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.

Positron emission tomography and magnetic resonance imaging in spinocerebellar ataxia type 2: a study of symptomatic and asymptomatic individuals

Spinocerebellar ataxia type 2 (SCA2) is an autosomal dominant neurodegenerative disorder characterized as an expanded CAG trinucleotide repeats in SCA2 gene resulting in abnormal polyglutamine sequence. We used positron emission tomography (PET) and magnetic resonance imaging (MRI) to clarify metabolic and atrophic changes of the brain in two symptomatic and three asymptomatic individuals who were genetically confirmed for SCA2. PET revealed decreased glucose metabolism in both patients and two of the three asymptomatic carriers in the cerebellum, pons, or both. No PET abnormality was found in the remaining one carrier who had only a very mildly expanded CAG repeat. MRI showed cerebellar and/or pontine atrophic changes in both patients and one of three carriers. The present study suggest that hypometabolism and atrophy of the cerebellum and pons may occur years before the clinical onset of SCA2. PET and MRI may be useful in the early detection of subclinical brain changes associated with SCA2.

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.

Single nucleotide polymorphisms in the gene encoding Krüppel-like factor 7 are associated with type 2 diabetes

AIMS/HYPOTHESIS

Although genetic susceptibility plays an important role in the pathogenesis of type 2 diabetes, most of the genes that influence susceptibility to type 2 diabetes have yet to be identified. Krüppel-like transcription factors are known to play important roles in development and cell differentiation, and have recently been implicated in the pathogenesis of type 2 diabetes. The present study aimed to examine the associations of single nucleotide polymorphisms (SNPs) in genes encoding members of the Krüppel-like-factor (KLF) family with type 2 diabetes in a large cohort of Japanese subjects.

METHODS

We genotyped 33 SNP loci found in 12 KLF genes in subjects with type 2 diabetes and in subjects from the general population using the PCR-Invader assay. We also examined the effects of the overexpression of KLF7 on adipogenesis in 3T3-L1 cells.

RESULTS

We identified a significant association between an SNP in KLF7 and type 2 diabetes (A vs C: p=0.004 after Bonferroni's correction, odds ratio=1.59, 95% CI 1.27-2.00). The expression of Klf7 decreased in response to the differentiation of 3T3-L1 adipocytes, and the overexpression of KLF7 resulted in significant inhibition of adipogenesis in 3T3-L1 cells.

CONCLUSIONS/INTERPRETATION

These results indicate that the gene encoding KLF7 is a novel candidate for conferring genetic susceptibility to type 2 diabetes.

Structural analysis of single wool fibre by scanning microbeam SAXS

The technique of scanning microbeam small-angle X-ray scattering (SAXS) has been applied to investigate the inhomogeneity in the nanostructure of a single bilateral wool fibre in relation to two types of cortices, the so-called orthocortex and paracortex, which are located at the outer side and the inner side of the curved fibre, respectively. On the basis of the equatorial scattering intensity profiles from both experiments and simulation, the inhomogeneity in the mean IF (intermediate filament)–IF distance, IF diameter and IF orientation, corresponding to the structural difference between the orthocortex and the paracortex in bilateral wool fibre, has been quantitatively obtained.

Low transposition frequency of the medaka fish Tol2 element may be due to extranuclear localization of its transposase

Transposase proteins of some highly active DNA-based transposable elements, such as the maize Activator element, are known to possess nuclear localization signals (NLSs). We examined if this is also the case for the transposase of the medaka fish Tol2 element, a member of the hAT (hobo/Activator/Tam3) transposable element family, using human and mouse culture cells. Unexpectedly, the transposase-lacZ fusion protein, in which the lacZ is a location marker, was found to be present in the cytoplasm rather than in the nucleus, suggesting that the Tol2 transposase contains a signal for extranuclear localization. The same staining pattern was also observed with a fusion protein containing a 33-amino-acid region at about the center of the primary structure of the transposase. The Tol2 element might have a mechanism to control its transposition frequency that includes extranuclear localization of its transposase.

Electric-field-induced transition between the polarization-modulated and ferroelectric smectic- C(S) P(F)* liquid crystalline states studied using microbeam x-ray diffraction

We report x-ray microbeam studies of a bent-core liquid crystalline material with chiral citronellyl tails. This material has an equilibrium polarization-modulated smectic- CP (PM-SmCP) state exhibiting the B7 texture upon slow cooing from the isotropic while a metastable chiral synclinic ferroelectric Sm-CP state (Sm- C(S) P(*)(F) ) is obtained on quenching from the isotropic. The polarization modulated phase PM-Sm C(S) P(*)(F) shows typical x-ray patterns having multiple satellite peaks around the first-order layer reflection, indicating undulated layers, while the metastable Sm- C(S) P(*)(F) state exhibits a single layering peak indicating flat layers. The Sm- C(S) P(*)(F) state is also induced by the application of an electric field larger than the threshold field ( E(th) ) and thermally returns to the polarization modulated PM-Sm C(S) P(*)(F) structure.

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.

Bottle choice tests for oxidized oil in rats

Bottle choice tests in rats are useful for the study of fat appetite. However, little is known about the feeding behavior of rats toward oxidized oil. In this study, 24-h two-bottle choice tests were performed in male Sprague-Dawley (SD) rats for 5 days. When rats were given a choice between thermally oxidized oil and fresh oil, they ingested more fresh oil. A choice test between vapor-added fresh oil and fresh oil showed that rancid flavor is involved in the avoidance of oxidized oil. Results with deodorized oxidized oil indicated that a nonvolatile product also influenced choice. In conclusion, rats could distinguish oxidized oil from fresh oil and preferred fresh oil.

Generation of a recombinant Sendai virus that is selectively activated and lyses human tumor cells expressing matrix metalloproteinases

Malignant tumor cells often express matrix metalloproteinases (MMPs) at a high level to enable their dissemination and metastasis. Sendai virus (SeV), a nonsegmented negative strand RNA virus, spreads in the target tissues in vivo via cleavage activation of the viral fusion glycoprotein by a tissue-specific, trypsin-like enzyme. By deleting the viral matrix protein, we previously generated a recombinant SeV that does not bud to mature virions, but is highly fusogenic and spreads extensively from cell to cell in a trypsin-dependent manner. Here, we changed the tryptic cleavage site of the fusion glycoprotein of this virus to a site susceptible to MMPs. The resulting recombinant virus was no longer activated by trypsin but spread efficiently in cultured cells supplemented with MMP2 or MMP9 and in human tumor cell lines expressing these MMPs. Furthermore, the virus spread extensively in tumor cells xenotrasplanted to nude mice without disseminating to the surrounding normal cells, leading to the inhibition of the tumor growth in the mice. These results demonstrate the selective targeting and killing of human tumor cells by recombinant SeV technology and greatly advance the reemerging concept of oncolytic virotherapy, which currently appears to rely largely upon a natural preference of certain viruses for cancer cells.

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.

Local layer structures in circular domains of an achiral bent-core mesogen observed by x-ray microbeam diffraction

The local layer structures have been investigated by x-ray microbeam diffraction in the circular domains of the SmCP phase of a banana-shaped molecule. Originally, the molecules form tilted layers with a certain tilt angle as well as nontilted ones. The application of a low electric field induces a tilted layer with a continuous change of the tilt angle; i.e., the tilted layer gradually changes the tilt angle, finally being upright at the center of circular domains. Upon application of a high electric field, the smectic layer forms a cylindrical-type structure. The layer structure changes from cylindrical to onionlike after turning off the high field.

Dynamic local-layer response of surface-stabilized ferroelectric liquid crystals to a high electric field by time-resolved x-ray microdiffraction

Time-resolved synchrotron x-ray microdiffraction measurements have directly revealed the dynamic local-layer response to the high electric field in a surface-stabilized ferroelectric liquid crystal. The irreversible layer transformation under the increasing electric field is found to consist of two stages; the initial vertical chevron structure transforms to the alternate vertical and horizontal chevrons and, with increasing field, the chevron angle decreases and the horizontal chevron structure develops. The time-resolved microdiffraction measurement has clarified the detailed reversible layer transformation between the mostly horizontal chevron at the high field and the so-called quasibookshelf at the low field during the ac field application. The transient layer response time is about 0.1-0.2 and 0.3-0.4 ms for falling and rising edges, respectively, and is slightly longer than the optical response time. The layer transformation is discussed in terms of electric torque and surface anchoring. The local-layer response in the antiferroelectric liquid crystal is also discussed for comparison.

Intraoral grafting of an ex vivo produced oral mucosa equivalent: a preliminary report

The objective of this study was to assess the efficacy of the use of an ex vivo produced oral mucosa equivalent (EVPOME) for intraoral grafting procedures. Autogenous keratinocytes were harvested from a punch biopsy 4 weeks prior to surgery, placed in a serum-free culture system and seeded onto a human cadaveric dermal equivalent, AlloDerm. Thirty patients with either a premalignant or cancerous lesion were triaged into two groups, depending on the stage of disease: Group 1: EVPOME or Group 2: AlloDerm, control without an epithelial layer. Clinically, EVPOME grafts were easy to handle and showed excellent compliance on grafting. Both, EVPOME and AlloDerm grafts, showed a 100% take rate. At 6 days post-grafting, the EVPOME clinically showed changes indicating vascular ingrowth and had cytologic evidence of the persistence of grafted cultured keratinocytes on the surface. The EVPOME grafts had enhanced maturation of the underlying submucosal layer associated with rapid epithelial coverage when compared to the AlloDerm grafts at biopsies taken at 28 days post-grafting. In summary, EVPOME appears to be an acceptable oral mucosal substitute for human intraoral grafting procedures and results in a more favorable wound healing response than AlloDerm alone.

Catalog of 258 single-nucleotide polymorphisms (SNPs) in genes encoding three organic anion transporters, three organic anion-transporting polypeptides, and three NADH:ubiquinone oxidoreductase flavoproteins

We present here a series of high-density maps of single-nucleotide polymorphisms (SNPs) detected in genes encoding three organic-anion transporters, three organic anion-transporting polypeptides, and three nicotinamide adenine dinucleotide, reduced:ubiquinone oxidoreductase flavoproteins. A total of 258 SNPs were identified among these nine genes through systematic screening of DNA from 48 Japanese individuals: 17 in 5' flanking regions, three in 5' untranslated regions, 13 in coding regions, 211 in introns, six in 3' untranslated regions, and 8 in 3' flanking regions. By comparing our data with SNPs deposited in the dbSNP database in the National Center for Biotechnology Information, we determined that 236 (91.5%) were novel. In addition, 46 genetic variations of other types were discovered within these loci. These high-resolution maps will serve as a useful resource for analyzing potential associations between variations in these nine genes and differences in human susceptibilities to common diseases or response to drug therapies.

High-density single-nucleotide polymorphism (SNP) map in the 96-kb region containing the entire human DiGeorge syndrome critical region 2 (DGCR2) gene at 22q11.2

We constructed a high-density single-nucleotide polymorphism (SNP) map in the 96-kb region containing the DiGeorge syndrome critical region 2 (DGCR2) gene at chromosome 22q11.2, a human counterpart of mouse seizure-related gene SEZ-12. A total of 102 SNPs were isolated from the region by systematic screening among 48 Japanese individuals: 9 SNPs in the 5' flanking region, 3 in the 5' untranslated region, 2 in the coding regions, 77 in introns, 7 in the 3' untranslated region, and 4 in the 3' flanking region. By a comparison of our data with SNPs deposited in the dbSNP database in the National Center for Biotechnology Information, 80 SNPs (78.4%) were considered to be novel. The ratio of transition to transversion was 3.08:1. In addition, eight other types of genetic variations (one GA dinucleotide polymorphism and seven insertion/deletion polymorphisms) were discovered. The high-resolution map that we constructed will be a useful resource for analyzing gene scans of complex diseases mapped to this local segment on chromosome 22.

Identification of 197 genetic variations in six human methyltranferase genes in the Japanese population

Methylation is an important event in the biotransformation pathway for many drugs and xenobiotic compounds. We screened DNA from 48 Japanese individuals for single-nucleotide polymorphisms (SNPs) in six methyltransferase (MT) genes (catechol-O-MT, COMT; guanidinoacetate N-MT, GAMT; histamine N-MT, HNMT; nicotinamide N-MT, NNMT; phosphatidylethanolamine N-MT, PEMT; and phenylethanolamine N-MT, PNMT) by direct sequencing of their entire genomic regions except for repetitive elements. This approach identified 190 SNPs and seven insertion/deletion polymorphisms among the six genes. Of the 190 SNPs, 33 were identified in the COMT gene, 6 in GAMT, 41 in HNMT, 8 in NNMT, 98 in PEMT, and 4 in PNMT. Nine were located in 5' flanking regions, 156 in introns, 10 in exons, and 15 in 3' flanking regions. These variants may contribute to a more precise understanding of possible correlations between genotypes and disease-susceptibility phenotypes or risk for side effects from drugs.

Catalog of 46 single-nucleotide polymorphisms (SNPs) in the microsomal glutathione S-transferase 1 (MGST1) gene

A major goal in our laboratory is to understand the role of common genetic variations among individual patients as regards susceptibility to common diseases and differences in therapeutic efficacy and/or side effects of drugs. As an addition to the high-density SNP (single-nucleotide polymorphism) maps of 12 glutathione S-transferase and related genes reported earlier, we provide here an SNP map of the microsomal glutathione S-transferase 1 (MGST1) gene. Among 48 healthy Japanese volunteers examined. we identified a total of 46 SNPs at this locus, 36 of which had not been reported before: 4 in the promoter region, 34 in introns, 3 in the 3' untranslated region, and 5 in the 3' flanking region. No SNP was found in 5'untranslated or coding regions. The ratio of transition to transversion was approximately 1.2:1. Among the 13 insertion-deletion polymorphisms was a 2-bp deletion in the coding region of MGST1 in DNA from one of the volunteers, which resulted in a frame-shift mutation. Since the gene product encoded by this mutant allele would lack the C-terminal half including the MAPEG (membrane-associated proteins in eicosanoid and glutathione metabolism) domain, MGST1 activity is likely to be reduced in the carrier's cells. The SNP map presented here adds to the archive of tools for studying complex genetic diseases, population migration patterns, and a variety of pharmacogenetic possibilities.

High-density single-nucleotide polymorphism (SNP) map of the 150-kb region corresponding to the human ATP-binding cassette transporter A1 (ABCA1) gene

Highly dense catalogs of human genetic variations, in combination with high-throughput genotyping technologies, are expected to clarify individual genetic differences in pharmacological responsiveness and predispositions to common diseases. Here we report single-nucleotide polymorphisms (SNPs) present among 48 Japanese individuals at the locus for the human ATP-binding cassette transporter A1 (ABCA1) gene. ABCA1 plays a key role in apolipoprotein-mediated cholesterol transport, and mutations in this gene are responsible for Tangier disease and familial high-density lipoprotein deficiency associated with reduced cholesterol efflux. We identified a total of 162 SNPs, 149 of which were novel, within the 150-kb region encompassing the entire ABCA1 gene. Eight of the SNPs lie within coding elements, two in 5' flanking regions, 147 in introns, and five in 3' untranslated regions, but none were found in 5' untranslated or 3' flanking regions. The ratio of transitions to transversions was approximately 2.37 to 1. Our dense SNP map of this region could serve as a powerful resource for studies of complex genetic diseases that may be associated with ABCA1 and of individual responses to drug therapy.

Catalog of 434 single-nucleotide polymorphisms (SNPs) in genes of the alcohol dehydrogenase, glutathione S-transferase, and nicotinamide adenine dinucleotide, reduced (NADH) ubiquinone oxidoreductase families

An approach based on development of a large archive of single-nucleotide polymorphisms (SNPs) throughout the human genome is expected to facilitate large-scale studies to identify genes associated with drug efficacy and side effects, or susceptibility to common diseases. We have already described collections of SNPs present among various genes encoding drug-metabolizing enzymes. Here we report SNPs for such enzymes at additional loci, including 8 alcohol dehydrogenases, 12 glutathione S-transferases, and 18 belonging to the NADH-ubiquinone oxidoreductase family. Among DNA samples from 48 Japanese volunteers, we identified a total of 434 SNPs at these 38 loci: 27 within coding elements, 52 in 5' flanking regions, five in 5' untranslated regions, 293 in introns, 20 in 3' untranslated regions, and 37 in 3' flanking regions. The ratio of transitions to transversions was approximately 2.1 to 1. Among the 27 coding SNPs, 13 were nonsynonymous changes that resulted in amino acid substitutions. Our collection of SNPs derived from this study should prove useful for investigations designed to detect associations between genetic variations and common diseases or responsiveness to drug therapy.

Screening of triterpenoids isolated from Phyllanthus flexuosus for DNA topoisomerase inhibitory activity

DNA topoisomerases (Topos) are enzymes that play a crucial role in DNA metabolism events such as replication, transcription, recombination, and chromosome segregation at mitosis. Thus, Topo inhibitors could be expected to have antitumor effects. Naturally occurring lupane- and oleanane-type triterpenoids isolated from the bark of Phyllanthus flexuosus were screened for human Topos I and II inhibitory activities. Olean-12-en-3 beta,15 alpha-diol (1), olean-12-en-3 beta,15 alpha,24-triol (3), lupeol (4), and betulin (6) were found to be selective catalytic inhibitors of human Topo II activity with IC(50) values in the range of 10-39 microM.