for injection at a final concentration of 150 ng/ l. After incubation at 25 for 24 hr, plasmid molecules were recovered from embryos by the method of Hirt (1967) and then introduced into the JM109 strain of E. coli by electroporation. The bacteria were screened for plasmids showing both the Kan R and Tet R phenotypes, which can be expected to include products of transposition. The drug concentrations were 50 g/ml for kanamycin and 6 g/ml for tetracycline. Sequencing analysis: Candidate transposition products were further selected by restriction mapping and sequenced for their Tol2 terminal and flanking regions, as described (Koga et al. 1995). The sequencing primers were nucleotides of the Tol2-tyr sequence for the left terminus and nucleotides for the right terminus. RESULTS Transposition assay: We carried out five experiments as listed in Table 1. In experiments A D, which included microinjection of plasmid DNAs, plasmids showing both the Kan R and Tet R phenotypes were found. Twenty plasmids each from the four experiments were randomly Figure 2. Transposition assay using plasmids. Plasmid molecules recovered from embryos were introduced into bacteria by electroporation. Most of the bacteria were plated on kanamycin- and tetracycline-containing media to screen for Tol2 insertion into the ptar01 plasmid. Small aliquots were plated on media containing only kanamycin to estimate the number of ptar01 molecules both with and without Tol2 insertion.

3 Medaka Transposable Element Tol TABLE 1 Numbers of colonies and distribution of plasmid sizes Drug a Plasmid size b Experiment Fish mrna Kan Tet Kan 7.7 kb 10 kb 12 kb A O. latipes No B O. latipes Yes C O. melastigma No D O. melastigma Yes E No a After electroporation, most of the bacterial mixture was plated on medium containing both kanamycin and tetracycline, Kan Tet indicating the number of colonies then observed. Small aliquots were also plated on medium containing only kanamycin. With the number of colonies on these media and the ratio of the mixture volumes, the total number of Kan R bacteria included was estimated as given in Kan. b Twenty plasmids each from experiments A D were checked for their sizes. If the pdon01 and ptar01 plasmids were combined and were flanked by sequences of ptar01 (Figure 4). into one molecule, the resultant plasmid would be ex- In addition, target site duplications of 8 bp were obpected to be 10 kb in size, like the plasmids of this size served in all cases (Figure 4). The insertion breakpoints observed in experiments A D. They all demonstrated according to the Tol2-flanking sequences are illustrated two SacI sites (examples shown in Figure 3) consistent in Figure 5. There was no apparent region where inserwith the inferred link. The fact that restriction patterns tion breakpoints were concentrated. for SacI differed among these 10-kb plasmids suggested that the integrations, on the assumption of this inference, were independent events. DISCUSSION There were also a few plasmids sized 12 kb with three SacI sites, as shown in Figure 3. Detection of de novo insertions: Our results provide Sequencing analysis: Of the 7.7-kb plasmids, five each evidence for de novo insertion of Tol2. Because excision from experiments B and D were randomly chosen and has already been detected, it can now be concluded sequenced for their Tol2 terminal and flanking regions. that Tol2 has all the activity necessary for cut-and-paste With all plasmids and for both Tol2 termini, the Tol2 transposition. sequences were observed as far as the last nucleotides We have not conducted further analysis of the 10- kb plasmids and the few larger plasmids because the purpose of our study was to detect insertion of Tol2, attained with the 7.7-kb plasmids. The 10-kb plasmids appear to have resulted from simple combination of pdon01 and ptar01 into one plasmid. If this is true, a possible mechanism for this event is homologous recombination, because the two vector plasmids (phsg399 and phsg299) share regions inherited from their common origin. Irrespective of the mechanisms involved, the recombination events occurred not in bacteria but in medaka fish cells because Kan R Tet R plasmids were not observed in experiment E. Precise insertion reaction leading to 7.7-kb plasmids also occurred in medaka fish cells. Evidence for transposase function: O. melastigma does not contain Tol2 in its genome. Therefore, the difference in results between experiments C and D implies that the mrna is essential for transposition of Tol2. It Figure 3. Electrophoresis of plasmid clones. Single plasmids isolated from experiments A D were digested with SacI of Tol2 that also functions as such in O. melastigma. is thus evident that the mrna encodes a transposase and electrophoresed on 0.6% agarose gels. In the example O. latipes contains 20 Tol2 copies and endogenous shown from experiment B, three clones (B-1, -5, and -7) exhimrna molecules are present in cells of this species bit single fragments of 7.7 kb, six clones (B-2, -3, -4, -6, -9, and -10) have a total length of 10 kb, and one clone (B-8) is (Koga et al. 1999). We infer from the results of experi- 12 kb. ments A and B that the amount is relatively low and

4 1246 A. Koga and H. Hori Figure 4. DNA sequences of Tol2 ends and their flanking regions. Five clones each from experiments B and D were sequenced. The regions outside Tol2 were all confirmed to be parts of the ptar01 plasmid. Target site duplications of 8 bp, in boldface type, were observed in all the cases. Figure 5. Locations of Tol2 insertions on the ptar01 plasmid. The stippled arrows indicate individual Tol2 copies, in accordance with the direction of the transposase gene in the element. Clones from experiment B are shown above and those from experiment D below the plasmid. the supply of exogenous mrna by microinjection was gene. Thus, the Tol2 element of the hat family can be responsible for invoking transposition of Tol2. expected to provide a gene tagging tool for molecular Development of a monitoring system: Our detection techniques as alternatives to those using mariner/tc1 system, if applied on a larger scale, would be useful for family elements. determining transposition frequency and, thus, finding We are grateful to H. Hashikawa, M. Sato, and S. Susaki for providing factors that affect the transposition. However, there is the O. melastigma samples. We also thank H. Ohtsubo and Y. Sekine a problem that remains to be solved and that is the for helpful discussions. This work was partly supported by grant no. presence of 10-kb plasmids. They can be eliminated by to A.K. and no to H.H. from the Ministry of Education, Science, Sports, and Culture of Japan, and also by the restriction enzyme digestion and agarose gel electro- Takeda Science Foundation to A.K. phoresis but a more efficient device is desirable. One possible approach is to use the Str S gene already contained in the ptar01 plasmid (see materials and methods). Screening with streptomycin, in addition to LITERATURE CITED kanamycin and tetracycline, would be useful for collect- Atkinson, P. W., W. D. Warren and D. A. O Brochta, 1993 The ing only insertions in the Str S gene. hobo transposable element of Drosophila can be cross-mobilized in houseflies and excises like the Ac element of maize. Proc. Natl. Potential as a gene tagging tool: Some elements of Acad. Sci. USA 90: the mariner/tc1 family have already been applied for Calvi, B. R., T. J. Hong, S. D. Findley and W. M. Gelbart, 1991 developing a gene tagging system in vertebrates. Howtransposons Evidence for a common evolutionary origin of inverted repeat in Drosophila and plants: hobo, Activator, and Tam3. ever, hat family elements have different features from Cell 66: those of the mariner/tc1 family, for example, being Dowe, M. F. Jr., G. W. Roman and A. S. Klein, 1990 Excision and larger in size. This might be an advantage for carrying transposition of two Ds transposons from the bronze mutable 4 derivative 6856 allele of Zea maize L. Mol. Gen. Genet. 221: 475 large DNA fragments. One element, Activator of maize, 485. has been shown to transpose preferentially within the Fadool, J. M., D. L. Hartl and J. E. Dowling, 1998 Transposition same chromosome (Greenblatt 1984; Dowe et al. of the mariner element from Drosophila mauritiana in zebrafish. 1990; Moreno et al. 1992) and, moreover, in a systematic Proc. Natl. Acad. Sci. USA 95: Greenblatt, I. M., 1984 A chromosomal replication pattern defurther analysis, preferentially to nearby regions (Mach- duced from pericarp phenotypes resulting from movements of ida et al. 1997). Such a transposition would be beneficial the transposable element, Modulator, in maize. Genetics 108: 471 to target nearby genes or regions. This might lead to 485. Hashimoto-Gotoh, T., A. Kume, W. Masahashi, S. Takeshita creation of chromosomal deletions and inversions and and A. Fukuda, 1986 Improved vector, phsg664, for direct to generating large numbers of mutations within a single streptomycin-resistance selection: cdna cloning with G:C-tailing

5 Medaka Transposable Element Tol procedure and subcloning of double-digest DNA fragments. medaka fish transposable element Tol2 deduced from mrna Gene 41: nucleotide sequences. FEBS Lett. 461: Hirt, B., 1967 Selective extraction of polyoma DNA from infected Koga, A., A. Shimada, A. Shima, M. Sakaizumi, H. Tachida et al., mouse cell cultures. J. Mol. Biol. 26: Evidence for recent invasion of the medaka fish genome Ivics, Z., P. B. Hackett, R. H. Plasterk and Z. Izsvák, 1997 Molec- by the Tol2 transposable element. Genetics 155: ular reconstruction of Sleeping Beauty, atc1-like transposon from Lam, W. L., T. S. Lee and W. Gilbert, 1996 Active transposition in fish, and its transposition in human cells. Cell 91: zebrafish. Proc. Natl. Acad. Sci. USA 93: Kawakami, K., and A. Shima, 1999 Identification of the Tol2 transposase Machida, C., H. Onouchi, J. Koizumi, S. Hamada, E. Semiarti et of the medaka fish Oryzias latipes that catalyzes excision of a al., 1997 Characterization of the transposition pattern of the nonautonomous Tol2 element in zebrafish Danio rerio. Gene 240: Ac element in Arabidopsis thaliana using endonuclease I-SceI. Proc Natl. Acad. Sci. USA 94: Kawakami, K., A. Koga, H. Hori and A. Shima, 1998 Excision of Moreno, M. A., J. Chen, I. Greenblatt and S. L. Dellaporta, 1992 the Tol2 transposable element of the medaka fish, Oryzias latipes, Reconstitutional mutagenesis of the maize P gene by short-range in zebrafish, Danio rerio. Gene 225: Ac transpositions. Genetics 131: Koga, A., and H. Hori, 1999 Homogeneity in the structure of the Raz, E., H. G. van Luenen, R. Schaerringer, R. H. A. Plasterk and medaka fish transposable element Tol2. Genet. Res. 73: W. Driever, 1997 Transposition of the nematode Caenorhabditis Koga, A., H. Inagaki, Y. Bessho and H. Hori, 1995 Insertion of a elegans Tc3 element in the zebrafish Danio rerio. Curr. Biol. 8: novel transposable element in the tyrosinase gene is responsible for an albino mutation in the medaka fish, Oryzias latipes. Mol. Takeshita, S., M. Sato, M. Toba, W. Masahashi and T. Hashimoto- Gen. Genet. 249: Gotoh, 1987 High-copy-number and low-copy-number plasmid Koga, A., M. Suzuki, H. Inagaki, Y. Bessho and H. Hori, vectors for lacz -complementation and chloramphenicol- or ka Transposable element in fish. Nature 383: 30. namycin-resistance selection. Gene 61: Koga, A., M. Suzuki, Y. Maruyama, M. Tsutsumi and H. Hori, 1999 Amino acid sequence of a putative transposase protein of the Communicating editor: J. A. Birchler