Atsushi Toyoda

Summary

Affiliation: National Institute of Genetics
Country: Japan

Publications

  1. doi Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes
    Toshiaki Watanabe
    Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Research Organization of Information and Systems, Mishima 411 8540, Japan
    Nature 453:539-43. 2008
  2. pmc Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes
    Toshiaki Watanabe
    Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto 606 8502, Japan
    Genes Dev 20:1732-43. 2006
  3. pmc Role for piRNAs and noncoding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locus
    Toshiaki Watanabe
    Division of Human Genetics and Department of Integrated Genetics, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka, 411 8540, Japan
    Science 332:848-52. 2011
  4. pmc Mobilization of a plant transposon by expression of the transposon-encoded anti-silencing factor
    Yu Fu
    Department of Integrated Genetics, National Institute of Genetics, Shizuoka, Japan
    EMBO J 32:2407-17. 2013
  5. pmc MITOPLD is a mitochondrial protein essential for nuage formation and piRNA biogenesis in the mouse germline
    Toshiaki Watanabe
    Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka, 411 8540, Japan
    Dev Cell 20:364-75. 2011
  6. pmc Mutations in cell elongation genes mreB, mrdA and mrdB suppress the shape defect of RodZ-deficient cells
    Daisuke Shiomi
    Microbial Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411 8540, Japan
    Mol Microbiol 87:1029-44. 2013
  7. pmc The ancestor of extant Japanese fancy mice contributed to the mosaic genomes of classical inbred strains
    Toyoyuki Takada
    Mammalian Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411 8540, Japan
    Genome Res 23:1329-38. 2013
  8. pmc Centromere-targeted de novo integrations of an LTR retrotransposon of Arabidopsis lyrata
    Sayuri Tsukahara
    Department of Integrated Genetics, National Institute of Genetics, Shizuoka 411 8540, Japan
    Genes Dev 26:705-13. 2012
  9. pmc Mitochondrial and plastid genomes of the colonial green alga Gonium pectorale give insights into the origins of organelle DNA architecture within the volvocales
    Takashi Hamaji
    Department of Botany, Graduate School of Science, Kyoto University, Oiwake cho, Kita shirakawa, Sakyo ku, Kyoto, Japan
    PLoS ONE 8:e57177. 2013
  10. pmc Genome features of "Dark-fly", a Drosophila line reared long-term in a dark environment
    Minako Izutsu
    Laboratory for Biodiversity, Global COE Program, Graduate School of Science, Kyoto University, Kyoto, Japan
    PLoS ONE 7:e33288. 2012

Collaborators

Detail Information

Publications29

  1. doi Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes
    Toshiaki Watanabe
    Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Research Organization of Information and Systems, Mishima 411 8540, Japan
    Nature 453:539-43. 2008
    ..Our results reveal a role for endogenous siRNAs in mammalian oocytes and show that organisms lacking RdRP activity can produce functional endogenous siRNAs from naturally occurring dsRNAs...
  2. pmc Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes
    Toshiaki Watanabe
    Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto 606 8502, Japan
    Genes Dev 20:1732-43. 2006
    ..These features are reminiscent of Tetrahymena approximately 23- to 24-nt small RNAs and Caenorhabditis elegans X-cluster small RNAs. A conserved novel small RNA pathway may be present in diverse animals...
  3. pmc Role for piRNAs and noncoding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locus
    Toshiaki Watanabe
    Division of Human Genetics and Department of Integrated Genetics, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka, 411 8540, Japan
    Science 332:848-52. 2011
    ..A direct repeat in the DMR, which is required for the methylation and imprinting of Rasgrf1, served as a promoter for this RNA. We propose a model in which piRNAs and a target RNA direct the sequence-specific methylation of Rasgrf1...
  4. pmc Mobilization of a plant transposon by expression of the transposon-encoded anti-silencing factor
    Yu Fu
    Department of Integrated Genetics, National Institute of Genetics, Shizuoka, Japan
    EMBO J 32:2407-17. 2013
    ..Proteins related to this anti-silencing factor, which we named VANC, are widespread in the non-TIR MULEs and may have contributed to the recent success of these TEs in natural Arabidopsis populations. ..
  5. pmc MITOPLD is a mitochondrial protein essential for nuage formation and piRNA biogenesis in the mouse germline
    Toshiaki Watanabe
    Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka, 411 8540, Japan
    Dev Cell 20:364-75. 2011
    ..Our results indicate a conserved role for MITOPLD/Zuc in the piRNA pathway and link mitochondrial membrane metabolism/signaling to small RNA biogenesis...
  6. pmc Mutations in cell elongation genes mreB, mrdA and mrdB suppress the shape defect of RodZ-deficient cells
    Daisuke Shiomi
    Microbial Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411 8540, Japan
    Mol Microbiol 87:1029-44. 2013
    ..Thus, we found that mutations in domain IA of MreB and in the periplasmic domain of PBP2 and RodA can restore growth and rod shape to ΔrodZ cells, possibly by changing the requirements of MreB in the process...
  7. pmc The ancestor of extant Japanese fancy mice contributed to the mosaic genomes of classical inbred strains
    Toyoyuki Takada
    Mammalian Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411 8540, Japan
    Genome Res 23:1329-38. 2013
    ..m. molossinus genome in classical inbred strains and largely contributed to its intersubspecific genome diversity. ..
  8. pmc Centromere-targeted de novo integrations of an LTR retrotransposon of Arabidopsis lyrata
    Sayuri Tsukahara
    Department of Integrated Genetics, National Institute of Genetics, Shizuoka 411 8540, Japan
    Genes Dev 26:705-13. 2012
    ..lyrata and A. thaliana. Our results revealed unexpectedly dynamic controls for evolution of the transposon-rich heterochromatic regions...
  9. pmc Mitochondrial and plastid genomes of the colonial green alga Gonium pectorale give insights into the origins of organelle DNA architecture within the volvocales
    Takashi Hamaji
    Department of Botany, Graduate School of Science, Kyoto University, Oiwake cho, Kita shirakawa, Sakyo ku, Kyoto, Japan
    PLoS ONE 8:e57177. 2013
    ..Overall, the G. pectorale organelle genomes raise several interesting questions about the origin of linear mitochondrial chromosomes within the Volvocales and the relationship between multicellularity and organelle genome expansion...
  10. pmc Genome features of "Dark-fly", a Drosophila line reared long-term in a dark environment
    Minako Izutsu
    Laboratory for Biodiversity, Global COE Program, Graduate School of Science, Kyoto University, Kyoto, Japan
    PLoS ONE 7:e33288. 2012
    ..Our results revealed unique features of the Dark-fly genome and provided a list of potential candidate genes involved in environmental adaptation...
  11. doi Loss of PINK1 in medaka fish (Oryzias latipes) causes late-onset decrease in spontaneous movement
    Hideaki Matsui
    Department of Neurology, Kyoto University, Graduate School of Medicine, 54 Shogoin Kawahara cho, Sakyo ku, Kyoto 606 8507, Japan
    Neurosci Res 66:151-61. 2010
    ..Thus, PINK1 contributes to the maintenance of dopamine metabolism, even before the selective death of dopaminergic neurons. Our animal model is therefore a valuable tool to detect pathogenesis in Parkinson's patients in the early stages...
  12. ncbi A 210-kb segment of tandem repeats and retroelements located between imprinted subdomains of mouse distal chromosome 7
    Hisao Shirohzu
    Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima 411 8540, Japan
    DNA Res 11:325-34. 2004
    ..We propose that this repeat segment could serve either as a boundary between the two subdomains or as a target for epigenetic chromatin modifications that regulate imprinting...
  13. pmc DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MIWI2 in murine fetal testes
    Satomi Kuramochi-Miyagawa
    Department of Pathology, Medical School, Graduate School of Frontier Biosciences, Research Institute for Microbial Diseases, Osaka University, Yamada oka 2 2 Suita, Osaka 565 0871, Japan
    Genes Dev 22:908-17. 2008
    ..Our data strongly suggest that MILI and MIWI2 play essential roles in establishing de novo DNA methylation of retrotransposons in fetal male germ cells...
  14. pmc Characterization of expressed sequence tags from a full-length enriched cDNA library of Cryptomeria japonica male strobili
    Norihiro Futamura
    Department of Molecular and Cell Biology, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305 8687, Japan
    BMC Genomics 9:383. 2008
    ..japonica should help us to clarify the overall expression of genes during the process of pollen development, we constructed a full-length enriched cDNA library that was derived from male strobili at various developmental stages...
  15. pmc Complete genome of the uncultured Termite Group 1 bacteria in a single host protist cell
    Yuichi Hongoh
    Environmental Molecular Biology Laboratory, RIKEN, Saitama 351 0198, Japan
    Proc Natl Acad Sci U S A 105:5555-60. 2008
    ..Our results provide a breakthrough to clarify the functions of and the interactions among the individual members of this multilayered symbiotic complex...
  16. doi An N-ethyl-N-nitrosourea-induced mutation in N-acetyltransferase 1 in mice
    Robert P Erickson
    Department of Pediatrics, University of Arizona, 1501 N Campbell Avenue, P O Box 245073, Tucson, AZ 85724, USA
    Biochem Biophys Res Commun 370:285-8. 2008
    ..Analysis of hepatic Nat1 activity with the selective substrate isoniazid showed that there was a significant reduction in enzymatic activity in the homozygous mutants compared to the parental strain...
  17. pmc Sequencing analysis of 20,000 full-length cDNA clones from cassava reveals lineage specific expansions in gene families related to stress response
    Tetsuya Sakurai
    Metabolomics Research Group, RIKEN Plant Science Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, 230 0045, Japan
    BMC Plant Biol 7:66. 2007
    ..A full-length cDNA library of cassava plants under normal, heat, drought, aluminum and post harvest physiological deterioration conditions was built; 19968 clones were sequence-characterized using expressed sequence tags (ESTs)...
  18. ncbi Cloning, nucleotide sequence and expression of the gene encoding the cellulose-binding protein A (CBPA) of Eubacterium cellulosolvens 5
    Atsushi Toyoda
    School of Agriculture, Ibaraki University, Ami, 300 0393, Ibaraki, Japan
    FEMS Microbiol Lett 207:141-6. 2002
    ..The cloned gene was inserted into an expression vector, pBAD-TOPO, and expressed in Escherichia coli as a fused protein. The fused protein was detected by immunoblotting using antiserum against CBPA...
  19. ncbi Identification of two novel primate-specific genes in DSCR
    Kunihiko Takamatsu
    Laboratory of Functional Genomics Human Genome Center, Institute of Medical Science, University of Tokyo, Japan
    DNA Res 9:89-97. 2002
    ..These results strongly suggest that DSCR9 and DSCR10 have emerged as a new class of gene in the primate lineage during evolution...
  20. ncbi Genomic organization and promoter analysis of the Dnmt3b gene
    Chisaki Ishida
    Division of Gene Therapy Science, Osaka University School of Medicine, 2 2 Yamada oka, Suita, 565 0870, Osaka, Japan
    Gene 310:151-9. 2003
    ..9 kb upstream of Dnmt3b downregulated this gene specifically in somatic cells but not in ES cells. These findings provide a basis for future detailed studies of the mechanisms controlling Dnmt3b expression...
  21. pmc Contribution of Asian mouse subspecies Mus musculus molossinus to genomic constitution of strain C57BL/6J, as defined by BAC-end sequence-SNP analysis
    Kuniya Abe
    Technology and Development Team for Mammalian Cellular Dynamics, BioResource Center, RIKEN Tsukuba Institute, Tsukuba, Ibaraki 305 0074, Japan
    Genome Res 14:2439-47. 2004
    ..2% of the genome showed an extremely low SNP rate (percentage identity = 0.9997); these sequences are likely derived from the molossinus genome...
  22. ncbi PCR detection of bovine mitochondrial DNA derived from meat and bone meal in feed
    Atsushi Toyoda
    College of Agriculture, Ibaraki University, Ibaraki 300 0393, Japan
    J Food Prot 67:2829-32. 2004
    ..However, the exclusion of this treatment improved the detection limit of bovine MBM in feed. This method appears suitable for the selective detection of bovine MBM in feed...
  23. ncbi Molecular characterization of ENU mouse mutagenesis and archives
    Yoshiyuki Sakuraba
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama 230 0045, Japan
    Biochem Biophys Res Commun 336:609-16. 2005
    ..The base-substitution spectra in this study were different from those of the phenotype-based mutagenesis. The ENU-based gene-driven mutagenesis in the mouse now becomes feasible and practical...
  24. pmc Cloning, sequencing, and expression of a Eubacterium cellulosolvens 5 gene encoding an endoglucanase (Cel5A) with novel carbohydrate-binding modules, and properties of Cel5A
    Kazutoyo Yoda
    College of Agriculture, Ibaraki University, Ami, Ibaraki 300 0393, Japan
    Appl Environ Microbiol 71:5787-93. 2005
    ..Removal of the CBMs from rCel5A reduced the catalytic activities with various polysaccharides remarkably. These observations show that CBMs play an important role in the catalytic function of the enzyme...
  25. pmc A large-scale full-length cDNA analysis to explore the budding yeast transcriptome
    Fumihito Miura
    Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277 8561, Japan
    Proc Natl Acad Sci U S A 103:17846-51. 2006
    ..The budding yeast will serve as a versatile model for the studies on these aspects of transcriptome, and the full-length cDNA clones can function as an invaluable resource in such studies...
  26. ncbi An oligodendrocyte enhancer in a phylogenetically conserved intron region of the mammalian myelin gene Opalin
    Jun Aruga
    Laboratory for Comparative Neurogenesis, RIKEN Brain Science Institute, Wako Shi, Saitama, Japan
    J Neurochem 102:1533-47. 2007
    ..These results suggest that LIF, cAMP signaling cascades and Myt1 play significant roles in the differentiation of oligodendrocytes through their action on the Opalin oligodendrocyte enhancer...
  27. pmc Functional annotation of 19,841 Populus nigra full-length enriched cDNA clones
    Tokihiko Nanjo
    Department of Molecular and Cell Biology, Forestry and Forest Products Research Institute FFPRI, 1 Matsunosato, Tsukuba, Ibaraki 305 8687 JAPAN
    BMC Genomics 8:448. 2007
    ..ESTs from full-length cDNA clones are especially powerful for accurate molecular annotation. We promoted collection and annotation of the ESTs from Populus full-length enriched cDNA clones as part of functional genomics of tree species...
  28. ncbi The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants
    Stefan A Rensing
    Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, D 79104 Freiburg, Germany
    Science 319:64-9. 2008
    ..The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics...
  29. ncbi Construction and analysis of a human-chimpanzee comparative clone map
    Asao Fujiyama
    RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Science 295:131-4. 2002
    ..We detected candidate positions, including two clusters on human chromosome 21 that suggest large, nonrandom regions of difference between the two genomes...