Takashi Ito

Summary

Affiliation: University of Tokyo
Country: Japan

Publications

  1. ncbi request reprint [Trends in interactomics]
    Takashi Ito
    Tanpakushitsu Kakusan Koso 50:2263-8. 2005
  2. pmc Mass spectrometry-based approaches toward absolute quantitative proteomics
    Keiji Kito
    Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277 8561, Japan
    Curr Genomics 9:263-74. 2008
  3. pmc Highly efficient PCR assay to discriminate allelic DNA methylation status using whole genome amplification
    Yoichi Yamada
    School of Electrical and Computer Engineering, College of Science and Engineering, Kanazawa University, Kanazawa 920 1192, Japan
    BMC Res Notes 4:179. 2011
  4. doi request reprint Unexpected complexity of the budding yeast transcriptome
    Takashi Ito
    Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277 8561, Japan
    IUBMB Life 60:775-81. 2008
  5. pmc Absolute quantification of the budding yeast transcriptome by means of competitive PCR between genomic and complementary DNAs
    Fumihito Miura
    Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277 8561, Japan
    BMC Genomics 9:574. 2008
  6. doi request reprint A proteomic screen reveals the mitochondrial outer membrane protein Mdm34p as an essential target of the F-box protein Mdm30p
    Kazuhisa Ota
    Department of Computational Biology and Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277 8561, Japan
    Genes Cells 13:1075-85. 2008
  7. 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
  8. doi request reprint Discrimination between stable and dynamic components of protein complexes by means of quantitative proteomics
    Keiji Kito
    Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
    Proteomics 8:2366-70. 2008
  9. pmc Circular permutation of ligand-binding module improves dynamic range of genetically encoded FRET-based nanosensor
    Satoshi Okada
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 5 1 5 Kashiwanoha, Kashiwa 277 8561, Japan
    Protein Sci 18:2518-27. 2009
  10. doi request reprint Remodeling of the SCF complex-mediated ubiquitination system by compositional alteration of incorporated F-box proteins
    Mitsunori Kato
    Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
    Proteomics 10:115-23. 2010

Collaborators

Detail Information

Publications36

  1. ncbi request reprint [Trends in interactomics]
    Takashi Ito
    Tanpakushitsu Kakusan Koso 50:2263-8. 2005
  2. pmc Mass spectrometry-based approaches toward absolute quantitative proteomics
    Keiji Kito
    Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277 8561, Japan
    Curr Genomics 9:263-74. 2008
    ..Here we review these mass spectrometry-based approaches for absolute quantification of proteome and discuss their implications...
  3. pmc Highly efficient PCR assay to discriminate allelic DNA methylation status using whole genome amplification
    Yoichi Yamada
    School of Electrical and Computer Engineering, College of Science and Engineering, Kanazawa University, Kanazawa 920 1192, Japan
    BMC Res Notes 4:179. 2011
    ..abstract:..
  4. doi request reprint Unexpected complexity of the budding yeast transcriptome
    Takashi Ito
    Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277 8561, Japan
    IUBMB Life 60:775-81. 2008
    ..The budding yeast may serve as an excellent model to study pervasive transcription and noncoding RNAs...
  5. pmc Absolute quantification of the budding yeast transcriptome by means of competitive PCR between genomic and complementary DNAs
    Fumihito Miura
    Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277 8561, Japan
    BMC Genomics 9:574. 2008
    ..It would help not only to precisely grasp the structure of the transcriptome but also to accelerate data exchange and integration...
  6. doi request reprint A proteomic screen reveals the mitochondrial outer membrane protein Mdm34p as an essential target of the F-box protein Mdm30p
    Kazuhisa Ota
    Department of Computational Biology and Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277 8561, Japan
    Genes Cells 13:1075-85. 2008
    ..These results indicate that Mdm34p is a physiologically important target of Mdm30p...
  7. 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...
  8. doi request reprint Discrimination between stable and dynamic components of protein complexes by means of quantitative proteomics
    Keiji Kito
    Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
    Proteomics 8:2366-70. 2008
    ..We successfully applied this strategy to analyze two yeast protein complexes, eIF2B-eIF2 and cyclin-Cdc28...
  9. pmc Circular permutation of ligand-binding module improves dynamic range of genetically encoded FRET-based nanosensor
    Satoshi Okada
    Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 5 1 5 Kashiwanoha, Kashiwa 277 8561, Japan
    Protein Sci 18:2518-27. 2009
    ..Thus, the circular permutation strategy would not only improve the performance of each nanosensor but also expand the repertoire of metabolites that can be measured by the FLIP nanosensor technology...
  10. doi request reprint Remodeling of the SCF complex-mediated ubiquitination system by compositional alteration of incorporated F-box proteins
    Mitsunori Kato
    Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
    Proteomics 10:115-23. 2010
    ..Compositional alteration of incorporated F-box proteins may redirect the activity of this system toward appropriate substrates to be ubiquitinated under individual conditions for the maintenance of cellular homeostasis...
  11. doi request reprint A parallel affinity purification method for selective isolation of polyubiquitinated proteins
    Kazuhisa Ota
    Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
    Proteomics 8:3004-7. 2008
    ..Accordingly, it would serve as a powerful method to facilitate mass-spectrometric identification of ubiquitinated proteins...
  12. pmc A yeast one-hybrid system to screen for methylated DNA-binding proteins
    Shu Ying Feng
    Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
    Nucleic Acids Res 38:e189. 2010
    ..We applied the dual-bait system to screen cDNA libraries and demonstrated efficient isolation of clones for methylated DNA-binding proteins. This system would serve as a unique research tool for epigenetics...
  13. ncbi request reprint A synthetic protein approach toward accurate mass spectrometric quantification of component stoichiometry of multiprotein complexes
    Keiji Kito
    Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, 5 1 5 Kashiwanoha, Kashiwa 277 8561, Japan
    J Proteome Res 6:792-800. 2007
    ..The PCS strategy would provide a versatile method to quantitatively analyze compositional alteration of multiprotein complexes or dynamics of protein-protein interactions in response to various stimuli...
  14. ncbi request reprint A novel Cdc42-interacting domain of the yeast polarity establishment protein Bem1. Implications for modulation of mating pheromone signaling
    Yoshihiro Yamaguchi
    Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, 5 1 5 Kashiwanoha, Kashiwa 277 8561, Japan
    J Biol Chem 282:29-38. 2007
    ..Intriguingly, Cdc42 can mediate an indirect interaction of the SH3b-CI to the CRIB domain of Ste20. These results suggest that the SH3b and the CI collaborate in tethering of Ste20 to Bem1 to ensure efficient mating pheromone signaling...
  15. ncbi request reprint A novel strategy to design highly specific PCR primers based on the stability and uniqueness of 3'-end subsequences
    Fumihito Miura
    Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo Kashiwa, Japan
    Bioinformatics 21:4363-70. 2005
    ..Since the primers designed by conventional methods often fail to work in these applications, an improved strategy is required, particularly, for a large-scale analysis...
  16. ncbi request reprint Diverse DNA methylation statuses at alternative promoters of human genes in various tissues
    Jieun Cheong
    Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5 1 5 Kashiwanoha, Kashiwa, Chiba, Japan
    DNA Res 13:155-67. 2006
    ..DNA methylation appears to play a significant role in differential usage of alternative promoters and may be related to functional diversification between CpG-island-containing promoters and CpG-island-less promoters...
  17. doi request reprint Synthetic Gene Circuit-Mediated Monitoring of Endogenous Metabolites: Identification of GAL11 as a Novel Multicopy Enhancer of S-Adenosylmethionine Level in Yeast
    Taichi Umeyama
    Department of Biophysics and Biochemistry, Graduate School of Science, and Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    ACS Synth Biol 2:425-30. 2013
    ..These results demonstrate the potential and utility of synthetic gene circuit-mediated metabolite monitoring. ..
  18. ncbi request reprint An evolutionary scenario for genomic imprinting of Impact lying between nonimprinted neighbors
    Kohji Okamura
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    DNA Res 11:381-90. 2004
    ..This model assumes that segmental duplication followed by enhancement of the promoter activity in the lineage to mouse is responsible for the species-specific imprinting of Impact...
  19. ncbi request reprint Comparative genomics approach toward critical determinants for the imprinting of an evolutionarily conserved gene Impact
    Kohji Okamura
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Biochem Biophys Res Commun 329:824-30. 2005
    ..It thus seems that lineage-specific enhancement of gene expression rather than the tandem repeat per se played a critical role in the evolution of imprinting of Impact...
  20. ncbi request reprint [Exploring interaction networks of the yeast proteins]
    Takashi Ito
    Tanpakushitsu Kakusan Koso 47:898-905. 2002
  21. pmc Transcriptional activators in yeast
    Björn Titz
    Institut fur Genetik, Forschungszentrum Karlsruhe, Box 3640, D 76021 Karlsruhe, Germany
    Nucleic Acids Res 34:955-67. 2006
    ....
  22. pmc A comprehensive analysis of allelic methylation status of CpG islands on human chromosome 21q
    Yoichi Yamada
    Division of Genome Biology, Cancer Research Institute, Kanazawa University, Kanazawa 920 0934, Japan
    Genome Res 14:247-66. 2004
    ..Thus, the cell seems to have a broader repertoire of methylating CGIs than previously thought, and our approach may contribute to uncover novel modes of allelic methylation...
  23. ncbi request reprint A yeast one-hybrid system to detect methylation-dependent DNA-protein interactions
    Shu Ying Feng
    Division of Genome Biology, Cancer Research Institute, Kanazawa University, Kanazawa 920 0934, Japan
    Biochem Biophys Res Commun 313:922-5. 2004
    ..This methylation-dependent one-hybrid system would provide a versatile tool for the search and analysis of proteins that recognize methylated DNA to participate in epigenetic regulation...
  24. ncbi request reprint Rapamycin-induced translational derepression of GCN4 mRNA involves a novel mechanism for activation of the eIF2 alpha kinase GCN2
    Hiroyuki Kubota
    Division of Genome Biology, Cancer Research Institute, Kanazawa University, 13 1 Takaramachi, Kanazawa 920 0934, Japan
    J Biol Chem 278:20457-60. 2003
    ..However, in contrast with amino acid starvation, rapamycin activates GCN2 without increasing the amount of uncharged tRNAs, but presumably by modifying the tRNA binding affinity of GCN2...
  25. ncbi request reprint A functional single-nucleotide polymorphism in the human cytidine deaminase gene contributing to ara-C sensitivity
    Lijie Yue
    Division of Cardiovascular Medicine, Vascular Medicine, Angiogenesis and Vascular Development, Department of Pediatrics, Kanazawa University Graduate School of Medical Science, Ishikawa, Japan
    Pharmacogenetics 13:29-38. 2003
    ....
  26. ncbi request reprint Roles for the two-hybrid system in exploration of the yeast protein interactome
    Takashi Ito
    Division of Genome Biology, Cancer Research Institute, Kanazawa University, Kanazawa 920 0934, Japan
    Mol Cell Proteomics 1:561-6. 2002
    ....
  27. pmc Barrier proteins remodel and modify chromatin to restrict silenced domains
    Masaya Oki
    Unit on Chromatin and Transcription, National Institute of Child Health and Human Development, Bethesda, Maryland 20892, USA
    Mol Cell Biol 24:1956-67. 2004
    ..Our data suggest that multiple overlapping mechanisms were involved in delimiting silenced and active domains in vivo...
  28. ncbi request reprint Analysis of gene network regulating yeast multidrug resistance by artificial activation of transcription factors: involvement of Pdr3 in salt tolerance
    Miyuki Onda
    Division of Genome Biology, Cancer Research Institute, Kanazawa University, Kanazawa 920 0934, Japan
    Gene 332:51-9. 2004
    ..The strategy would thus contribute not only to identify target genes but to reveal redundancy and specificity in complex gene regulatory networks...
  29. ncbi request reprint Transcriptomic and proteomic analysis of a 14-3-3 gene-deficient yeast
    Tohru Ichimura
    Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji shi, Tokyo 192 0397, Japan
    Biochemistry 43:6149-58. 2004
    ..This study presents the first comprehensive overview of the genes and proteins that are affected by the depletion of Bmh1/2p and extends the scope of knowledge of the regulatory roles of Bmh1/2p in S. cerevisiae...
  30. ncbi request reprint Structure and function of the PB1 domain, a protein interaction module conserved in animals, fungi, amoebas, and plants
    Hideki Sumimoto
    Medical Institute of Bioregulation, Kyushu University, Maidashi, Higashi ku, Fukuoka, Japan
    Sci STKE 2007:re6. 2007
    ..This Review describes various aspects of PB1 domains at the molecular and cellular levels...
  31. ncbi request reprint Proteomic analysis of in vivo 14-3-3 interactions in the yeast Saccharomyces cerevisiae
    Kazue Kakiuchi
    Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo 192 0397, Japan
    Biochemistry 46:7781-92. 2007
    ....
  32. ncbi request reprint Molecular characterization of the PEX5 gene encoding peroxisomal targeting signal 1 receptor from the methylotrophic yeast Pichia methanolica
    Takashi Ito
    Department of Food Science and Technology, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri, Hokkaido 099 2493, Japan
    Yeast 24:589-97. 2007
    ..methanolica, including methanol metabolism, and in peroxisomal localization and activation of methanol-metabolizing enzymes, e.g. AOD isozymes, DHAS and CTA...
  33. ncbi request reprint Distribution, diversity and regulation of alcohol oxidase isozymes, and phylogenetic relationships of methylotrophic yeasts
    Takashi Ito
    Department of Food Science and Technology, Faculty of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido, Japan
    Yeast 24:523-32. 2007
    ....
  34. ncbi request reprint Peroxisomal metabolism is regulated by an oxygen-recognition system through organelle crosstalk between the mitochondria and peroxisomes
    Shuki Fujimura
    Department of Food Science and Technology, Faculty of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido, Japan
    Yeast 24:491-8. 2007
    ....
  35. ncbi request reprint The yeast eIF4E-associated protein Eap1p attenuates GCN4 translation upon TOR-inactivation
    Ryu Matsuo
    Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
    FEBS Lett 579:2433-8. 2005
    ....
  36. ncbi request reprint OPR, PC and AID: all in the PB1 family
    Chris P Ponting
    Trends Biochem Sci 27:10. 2002