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Uchiyama T, Fujino K, Ogawa T, Wakatsuki A, Kishima Y, Mikami T, Sano Y. Stable transcription activities dependent on an orientation of Tam3 transposon insertions into Antirrhinum and yeast promoters occur only within chromatin. PLANT PHYSIOLOGY 2009; 151:1557-69. [PMID: 19759347 PMCID: PMC2773084 DOI: 10.1104/pp.109.142356] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Accepted: 09/09/2009] [Indexed: 05/28/2023]
Abstract
Transposon insertions occasionally occur in the promoter regions of plant genes, many of which are still capable of being transcribed. However, it remains unclear how transcription of such promoters is able to occur. Insertion of the Tam3 transposon into various genes of Antirrhinum majus can confer leaky phenotypes without its excision. These genes, named Tam3-permissible alleles, often contain Tam3 in their promoter regions. Two alleles at different anthocyanin biosynthesis loci, nivea(recurrensTam3) (niv(rec)) and pallida(recurrensTam3) (pal(rec)), both contain Tam3 at a similar position immediately upstream of the promoter TATA-box; however, these insertions had different phenotypic consequences. Under conditions where the inserted Tam3 is immobilized, the niv(rec) line produces pale red petals, whereas the pal(rec) line produces no pigment. These pigmentation patterns are correlated with the level of transcripts from the niv(rec) or pal(rec) alleles, and these transcriptional activities are independent of DNA methylation in their promoter regions. In niv(rec), Tam3 is inserted in an orientation that results in the 3' end of Tam3 adjacent to the 5' region of the gene coding sequence. In contrast, the pal(rec) allele contains a Tam3 insertion in the opposite orientation. Four of five different nonrelated genes that are also Tam3-permissible alleles and contain Tam3 within the promoter region share the same Tam3 orientation as niv(rec). The different transcriptional activities dependent on Tam3 orientation in the Antirrhinum promoters were consistent with expression of luciferase reporter constructs introduced into yeast chromosomes but not with transient expression of these constructs in Antirrhinum cells. These results suggest that for Tam3 to sustain stable transcriptional activity in various promoters it must be embedded in chromatin.
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Uchiyama T, Saito Y, Kuwabara H, Fujino K, Kishima Y, Martin C, Sano Y. Multiple regulatory mechanisms influence the activity of the transposon, Tam3, of Antirrhinum. THE NEW PHYTOLOGIST 2008; 179:343-355. [PMID: 19086175 DOI: 10.1111/j.1469-8137.2008.02477.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
In Antirrhinum, several unique regulations of the transposon, Tam3, have been described. Tam3 activity in Antirrhinum is strictly controlled by the growing temperature of plants (low-temperature-dependent transposition: LTDT), by chromosomal position of Tam3 copy and by two specific repressor genes Stabiliser (St) and New Stabiliser (NSt). Here, the effects of the St and NSt loci on Tam3 transposition are compared. In cotyledons and hypocotyls, Tam3 is active even at high growing temperatures, indicating that LTDT does not operate when these organs are developing. This developmental regulation of Tam3 activity is differentially influenced by the St and NSt loci: St permits Tam3 transposition in cotyledons and hypocotyls, whereas NSt suppresses it in these organs. The effects of these host genes on Tam3 activity at the molecular level were examined. It was found that neither of these genes inhibits the transcription of the Tam3 transposase gene nor its translation, and that the Tam3 transposase has the potential to catalyze transposition in the St and NSt lines. The differences between the effects of St and NSt imply that they regulate Tam3 activity independently. Our molecular data indicate that their influence on Tam3 transposition seems to be nonepigenetic; possible mechanisms for their activity are discussed.
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Takata M, Kiyohara A, Takasu A, Kishima Y, Ohtsubo H, Sano Y. Rice transposable elements are characterized by various methylation environments in the genome. BMC Genomics 2007; 8:469. [PMID: 18093338 PMCID: PMC2222647 DOI: 10.1186/1471-2164-8-469] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2007] [Accepted: 12/20/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recent studies using high-throughput methods have revealed that transposable elements (TEs) are a comprehensive target for DNA methylation. However, the relationship between TEs and their genomic environment regarding methylation still remains unclear. The rice genome contains representatives of all known TE families with different characteristics of chromosomal distribution, structure, transposition, size, and copy number. Here we studied the DNA methylation state around 12 TEs in nine genomic DNAs from cultivated rice strains and their closely related wild strains. RESULTS We employed a transposon display (TD) method to analyze the methylation environments in the genomes. The 12 TE families, consisting of four class I elements, seven class II elements, and one element of a different class, were differentially distributed in the rice chromosomes: some elements were concentrated in the centromeric or pericentromeric regions, but others were located in euchromatic regions. The TD analyses revealed that the TE families were embedded in flanking sequences with different methylation degrees. Each TE had flanking sequences with similar degrees of methylation among the nine rice strains. The class I elements tended to be present in highly methylated regions, while those of the class II elements showed widely varying degrees of methylation. In some TE families, the degrees of methylation were markedly lower than the average methylation state of the genome. In two families, dramatic changes of the methylation state occurred depending on the distance from the TE. CONCLUSION Our results demonstrate that the TE families in the rice genomes can be characterized by the methylation states of their surroundings. The copy number and degree of conservation of the TE family are not likely to be correlated with the degree of methylation. We discuss possible relationships between the methylation state of TEs and their surroundings. This is the first report demonstrating that TEs in the genome are associated with a particular methylation environment that is a feature of a given TE.
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Noro Y, Takano-Shimizu T, Syono K, Kishima Y, Sano Y. Genetic variations in rice in vitro cultures at the EPSPs-RPS20 region. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 114:705-11. [PMID: 17177062 DOI: 10.1007/s00122-006-0470-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2006] [Accepted: 11/17/2006] [Indexed: 05/13/2023]
Abstract
In vitro cultures of plant cells have often been utilized to generate genetic variations, which are designated somaclonal variations. Little is known about the major genetic alterations in the cultured cells and the nature of these genetic changes. Here, we examined different lines of rice Oc cells that have been cultured for more than 20 years on agar media or in liquid media. We surveyed 35 clones obtained from PCR amplification of the 3-kb EPSPs-RPS20 region. The sequence divergence among the Oc cells was even greater than that between Japonica and Indica rice cultivars. The divergent sequences appeared to be maintained as multiple copies in a single cell. Surprisingly, the nucleotide substitutions in the Oc cells were characterized by an extremely high frequency of transition mutations of A/T-to-G/C, a feature which is similar to that of the mutations caused by chemical mutagens such as 5-bromouracil and 2-aminopurine. Although no replacements in the exons of this region were observed among the AA-genome Oryza species, our results revealed that the nucleotide substitutions of the cultured cell lines occurred more frequently at replacement sites in the exons than at synonymous sites. These distinct mutation biases found in rice in vitro cultures might contribute importantly to somaclonal variations.
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Hashida SN, Uchiyama T, Martin C, Kishima Y, Sano Y, Mikami T. The temperature-dependent change in methylation of the Antirrhinum transposon Tam3 is controlled by the activity of its transposase. THE PLANT CELL 2006; 18:104-18. [PMID: 16326924 PMCID: PMC1323487 DOI: 10.1105/tpc.105.037655] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The Antirrhinum majus transposon Tam3 undergoes low temperature-dependent transposition (LTDT). Growth at 15 degrees C permits transposition, whereas growth at 25 degrees C strongly suppresses it. The degree of Tam3 DNA methylation is altered somatically and positively correlated with growth temperature, an exceptional epigenetic system in plants. Using a Tam3-inactive line, we show that methylation change depends on Tam3 activity. Random binding site selection analysis and electrophoretic mobility shift assays revealed that the Tam3 transposase (TPase) binds to the major repeat in the subterminal regions of Tam3, the site showing the biggest temperature-dependent change in methylation state. Methylcytosines in the motif impair the binding ability of the TPase. Proteins in a nuclear extract from plants grown at 15 degrees C but not 25 degrees C bind to this motif in Tam3. The decrease in Tam3 DNA methylation at low temperature also requires cell division. Thus, TPase binding to Tam3 occurs only during growth at low temperature and immediately after DNA replication, resulting in a Tam3-specific decrease in methylation of transposon DNA. Consequently, the Tam3 methylation level in LTDT is regulated by Tam3 activity, which is dependent on the ability of its TPase to bind DNA and affected by growth temperature. Thus, the methylation/demethylation of Tam3 is the consequence, not the cause, of LTDT.
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Hashida SN, Kishima Y, Mikami T. DNA methylation is not necessary for the inactivation of the Tam3 transposon at non-permissive temperature in Antirrhinum. JOURNAL OF PLANT PHYSIOLOGY 2005; 162:1292-6. [PMID: 16323282 DOI: 10.1016/j.jplph.2005.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
It has been proposed that DNA methylation plays an important role in the inactivation of transposons. This view stems from a comparison of the degree of methylation of transposons in the active and inactive state. However, direct evidence for the degree of methylation required for the suppression of transposition has not been reported. Transposon Tam3 in Antirrhinum majus undergoes somatic reversal of its transposition activity, which is tightly controlled by temperature: low temperature around 15 degrees C permits transposition, high temperatures around 25 degrees C strongly inhibits it. Our previous study had shown that the methylation state of the Tam3 end regions is negatively correlated with the Tam3 transposition frequency. The results of the present study reveal that the inactive state of Tam3 copies at high temperature is unlikely to be directly coupled to the methylation state. Treatment with methylation inhibitors (5-azacytidine or 5-azacytidine+ethionine) does not affect Tam3 excision frequency in calli derived from Antirrhinum hypocotyls. The results suggest that methylation is not essential for the suppression of Tam3 transposition at high temperature, but rather that some other mechanism(s) involved in the control of Tam3 transposition may be obscured by methylation.
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Kobayashi S, Noro Y, Nagano H, Yoshida KT, Takano-Shimizu T, Kishima Y, Sano Y. Evidence for an evolutionary force that prevents epigenetic silencing between tail-to-tail rice genes with a short spacer. Gene 2005; 346:231-40. [PMID: 15716045 DOI: 10.1016/j.gene.2004.11.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2004] [Revised: 10/22/2004] [Accepted: 11/17/2004] [Indexed: 10/25/2022]
Abstract
During the course of evolution, the genome should have toned down various types of genomic noise, such as those that cause the unstable expression or gene silencing observed in transgenic organisms. We found a rice genomic segment where two genes, encoding 5-enolpyruvylshikimate-3-phosphate synthase (EPSPs) and ribosomal protein small subunit 20 (rps20), are located in a tail-to-tail orientation and separated by only 300 bp of spacer. It is possible that this kind of structure would give rise to unstable expression due to antisense RNA derived from the neighboring gene. We examined this possibility using Northern blot, reverse transcription-polymerase chain reaction (RT-PCR), and 3' RACE analyses, but obtained no evidence for instability or antisense RNAs of these housekeeping genes. Comparison of the sequences in the corresponding regions among related rice species revealed a lower level of genetic divergence of both the 3'-untranslated region (3'-UTRs) than of the other noncoding regions; in particular both of the boundaries between the 3'-UTRs and the spacer were markedly conserved. The conservation of both the terminal regions is most likely the result of purifying selection, implying a functional role for the strict termination of the transcription of these genes to prevent gene-silencing-related events.
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Hashida SN, Kitamura K, Mikami T, Kishima Y. Temperature shift coordinately changes the activity and the methylation state of transposon Tam3 in Antirrhinum majus. PLANT PHYSIOLOGY 2003; 132:1207-16. [PMID: 12857803 PMCID: PMC167061 DOI: 10.1104/pp.102.017533] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2002] [Revised: 01/20/2003] [Accepted: 03/06/2003] [Indexed: 05/21/2023]
Abstract
The transposition frequency of Tam3 in Antirrhinum majus, unlike that of most other cut-and-paste-type transposons, is tightly controlled by temperature: Tam3 transposes rarely at 25 degrees C, but much more frequently at 15 degrees C. Here, we studied the mechanism of the low-temperature-dependent transposition (LTDT) of Tam3. Our results strongly suggest that LTDT is not likely to be due to either transcriptional regulation or posttranscriptional regulation of the Tam3 TPase gene. We found that temperature shift induced a remarkable change of the methylation state unique to Tam3 sequences in the genome: Higher temperature resulted in hypermethylation, whereas lower temperature resulted in reduced methylation. The methylation state was reversible within a single generation in response to a temperature shift. Although our data demonstrate a close link between LTDT and the methylation of Tam3, they also suggest that secondary factor(s) other than DNA methylation is involved in repression of Tam3 transposition.
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Nagano H, Kunii M, Azuma T, Kishima Y, Sano Y. Characterization of the repetitive sequences in a 200-kb region around the rice waxy locus: diversity of transposable elements and presence of veiled repetitive sequences. Genes Genet Syst 2002; 77:69-79. [PMID: 12087189 DOI: 10.1266/ggs.77.69] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Repetitive genomic sequences might have various structural features and properties distinct from those of the known transposable elements (TE). Here, the content and properties of the repetitive sequences present in a 200-kb region around the rice waxy locus were analyzed using the available rice genomic database. In our previous Southern blotting analysis, 70% of the segments in this region showed smeared patterns, but according to the present database analysis, the proportion of repetitive sequences in this region was only 15%. The repetitive segments in this 200-kb region comprised 75 repetitive sequences that we classified into 46 subfamilies: 21 subfamilies were known TEs or repetitive sequences and 25 subfamilies consisted of newly identified TEs or novel types of repetitive sequences. The region contains no long terminal repeat (LTR) retrotransposable elements, but miniature inverted repeat transposable elements (MITEs) constituted a major class among the elements identified. These MITEs showed remarkable structural divergence: 12 elements were found to be new members of known MITE superfamilies, while five elements had novel terminal structures, and did not belong to any known TE families. Interestingly, about 10% of the repetitive sequences, including virus-like sequences did not have any of the usual characteristics of TEs, suggesting that a certain proportion of repetitive sequences that might not share the transpositional mechanisms of known elements are dispersed in the compact rice genome.
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Kitamura K, Hashida SN, Mikami T, Kishima Y. Position effect of the excision frequency of the Antirrhinum transposon Tam3: implications for the degree of position-dependent methylation in the ends of the element. PLANT MOLECULAR BIOLOGY 2001; 47:475-490. [PMID: 11669573 DOI: 10.1023/a:1011892003996] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We identified eight independent Tam3 copies residing in the same Antirrhinum majus genome. All the copies showed excision at 15 degrees C, but not at 25 degrees C. Under conditions promoting excision, each copy appeared to transpose in the leaves and flower lobes with a nearly constant frequency, whereas individual transposition abilities varied widely: the most active copy had an excision frequency more than 100-fold greater than that of the least active one. Despite the different transposition abilities, the structures of the eight Tam3 copies were almost identical. These results made it clear that the transpositional ability of Tam3 is regulated by chromosomal position, but they do not imply position-dependent transposase activity. The position effect of the Tam3 transposition was found to be correlated to the methylation state of the copy's end regions: DNA methylation in the Tam3 end regions tended to suppress the excision activity, and the degree of methylation was dependent on the chromosomal position. Our results also provide evidence of de novo methylation provoked by transposition of the endogenous element. We propose a mechanism of transpositional regulation of plant transposons that responds to the degree of methylation as determined by chromosomal position.
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Nakamura H, Enomoto H, Kishima Y, Yoshida K, Kuroda T. [Hepatoma-derived growth factor (HDGF) and HDGF family]. NIHON RINSHO. JAPANESE JOURNAL OF CLINICAL MEDICINE 2001; 59 Suppl 6:834-8. [PMID: 11762067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
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Ogawa H, Kuroda T, Inada M, Yamamoto M, Enomoto H, Kishima Y, Yoshida K, Ito H, Ogawa H, Nakamura H. Intestinal Behçet's disease associated with myelodysplastic syndrome with chromosomal trisomy 8--a report of two cases and a review of the literature. HEPATO-GASTROENTEROLOGY 2001; 48:416-20. [PMID: 11379321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Two cases of intestinal Behçet's disease, which developed in the state of myelodysplastic syndrome with trisomy 8, are presented. Both cases are included in the incomplete type of Behçet's disease, with recurrent aphthous stomatitis, skin lesions, genital ulcers or vascular involvement and punched-out ulcers in the cecum, without ocular involvement. The chromosomal analyses revealed chromosomal abnormalities, including trisomy 8, in both cases. Chromosomal trisomy 8 was shown in all 6 cases with the intestinal Behçet's disease associated with myelodysplastic syndrome reported previously, including our patients. Their histories indicated that myelodysplastic syndrome might have started before the development of intestinal Beçet's disease. Theses findings suggested that chromosomal trisomy 8 might play an important role in the pathogenesis, at least in some groups, of intestinal Behçet's disease.
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Kambe H, Kishima Y, Kuroda T, Enomoto H, Ogawa H, Nakmaura H. Protein kinase C inhibitor, H-7 suppresses the growth activity of hepatoma-derived growth factor. HEPATO-GASTROENTEROLOGY 2000; 47:1645-8. [PMID: 11149024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
BACKGROUND/AIMS A well-differentiated hepatocellular carcinoma-derived cell line, HuH-7 proliferates autonomously in serum-free medium. Human hepatoma-derived growth factor, which was purified from the conditioned medium of HuH-7 cells, stimulates the growth of HuH-7 cells by an autocrine fashion, and fibroblasts and endothelial cells by a paracrine fashion. We investigated the role of protein kinase C in the proliferation of HuH-7 cells and the growth activity of hepatoma-derived growth factor. METHODOLOGY The effects of a selective protein kinase C inhibitor, H-7 on the proliferation of HuH-7 and 3T3 fibroblasts stimulated by hepatoma-derived growth factor were examined by DNA synthesis and cell growth assay. RESULTS H-7 suppressed the growth of HuH-7 cells. The ID50 of H-7 on the growth of HuH-7 cells was about 25 microM, and the growth of HuH-7 cells was almost completely inhibited by not less than 50 microM of H-7. H-7 inhibited the growth activity of hepatoma-derived growth factor for Swiss 3T3 fibroblasts. The ID50 of H-7 on the activity of hepatoma-derived growth factor for 3T3 fibroblasts was about 25 microM, too. HA1004, used as a negative control of H-7, failed to inhibit the growth of HuH-7 cells and the activity of hepatoma-derived growth factor. The growth of HuH-7 cells was stimulated significantly by about 40% by a protein kinase C activator, SC-9. H-7 did not suppress hepatoma-derived growth factor production in HuH-7 cells. CONCLUSIONS These findings suggest that protein kinase C plays an important role in the growth of HuH-7 hepatoma cells and may be participated as a pathway in signal transduction of hepatoma-derived growth factor.
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Ikegame K, Yamamoto M, Kishima Y, Enomoto H, Yoshida K, Suemura M, Kishimoto T, Nakamura H. A new member of a hepatoma-derived growth factor gene family can translocate to the nucleus. Biochem Biophys Res Commun 1999; 266:81-7. [PMID: 10581169 DOI: 10.1006/bbrc.1999.1733] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Hepatoma-derived growth factor (HDGF) and HDGF-related proteins (HRP) belong to a gene family with a well-conserved amino acid sequence at the N-terminus (the hath region). A new member of the HDGF family in humans and mice was identified and cloned; we call it HRP-3. The deduced amino acid sequence from HRP-3 cDNA contained 203 amino acids without a signal peptide for secretion. HRP-3 has its 97-amino-acid sequence at the N-terminus, which is highly conserved with the hath region of the HDGF family proteins. It also has a putative bipartite nuclear localizing signal (NLS) sequence in a similar location in its self-specific region of HDGF and HRP-1. Northern blot analysis shows that HRP-3 is expressed predominantly in the testis and brain, to an intermediate extent in the heart, and to a slight extent in the ovaries, kidneys, spleen, and liver in humans. Transfection of green fluorescent protein (GFP)-tagged HRP-3 cDNA showed that HRP-3 translocated to the nucleus of 293 cells. GFP-HRP-3 transfectants significantly increased their DNA synthesis more than cells transfected with vector only. The HRP-3 gene was mapped to chromosome 15, region q25 by FISH analysis. These findings suggest that a new member of the HDGF gene family, HRP-3, may function mainly in the nucleus of the brain, testis, and heart, probably for cell proliferation.
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Nagano H, Wu L, Kawasaki S, Kishima Y, Sano Y. Genomic organization of the 260 kb surrounding the waxy locus in a Japonica rice. Genome 1999; 42:1121-6. [PMID: 10659779 DOI: 10.1139/g99-068] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The present study was carried out to characterize the molecular organization in the vicinity of the waxy locus in rice. To determine the structural organization of the region surrounding waxy, contiguous clones covering a total of 260 kb were constructed using a bacterial artificial chromosome (BAC) library from the Shimokita variety of Japonica rice. This map also contains 200 overlapping subclones, which allowed construction of a fine physical map with a total of 64 HindIII sites. During the course of constructing the map, we noticed the presence of some repeated regions which might be related to transposable elements. We divided the 260-kb region into 60 segments (average size of 5.7 kb) to use as probes to determine their genomic organization. Hybridization patterns obtained by probing with these segments were classified into four types: class 1, a single or a few bands without a smeared background; class 2, a single or a few bands with a smeared background; class 3, multiple discrete bands without a smeared background; and class 4, only a smeared background. These classes constituted 6.5%, 20.9%, 3.7%, and 68.9% of the 260-kb region, respectively. The distribution of each class revealed that repetitive sequences are a major component in this region, as expected, and that unique sequence regions were mostly no longer than 6 kb due to interruption by repetitive sequences. We discuss how the map constructed here might be a powerful tool for characterization and comparison of the genome structures and the genes around the waxy locus in the Oryza species.
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Yamashita S, Takano-Shimizu T, Kitamura K, Mikami T, Kishima Y. Resistance to gap repair of the transposon Tam3 in Antirrhinum majus: a role of the end regions. Genetics 1999; 153:1899-908. [PMID: 10581294 PMCID: PMC1460842 DOI: 10.1093/genetics/153.4.1899] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The extremely homogeneous organization of the transposon family Tam3 in Antirrhinum majus is in sharp contrast to the heterogeneity of the copies constituting many other transposon families. To address the issue of the Tam3 structural uniformity, we examined two possibilities: (1) recent invasion of Tam3 and (2) failure of gap repair, which is involved in conversion from autonomous forms to defective forms. The phylogenetic analysis of 17 Tam3 copies suggested that the invasion of Tam3 into the Antirrhinum genome occurred at least 5 mya, which is sufficiently long ago to have produced many aberrant copies by gap repair. Thus, we investigated gap repair events at the nivea(recurrens:Tam3) (niv(rec)::Tam3) allele, where Tam3 is actively excised. We show here that the gap repair of de novo somatic Tam3 excision was arrested immediately after initiation of the process. All of the identified gap repair products were short stretches, no longer than 150 bp from the ends. The Tam3 ends have hairpin structures with low free energies. We observed that the gap repair halted within the hairpin structure regions. Such small gap repair products appear to be distributed in the Antirrhinum genome, but are unlikely to be active. Our data strongly suggest that the structural homogeneity of Tam3 was caused by immunity to gap repair at the hairpins in both of the end regions. The frequency of extensive gap repair of de novo excision products in eukaryotic transposons was found to be correlated with the free energies of the secondary structures in the end regions. This fact suggests that the fates of transposon families might depend on the structures of their ends.
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Kishima Y, Yamashita S, Martin C, Mikami T. Structural conservation of the transposon Tam3 family in Antirrhinum majus and estimation of the number of copies able to transpose. PLANT MOLECULAR BIOLOGY 1999; 39:299-308. [PMID: 10080696 DOI: 10.1023/a:1006129413306] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We have investigated the organization of the transposon Tam3 family in Antirrhinum majus. Genomic hybridization experiments and characterization of 40 independent Tam3 clones isolated from an A. majus plant revealed that the Tam3 family is quite conserved and the copy sizes are uniform. We did not find any copy with a deleted internal sequence, unlike what is usually observed in other transposons. This exceptionally conserved structure of the Tam3 family was confirmed by PCR and sequencing analyses. Sequencing analysis identified eight copies with sequences completely identical to that of the Tam3 transposase gene. These results suggested that a considerable number of autonomous Tam3 copies are present in the genome of A. majus. Among 24 copies which are surrounded by single copy regions of the genome, 14 copies are present as specific insertions in the line which we used, but absent in other lines. These copies are therefore predicted to be movable. If this ratio is the same for all Tam3 copies in a genome, then a maximum of 60% of the copies are estimated to be movable in the genome. The relatively high frequency of gene tagged by Tam3 might reflect the large number of movable copies in the genome.
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Nagano H, Wu L, Kawasaki S, Kishima Y, Sano Y. Genomic organization of the 260 kb surrounding the waxy locus in a Japonica rice. Genome 1999. [DOI: 10.1139/gen-42-6-1121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Yamashita S, Mikami T, Kishima Y. Tam3 in Antirrhinum majus is exceptional transposon in resistant to alteration by abortive gap repair: identification of nested transposons. MOLECULAR & GENERAL GENETICS : MGG 1998; 259:468-74. [PMID: 9790577 DOI: 10.1007/s004380050837] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Most transposon families consist of heterogeneous copies with varying sizes. In contrast, the Tam3 copies in Antirrhinum majus are known to have exceptionally conserved structures of uniform size. Gap repair has been reported to be involved in the structural alteration of copies from several transposon families. In this study, we have asked whether or not gap repair has affected Tam3 copies. Five Tam3 copies carrying aberrant sequences were selected from 40 independent Tam3 clones and their sequences were analyzed. Two of the five copies contain insertions in the Tam3 sequence. These two insertions, designated Tam356 and Tam661, are typical transposon-like sequences, which have terminal inverted repeats and cause target site duplication. These nested transposons were obviously associated with transpositional events, and did not originate from the gap-repair process. The remaining three copies had lost large parts of the Tam3 sequence. We could not find any relationship between the deletions of Tam3 sequence in the three copies and gap repair. PCR analysis of a Tam3 excision site in the nivea(recurrence:Tam3) mutant also showed that most of the repair events after the Tam3 excision involved end-joining. In addition to the results obtained here, among the other clones isolated, we could not find any of the internally deleted copies that comprise a major part of other transposon families. All of these data suggest that some feature of the Tam3 structure suppresses the structural alterations that are otherwise generated during the gap repair process.
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Aii J, Kishima Y, Mikami T, Adachi T. Expansion of the IR in the chloroplast genomes of buckwheat species is due to incorporation of an SSC sequence that could be mediated by an inversion. Curr Genet 1997; 31:276-9. [PMID: 9065392 DOI: 10.1007/s002940050206] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The chloroplast genomes in buckwheat species contain large inverted repeats which are at least 4 kbp longer than the majority of those in land plants. The length of the buckwheat inverted repeats was attributable to an additional region located adjacent to the borders of the small single-copy region. We have cloned and sequenced a 5. 2-kbp SmaI fragment corresponding to this extra region in the inverted repeats. A homology search revealed that the sequence of the SmaI fragment is highly homologous to one side of the small single-copy region of the inverted repeats in dicot chloroplast DNAs such as tobacco and beechdrops. Interestingly, a 3.7-kbp segment in the middle of the SmaI fragment is inserted in the opposite orientation relative to those of the other dicot species, and 17-bp direct repeats are found located at both the ends of the additional region. These results suggest that expansion of the inverted repeats in buckwheat chloroplast DNA might have been associated with an inversion.
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Ohnishi N, Kishima Y, Hashimoto K, Kiwamoto H, Esa A, Sugiyama T, Park YC, Kurita T. [Morphometric study of low compliant bladder]. HINYOKIKA KIYO. ACTA UROLOGICA JAPONICA 1994; 40:657-61. [PMID: 7942361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Low compliant bladder is an important cause of detrusor dysfunction, although its cause is unknown. Two groups of patients who developed low compliant bladder have been studied by the morphometric technique. One group consisted of patients with neurogenic low compliant bladder, and the other group consisted of patients with non-neurogenic low compliant bladder. Control materials were obtained from postmortal samples offered from the department of anatomy. Bladder wall samples were obtained during bladder augmentation surgery. Morphometric computer analysis was used to measure the proportions of connective tissue and muscle layer in the bladder wall samples. In the non-neurogenic group, there was a significant increase in connective tissue and a marked decrease in muscle layer proportion than the control group. On the other hand, there was a mild increase in connective tissue, but no decrease in muscle layer proportion was observed in patients with neurogenic low compliant bladder. Comparison of the results obtained from the two groups suggested that low bladder compliance in neurogenic patients is mainly caused by functional alteration of the bladder wall, whereas that in non-neurogenic patients is caused by an organic change of the bladder wall.
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Ohnishi N, Kishima Y, Hashimoto K, Kiwamoto H, Esa A, Sugiyama T, Park YC, Kurita T. [A new method of measurement of the urinary bladder blood flow in patients with low compliant bladder]. HINYOKIKA KIYO. ACTA UROLOGICA JAPONICA 1994; 40:663-7. [PMID: 7942362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Laser-doppler blood flowmetry, a new instrument for measurement of tissue blood flow, was used to evaluate the changes occurring in the bladder blood flow and the intravesical pressure during bladder distension in 4 patients with normal detrusor function, 4 patients with neurogenic bladder dysfunction and one patient with non-neurogenic contracted bladder. In patients with normal detrusor function and normal compliance, the bladder blood flow relatively decreased, but the intravesical pressure was not affected by the bladder distension. On the other hand, the bladder distension in patients with low compliant bladder caused a significant decrease of the bladder blood flow and marked increase of the intravesical pressure. These observations suggest that the reduction of the bladder compliance is related to the decrease of the bladder blood flow. Furthermore, the bladder over distension and the high intravesical pressure in patients with low compliant bladder are thought to induce deterioration of bladder compliance and upper urinary tract.
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Shimada K, Hosokawa S, Sakaue K, Kishima Y. [Fetal genitourinary abnormalities associated with oligohydramnios]. Nihon Hinyokika Gakkai Zasshi 1994; 85:990-5. [PMID: 8065082 DOI: 10.5980/jpnjurol1989.85.990] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
After 16 weeks of gestation, amniotic fluid mainly consisted of fetal urine. Therefore, the association of oligohydramnios with fetal urinary tract abnormalities implies severe deterioration of renal function. The relationship of the kidney and amniotic fluid in pulmonary development has been investigated, and fetuses with oligohydramnios starting in the second trimester are considered to have uniformly fatal outcomes. We analysed underlying urological disorders, gestational age at presentation, and ultimate outcomes in 45 fetuses with severe oligohydramnios, and especially focused on clinical courses and prognosis of 7 surviving patients. Clinical and/or autopsy diagnosis included bilateral renal hypodysplasia in 20 patients, urethral atresia with/without prune belly deformity in 9, posterior urethral valve in 6, polycystic kidney disease in 4, hydrometrocolpos in 2, hereditary renal dysplasia in 2, and the others. The average gestational age at detection of severe oligohydramnios was about 30 weeks, ranging from 16 weeks in patient with urethral atresia. Urological disorders of 7 surviving patients consisted of 4 posterior urethral valves, one hydrometrocolpos, one hydronephrosis of the solitary kidney, and one bilateral megaureter. In these 7 patients severe oligohydramnios striated in the third trimester. Four patients required ventilator supports together with the administration of surfactant, but they were weaned in one to 4 days. There was no evidence of pulmonary hypoplasia on chest X-ray films. Urological emergency drainage was necessary in all patients on the day of delivery to 2 days postnatally. One patient with posterior urethral valve developed ESRF 6 months after birth. Two patients have a normal serum creatinine, but another 4 have slight elevation of SCr for their age.(ABSTRACT TRUNCATED AT 250 WORDS)
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Hashimoto K, Kishima Y, Onishi N, Esa A, Sugiyama T, Park Y, Kohri K, Akiyama T, Kurita T. [Transurethral teflon paste injection for vesicoureteral reflux in neurogenic bladder dysfunction]. Nihon Hinyokika Gakkai Zasshi 1993; 84:2118-23. [PMID: 8309118 DOI: 10.5980/jpnjurol1989.84.2118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We experienced transurethral teflon paste injection for 12 refluxing ureters of 7 patients with neurogenic bladder dysfunction. Preoperative assessment of cystometry showed hypoactive bladder function with normal bladder compliance in 4 patients, and low compliance bladder (< 10 ml/cmH2O) in 1. Voiding cystography revealed grade 1 reflux in 2 ureters, grade 2 in 3, grade 3 in 2, grade 4 in 2, and grade 5 in 2. One ureter did not show reflux. Zero point two to 1.6 ml of teflon paste was injected on each ureter under cystoscopic observation. These patients were followed for a mean of 25.1 months. Reflux disappeared immediately after the first operations in all patients, however recurrence was observed in 2 ureters, in which improvement of reflux (grade 5 to 2) was achieved in 1 ureter but no improvement (grade 2 to 2) in another. Pyelonephritis was not encountered in any patients after injection. No complication was observed through the follow up period. In conclusion, we advocate that endoscopic teflon paste injection is a useful alternative to ureteroneocystostomy in the treatment of reflux in patients with neurogenic bladder dysfunction.
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Nakanishi T, Tamura T, Miyazaki H, Osawa K, Fukuro Y, Kishima Y, Shoji T, Sasaoka T, Kubota S. [A case of hemodialysis-induced brain disease with intracranial calcinosis]. NIHON NAIKA GAKKAI ZASSHI. THE JOURNAL OF THE JAPANESE SOCIETY OF INTERNAL MEDICINE 1993; 82:280-2. [PMID: 8492033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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