Yoshikazu Nakamura

Summary

Affiliation: University of Tokyo
Country: Japan

Publications

  1. ncbi request reprint Making sense of mimic in translation termination
    Yoshikazu Nakamura
    Department of Basic Medical Sciences, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
    Trends Biochem Sci 28:99-105. 2003
  2. pmc NMR structures of double loops of an RNA aptamer against mammalian initiation factor 4A
    Taiichi Sakamoto
    Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 33:745-54. 2005
  3. pmc RNA plasticity and selectivity applicable to therapeutics and novel biosensor development
    Yoshikazu Nakamura
    Department of Basic Medical Sciences, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Genes Cells 17:344-64. 2012
  4. ncbi request reprint How protein reads the stop codon and terminates translation
    Y Nakamura
    Department of Tumor Biology, The Institute of Medical Science, The University of Tokyo, Japan
    Genes Cells 3:265-78. 1998
  5. ncbi request reprint A tripeptide discriminator for stop codon recognition
    Yoshikazu Nakamura
    Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, 108 8630, Tokyo, Japan
    FEBS Lett 514:30-3. 2002
  6. ncbi request reprint Molecular mimicry between protein and tRNA
    Y Nakamura
    Department of Basic Medical Sciences, The Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    J Mol Evol 53:282-9. 2001
  7. ncbi request reprint [The stream of RNA science]
    Yoshikazu Nakamura
    Tanpakushitsu Kakusan Koso 48:319-28. 2003
  8. ncbi request reprint [Translation termination factors and prions]
    Yoshikazu Nakamura
    Tanpakushitsu Kakusan Koso 51:2574-82. 2006
  9. ncbi request reprint Yeast [PSI+] "prions" that are crosstransmissible and susceptible beyond a species barrier through a quasi-prion state
    T Nakayashiki
    Department of Basic Medical Sciences and, Institute of Medical Science, University of Tokyo, 108 8639, Tokyo, Japan
    Mol Cell 7:1121-30. 2001
  10. ncbi request reprint [Life driven by RNA]
    Yoshikazu Nakamura
    Tanpakushitsu Kakusan Koso 51:2409-12. 2006

Collaborators

Detail Information

Publications154 found, 100 shown here

  1. ncbi request reprint Making sense of mimic in translation termination
    Yoshikazu Nakamura
    Department of Basic Medical Sciences, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
    Trends Biochem Sci 28:99-105. 2003
    ..All of this evidence seriously questions the simple concept of structural mimicry between proteins and RNA and, thus, leaves only functional mimicry of protein factors of translation to be investigated...
  2. pmc NMR structures of double loops of an RNA aptamer against mammalian initiation factor 4A
    Taiichi Sakamoto
    Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 33:745-54. 2005
    ..The Watson-Crick edges of C7 and C9 in the AUCGCA loop may directly interact with eIF4A...
  3. pmc RNA plasticity and selectivity applicable to therapeutics and novel biosensor development
    Yoshikazu Nakamura
    Department of Basic Medical Sciences, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Genes Cells 17:344-64. 2012
    ....
  4. ncbi request reprint How protein reads the stop codon and terminates translation
    Y Nakamura
    Department of Tumor Biology, The Institute of Medical Science, The University of Tokyo, Japan
    Genes Cells 3:265-78. 1998
    ....
  5. ncbi request reprint A tripeptide discriminator for stop codon recognition
    Yoshikazu Nakamura
    Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, 108 8630, Tokyo, Japan
    FEBS Lett 514:30-3. 2002
    ..Here we review the experimental background and process leading to this discovery, and strengthen functional evidence for the tripeptide determinant for deciphering stop codons in mRNAs in prokaryotes...
  6. ncbi request reprint Molecular mimicry between protein and tRNA
    Y Nakamura
    Department of Basic Medical Sciences, The Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    J Mol Evol 53:282-9. 2001
    ..Structural, functional, and evolutionary aspects of molecular mimicry will be discussed...
  7. ncbi request reprint [The stream of RNA science]
    Yoshikazu Nakamura
    Tanpakushitsu Kakusan Koso 48:319-28. 2003
  8. ncbi request reprint [Translation termination factors and prions]
    Yoshikazu Nakamura
    Tanpakushitsu Kakusan Koso 51:2574-82. 2006
  9. ncbi request reprint Yeast [PSI+] "prions" that are crosstransmissible and susceptible beyond a species barrier through a quasi-prion state
    T Nakayashiki
    Department of Basic Medical Sciences and, Institute of Medical Science, University of Tokyo, 108 8639, Tokyo, Japan
    Mol Cell 7:1121-30. 2001
    ..cerevisiae but in K. lactis. These two Sup35 proteins contain unique multiple imperfect oligopeptide repeats responsible for crosstransmission and high spontaneous propagation of novel [PSI(+)] elements...
  10. ncbi request reprint [Life driven by RNA]
    Yoshikazu Nakamura
    Tanpakushitsu Kakusan Koso 51:2409-12. 2006
  11. ncbi request reprint Isolation and characterization of a human cDNA clone (GCN5L1) homologous to GCN5, a yeast transcription activator
    M Inoue
    Laboratory of Molecular Medicine, University of Tokyo, Japan
    Cytogenet Cell Genet 73:134-6. 1996
    ..We isolated a genomic clone corresponding to this cDNA from a human cosmid library and mapped it to chromosome 12q13 --> q14 by fluorescent in situ hybridization (FISH)...
  12. ncbi request reprint Conformation preserved in a weak-to-strong or strong-to-weak [PSI+] conversion during transmission to Sup35 prion variants
    Colin G Crist
    Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Tokyo 108 8639, Japan
    Biochimie 88:485-96. 2006
    ..A mechanism of "conformational memory" to remember specific [PSI(+)] conformations during transmission is proposed...
  13. pmc RNA aptamers to mammalian initiation factor 4G inhibit cap-dependent translation by blocking the formation of initiation factor complexes
    Shin Miyakawa
    Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, Minato ku, Tokyo 108 8639, Japan
    RNA 12:1825-34. 2006
    ..Therefore, we speculate that these seven sets of aptamers may bind to different regions in eIF4G in different fashions...
  14. ncbi request reprint Molecular cloning, characterization, and chromosomal mapping of a novel human gene (GTF3A) that is highly homologous to Xenopus transcription factor IIIA
    H Arakawa
    Department of Biochemistry, Cancer Institute, Tokyo, Japan
    Cytogenet Cell Genet 70:235-8. 1995
    ..Northern analysis showed expression in various tissues examined. The human TFIIIA gene (GTF3A) was localized to chromosome band 13q12.3-->q13.1 by fluorescent in situ hybridization (FISH)...
  15. ncbi request reprint Structural organization, complete genomic sequences and mutational analyses of the Fukuyama-type congenital muscular dystrophy gene, fukutin
    K Kobayashi
    Laboratory of Genome Medicine, Human Genome Center, Institute of Medical Science, University of Tokyo, Japan
    FEBS Lett 489:192-6. 2001
    ..Analysis of expressed sequence tag clusters within the region revealed two novel genes upstream of the fukutin gene. These data provide fundamental information to support detailed genetic and functional analyses of the fukutin gene...
  16. pmc A regulatory role of the Rnq1 nonprion domain for prion propagation and polyglutamine aggregates
    Hiroshi Kurahashi
    Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Mol Cell Biol 28:3313-23. 2008
    ....
  17. ncbi request reprint Heterologous expression of Aquifex aeolicus ribosome recycling factor in Escherichia coli is dominant lethal by forming a complex that lacks functional co-ordination for ribosome disassembly
    Tohru Yamami
    Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Mol Microbiol 55:150-61. 2005
    ..coli. These aaRRF mutations are spatially distinct from mutations previously described and suggest a novel active centre for coupling EF-G's G domain motor action to ribosome disassembly...
  18. pmc Role of phospholipase C-L2, a novel phospholipase C-like protein that lacks lipase activity, in B-cell receptor signaling
    Kei Takenaka
    Department of Biochemistry, The Institute of Medical Science, University of Tokyo, Tokyo 108 8639, Japan
    Mol Cell Biol 23:7329-38. 2003
    ..These mice had a stronger T-cell-independent antigen response. These results indicate that PLC-L2 is a novel negative regulator of BCR signaling and immune responses...
  19. ncbi request reprint Isolation and mapping of a human gene (SEC14L), partially homologous to yeast SEC14, that contains a variable number of tandem repeats (VNTR) site in its 3' untranslated region
    K Chinen
    Laboratory of Molecular Medicine, University of Tokyo, Japan
    Cytogenet Cell Genet 73:218-23. 1996
    ..elegans, evolutionary conservation is indicated. SEC14L, which was expressed in all human tissues examined, was localized to chromosome bands 17q25.1 --> q25.2 by fluorescence in situ hybridization...
  20. ncbi request reprint Cloning, characterization and chromosomal assignment of the human genes homologous to yeast PMS1, a member of mismatch repair genes
    A Horii
    Department of Biochemistry, Cancer Institute, Tokyo, Japan
    Biochem Biophys Res Commun 204:1257-64. 1994
    ..DNA sequencing analyses indicated that human PMS genes constituted a multiple gene family and that some of the family members have been mapped to chromosomal bands 7q11.23 and 7q22 by fluorescent in situ hybridization...
  21. ncbi request reprint Molecular cloning, mapping, and characterization of two novel human genes, ORCTL3 and ORCTL4, bearing homology to organic-cation transporters
    T Nishiwaki
    Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
    Cytogenet Cell Genet 83:251-5. 1998
    ..The two genes are clustered within a 52-kb region of genomic DNA and ORCTL4 lies about 27 kb telomeric to ORCTL3 in the genomic DNA sequence in a tail-to-head orientation...
  22. ncbi request reprint Prion domain interaction responsible for species discrimination in yeast [PSI+] transmission
    Hideyuki Hara
    Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Genes Cells 8:925-39. 2003
    ..The N-terminal of Sup35 of Saccharomyces cerevisiae, necessary for [PSI+], contains two species-signature elements-a Gln/Asn-rich region (residues 1-41; designated NQ) that is followed by oligopeptide repeats (designated NR)...
  23. ncbi request reprint Ribosome recycling factor disassembles the post-termination ribosomal complex independent of the ribosomal translocase activity of elongation factor G
    Toshinobu Fujiwara
    Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Mol Microbiol 53:517-28. 2004
    ..These findings suggest that RRF is not a functional mimic of tRNA and disassembles the post-termination ribosomal complex independently of the translocation activity of EF-G...
  24. ncbi request reprint The role of N-terminal domain of translational release factor eRF3 for the control of functionality and stability in S. cerevisiae
    Hiroyuki Kodama
    Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Genes Cells 12:639-50. 2007
    ..These findings suggest that NED functions to switch the functional mode of eRF3 depending on the nature of binding factors...
  25. ncbi request reprint Transient idling of posttermination ribosomes ready to reinitiate protein synthesis
    Andrey L Karamyshev
    Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Biochimie 86:933-8. 2004
    ....
  26. ncbi request reprint Isolation of 115 human chromosome 8-specific expressed-sequence tags by exon amplification
    K Koyama
    Department of Biochemistry, Cancer Institute, Tokyo, Japan
    Genomics 26:245-53. 1995
    ..The expressed-sequence tags isolated here will be useful resources for a transcriptional map of chromosome 8 and for isolation of new genes...
  27. ncbi request reprint Isolation, characterization, and mapping of the mouse and human WDR8 genes, members of a novel WD-repeat gene family
    Y Koshizuka
    Laboratory of Genome Medicine, University of Tokyo, Tokyo, Japan
    Genomics 72:252-9. 2001
    ..The WDR8 protein is highly conserved among a variety of species, but is distinctly different from other WD-repeat proteins, indicating that it represents a novel subfamily of the WD-repeat gene family...
  28. ncbi request reprint Isolation and mapping of a human gene (RPD3L1) that is homologous to RPD3, a transcription factor in Saccharomyces cerevisiae
    Y Furukawa
    Laboratory of Molecular Medicine, University of Tokyo, Japan
    Cytogenet Cell Genet 73:130-3. 1996
    ..It shares 62% identity in nucleotide sequence and 52% identity in amino acid sequence to RPD3. This gene is expressed at various levels in all tissues examined. Furthermore, we were able to map it to chromosome band 1p34.1 by FISH...
  29. pmc A bipolar functionality of Q/N-rich proteins: Lsm4 amyloid causes clearance of yeast prions
    Keita Oishi
    Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo, 108 8639, Japan
    Microbiologyopen 2:415-30. 2013
    ..We also found that the antiprion activity is a general property of [PSI(+) ]-inducible factors. These data provoked a novel "unified" model that explains both prion induction and elimination by a single scheme...
  30. doi request reprint Clearance of yeast prions by misfolded multi-transmembrane proteins
    Chie Arai
    Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Tokyo 108 8639, Japan
    Biochimie 95:1223-32. 2013
    ..These findings suggest that the GET pathway plays a pivotal role in quality assurance of MTM proteins, and entraps misfolded MTM proteins into ER compartments, leading to loss-of-prion through a yet undefined mechanism...
  31. doi request reprint Selfish prion of Rnq1 mutant in yeast
    Hiroshi Kurahashi
    Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Genes Cells 14:659-68. 2009
    ..Thus, the [RNQ1Delta100(+)] prion demonstrates selfish activity to eliminate a heterologous prion in S. cerevisiae, showing the first instance of a selfish prion variant in living organisms...
  32. ncbi request reprint An ancient retrotransposal insertion causes Fukuyama-type congenital muscular dystrophy
    K Kobayashi
    Laboratory of Genome Medicine, Human Genome Center, Institute of Medical Science, University of Tokyo, Japan
    Nature 394:388-92. 1998
    ..To our knowledge, FCMD is the first human disease to be caused by an ancient retrotransposal integration...
  33. ncbi request reprint Human metalloprotease/disintegrin-like (MDC) gene: exon-intron organization and alternative splicing
    T Katagiri
    Department of Biochemistry, Cancer Institute, Tokyo, Japan
    Cytogenet Cell Genet 68:39-44. 1995
    ..These results show that human MDC contains a mosaic of exons capable of encoding several functional domains...
  34. ncbi request reprint Elongation factor G participates in ribosome disassembly by interacting with ribosome recycling factor at their tRNA-mimicry domains
    Koichi Ito
    Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Mol Cell 9:1263-72. 2002
    ..These mutational studies suggest that EF-G motor action is transmitted to RRF by specific surface contacts between the domains that mimic the anticodon arm...
  35. doi request reprint Lipid rafts and caveolin-1 are required for invadopodia formation and extracellular matrix degradation by human breast cancer cells
    Hideki Yamaguchi
    Laboratory of Genome and Biosignal, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
    Cancer Res 69:8594-602. 2009
    ..These results indicate that invadopodia are the sites where enrichment and trafficking of lipid rafts occur and that Cav-1 is an essential regulator of MT1-MMP function and invadopodia-mediated breast cancer cell invasion...
  36. pmc A systematic evaluation of the function of the protein-remodeling factor Hsp104 in [PSI+] prion propagation in S. cerevisiae by comprehensive chromosomal mutations
    Aiko Takahashi
    Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, Tokyo, Japan
    Prion 1:69-77. 2007
    ....
  37. ncbi request reprint Isolation and mapping of a human gene (RABL) encoding a small GTP-binding protein homologous to the Ras-related RAB gene
    H J Han
    Department of Biochemistry, Cancer Institute, Tokyo, Japan
    Cytogenet Cell Genet 73:137-9. 1996
    ..This gene was expressed ubiquitously in all human tissues examined. By fluorescence in situ hybridization we mapped RABL to chromosome band 17q21.2...
  38. ncbi request reprint Characterization of the human p57KIP2 gene: alternative splicing, insertion/deletion polymorphisms in VNTR sequences in the coding region, and mutational analysis
    T Tokino
    Laboratory of Molecular Medicine, The Institute of Medical Science, The University of Tokyo, Japan
    Hum Genet 97:625-31. 1996
    ..5'-CCGGCC-3', are tandemly repeated...
  39. pmc The stretch of C-terminal acidic amino acids of translational release factor eRF1 is a primary binding site for eRF3 of fission yeast
    K Ito
    Department of Tumor Biology, The Institute of Medical Science, The University of Tokyo, Japan
    RNA 4:958-72. 1998
    ..These results cannot be accounted for by the simple "eRF3-EF-Tu mimicry" model, but may provide new insight into the eRF3 function for translation termination in eukaryotes...
  40. ncbi request reprint Emerging understanding of translation termination
    Y Nakamura
    Department of Tumor Biology, The Institute of Medical Science, The University of Tokyo, Minato ku, Japan
    Cell 87:147-50. 1996
  41. ncbi request reprint Molecular cloning of a novel human cDNA homologous to CDC10 in Saccharomyces cerevisiae
    S Nakatsuru
    Department of Biochemistry, Cancer Institute, Tokyo, Japan
    Biochem Biophys Res Commun 202:82-7. 1994
    ..Each of these sequence homologues, including Saccharomyces cerevisiae CDC10, contains the GTP-binding motif. Northern blot analyses indicated that the hCDC10 gene is expressed ubiquitously in normal tissues...
  42. ncbi request reprint Isolation and characterization of a novel gene encoding nuclear protein at a locus (D11S636) tightly linked to multiple endocrine neoplasia type 1 (MEN1)
    T Toda
    Department of Biochemistry, Cancer Institute, Tokyo, Japan
    Hum Mol Genet 3:465-70. 1994
    ..These data suggest that ZFM1 might be a candidate for mutations that cause MEN1...
  43. pmc Properties of peptide chain release factor 2 from Streptomyces coelicolor A3(2): conserved primary structure but no frameshift regulation
    H Ogawara
    Department of Biochemistry, Meiji College of Pharmacy, Tokyo, Japan
    J Bacteriol 177:5342-5. 1995
    ..coelicolor A3(2). However, about 80 bp upstream of the gene there is an operon which is composed of two genes encoding eukaryotic-type serine/threonine kinases...
  44. ncbi request reprint Genomic organization and mutational analysis of KVLQT1, a gene responsible for familial long QT syndrome
    T Itoh
    Human Genome Center, Institute of Medical Science, University of Tokyo, Japan
    Hum Genet 103:290-4. 1998
    ..This work will enable us to search more thoroughly for LQTS mutations associated with KVLQT1, and eventually will help us in finding genotype/phenotype relationships...
  45. ncbi request reprint Sequence analysis of a 685-kb genomic region on chromosome 3p22-p21.3 that is homozygously deleted in a lung carcinoma cell line
    S Ishikawa
    Laboratory of Molecular Medicine, University of Tokyo, Japan
    DNA Res 4:35-43. 1997
    ..Repetitive sequences contained in the genomic region included 151 copies of the Alu sequence (1 copy/every 4.5 kb), 19 copies of the L1 sequence (1 copy/every 36 kb), and 10 copies of the THE sequence...
  46. ncbi request reprint Genomic organization and mutational analysis of HERG, a gene responsible for familial long QT syndrome
    T Itoh
    Laboratory of Molecular Medicine, Institute of Medical Science, University of Tokyo, Japan
    Hum Genet 102:435-9. 1998
    ..Each mutation was present in affected relatives of the respective proband. This work should increase the efficiency of screening mutations associated with HERG...
  47. ncbi request reprint Complete genomic structure DNA polymorphisms, and alternative splicing of the human AF-6 gene
    S Saito
    Center for Molecular Biology and Cytogenetics, SRL, Inc, Tokyo, Japan
    DNA Res 5:115-20. 1998
    ..These results may contribute to an understanding of the mechanism causing chromosomal translocations in leukemic cells...
  48. doi request reprint [PSI(+)] aggregate enlargement in rnq1 nonprion domain mutants, leading to a loss of prion in yeast
    Hiroshi Kurahashi
    Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, Shirokanedai, Minato ku, Japan
    Genes Cells 16:576-89. 2011
    ....
  49. pmc Generation of a mouse model with down-regulated U50 snoRNA (SNORD50) expression and its organ-specific phenotypic modulation
    Yuuichi Soeno
    Department of Pathology, School of Life Dentistry, The Nippon Dental University, Tokyo, Japan
    PLoS ONE 8:e72105. 2013
    ....
  50. doi request reprint A novel class of bacterial translation factor RF3 mutations suggests specific structural domains for premature peptidyl-tRNA drop-off
    Yuya Watanabe
    Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo IMSUT, Tokyo, Japan
    FEBS Lett 584:790-4. 2010
    ..In this report, we demonstrate a novel class of RF3 mutations specifically defective in the tRNA drop-off reaction. These mutations suggest differential molecular pathways closely related to the guanine nucleotide modes of RF3...
  51. pmc Localization of prion-destabilizing mutations in the N-terminal non-prion domain of Rnq1 in Saccharomyces cerevisiae
    Shoichiro Shibata
    Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, Minato ku, Tokyo, Japan
    Prion 3:250-8. 2009
    ..These findings indicate that the N-terminal non-prion domain of Rnq1 harbors a potent activity to regulate the maintenance of the [PIN(+)] prion...
  52. ncbi request reprint Overexpression and purification of recombinant eRF1 proteins of rabbit and Tetrahymena thermophila
    A L Karamyshev
    Department of Tumor Biology, Institute of Medical Science, University of Tokyo, Tokyo, 108 8630, Japan
    Biochemistry (Mosc) 64:1391-400. 1999
    ..cerevisiae, though the complementation activity was significantly impaired by the histidine tag, whereas Tt-eRF1 failed to complement the sup45 (ts) allele...
  53. pmc Functional mapping of ribosome-contact sites in the ribosome recycling factor: a structural view from a tRNA mimic
    T Fujiwara
    Department of Basic Medical Sciences, The Institute of Medical Science, The University of Tokyo, Japan
    RNA 7:64-70. 2001
    ....
  54. ncbi request reprint Mutational analysis of the RET proto-oncogene in 71 Japanese patients with medullary thyroid carcinoma
    S Shirahama
    Center for Molecular Biology and Cytogenetics, SRL Inc, Tokyo, Japan
    J Hum Genet 43:101-6. 1998
    ....
  55. ncbi request reprint Isolation and characterization of a human cDNA homologous to the Xenopus laevis XCAP-C gene belonging to the structural maintenance of chromosomes (SMC) family
    T Nishiwaki
    Laboratory of Molecular Medicine, Institute of Medical Science, University of Tokyo, Japan
    J Hum Genet 44:197-202. 1999
    ..We also determined its chromosomal location at 3q26.1 by fluorescence in situ hybridization...
  56. ncbi request reprint Molecular cloning and mapping of a human cDNA (SC5DL) encoding a protein homologous to fungal sterol-C5-desaturase
    M Matsushima
    Laboratory of Molecular Medicine, University of Tokyo, Japan
    Cytogenet Cell Genet 74:252-4. 1996
    ..The gene was expressed in all normal human tissues examined. We determined its location to chromosome 11q23.3 by fluorescence in situ hybridization...
  57. ncbi request reprint Isolation and mapping of RAB2L, a human cDNA that encodes a protein homologous to RalGDS
    M Isomura
    Laboratory of Molecular Medicine, University of Tokyo, Japan
    Cytogenet Cell Genet 74:263-5. 1996
    ..Northern analysis revealed that the gene RAB2L is expressed in all human tissues examined. We assigned this gene locus to chromosome band 6p21.3 by fluorescence in situ hybridization...
  58. pmc High affinity RNA for mammalian initiation factor 4E interferes with mRNA-cap binding and inhibits translation
    Kiyotaka Mochizuki
    Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    RNA 11:77-89. 2005
    ..The genetic mutation and affinity study of variant eIF4E proteins suggests that aptamer 1 binds to eIF4E adjacent to the entrance of the cap-binding slot and blocks the cap-binding pocket, thereby inhibiting translation initiation...
  59. ncbi request reprint Channel mutations in Hsp104 hexamer distinctively affect thermotolerance and prion-specific propagation
    Hiroshi Kurahashi
    Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Mol Microbiol 63:1669-83. 2007
    ..The mutations that are specific to prion propagation are clustered around the lateral channel of the Hsp104 hexamer, suggesting a crucial and specific role of this channel for prion propagation...
  60. pmc Structural and molecular basis for hyperspecificity of RNA aptamer to human immunoglobulin G
    Shin Miyakawa
    RIBOMIC Inc, 3 16 13 Shirokanedai, Minato ku, Tokyo 108 0071, Japan
    RNA 14:1154-63. 2008
    ..Using Apt8-2 would have several potential advantages, raising the possibility of developing new applications based on aptamer design...
  61. ncbi request reprint Isolation and mapping of a human gene (DIFF6) homologous to yeast CDC3, CDC10, CDC11, and CDC12, and mouse Diff6
    T Mori
    Laboratory of Molecular Medicine, University of Tokyo, Japan
    Cytogenet Cell Genet 73:224-7. 1996
    ..5 kb long, was expressed ubiquitously in all human tissues examined, but a 2.0-kb alternative transcript lacking any long AU-rich element in the 3' non-coding region was expressed abundantly only in testis, heart and skeletal muscle...
  62. ncbi request reprint Mutational analysis of mismatch repair genes, hMLH1 and hMSH2, in sporadic endometrial carcinomas with microsatellite instability
    K Kobayashi
    Laboratory of Molecular Medicine, Institute of Medical Science, University of Tokyo, Japan
    Jpn J Cancer Res 87:141-5. 1996
    ....
  63. ncbi request reprint Identification, genomic organization, and alternative splicing of KNSL3, a novel human gene encoding a kinesin-like protein
    S Okamoto
    Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo Japan
    Cytogenet Cell Genet 83:25-9. 1998
    ..These observations may contribute to an understanding of the specificity of different kinesins with respect to organelle binding...
  64. ncbi request reprint Mutations in the N-terminal globular domain of the type X collagen gene (COL10A1) in patients with Schmid metaphyseal chondrodysplasia
    S Ikegawa
    Laboratory of Molecular Medicine, University of Tokyo, Japan
    Hum Mutat 9:131-5. 1997
    ....
  65. pmc C-terminal interaction of translational release factors eRF1 and eRF3 of fission yeast: G-domain uncoupled binding and the role of conserved amino acids
    K Ebihara
    Department of Tumor Biology, The Institute of Medical Science, The University of Tokyo, Japan
    RNA 5:739-50. 1999
    ..e., probably uncoupled with GTP hydrolysis), whereas aminoacyl-tRNA binding depends on that of EF-Tu/EF-1alpha(i.e., coupled with GTP hydrolysis), which sheds some light on the mechanism of eRF3 function...
  66. ncbi request reprint Isolation of two isoforms of the PAX3 gene transcripts and their tissue-specific alternative expression in human adult tissues
    K Tsukamoto
    Department of Biochemistry, Cancer Institute, Tokyo, Japan
    Hum Genet 93:270-4. 1994
    ..PAX3B was expressed in most of the tissues examined, but the PAX3A type of transcript was detected only in the cerebellum, esophagus, and skeletal muscle...
  67. ncbi request reprint Localization of nusA-suppressing amino acid substitutions in the conserved regions of the beta' subunit of Escherichia coli RNA polymerase
    K Ito
    Department of Tumor Biology, University of Tokyo, Japan
    Mol Gen Genet 251:699-706. 1996
    ..These results suggested that the conserved domains of the beta' subunit of E. coli RNA polymerase are involved in transcript termination or interaction with termination factor(s)...
  68. ncbi request reprint Amber mutations in ribosome recycling factors of Escherichia coli and Thermus thermophilus: evidence for C-terminal modulator element
    T Fujiwara
    Department of Tumor Biology, The Institute of Medical Science, The University of Tokyo, Takanawa, Japan
    FEBS Lett 447:297-302. 1999
    ..thermophilus RRF, demonstrating the modulator activity of the C-terminal tail. Rapid purification of T. thermophilus RRF was achieved by T7-RNA polymerase-driven overexpression for crystallography...
  69. ncbi request reprint Assignment of the human caltractin gene (CALT) to Xq28 by fluorescence in situ hybridization
    T Tanaka
    Department of Biochemistry, Cancer Institute, Tokyo, Japan
    Genomics 24:609-10. 1994
  70. ncbi request reprint Isolation and mapping of a novel human gene encoding a protein containing zinc-finger structures
    H Saito
    Department of Biochemistry, Cancer Institute, Tokyo, Japan
    Genomics 31:376-9. 1996
    ..The 4.3-kb transcript was expressed in all adult human tissues examined by Northern analysis. The gene was assigned to chromosomal band 19q13.4 by fluorescence in situ hybridization...
  71. pmc A bipolar personality of yeast prion proteins
    Hiroshi Kurahashi
    Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, Tokyo, Japan
    Prion 5:305-10. 2011
    ..Possible mechanisms underlying the apparent bipolar activity of yeast prions will be discussed...
  72. pmc A G-protein gamma subunit mimic is a general antagonist of prion propagation in Saccharomyces cerevisiae
    Masao Ishiwata
    Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, Minato ku, Tokyo 108 8639, Japan
    Proc Natl Acad Sci U S A 106:791-6. 2009
    ..Assuming the ability of Gpg1 to form G-protein heterotrimeric complexes, Gpg1 is likely to play a versatile function of reversing the prion state and modulating the G-protein signaling pathway...
  73. pmc Phospholipase Cdelta1 is required for skin stem cell lineage commitment
    Yoshikazu Nakamura
    Department of Biochemistry, The Institute of Medical Science, University of Tokyo, Tokyo 108 8639, Japan
    EMBO J 22:2981-91. 2003
    ..From these results, we conclude that PLCdelta(1) is required for skin stem cell lineage commitment...
  74. pmc Antizyme frameshifting as a functional probe of eukaryotic translational termination
    Zemfira N Karamysheva
    Department of Biochemistry II, The Jikei University, School of Medicine, 3 25 8 Nishi shinbashi, Minato ku, Tokyo 105 8461, Japan
    Nucleic Acids Res 31:5949-56. 2003
    ..The system affords a convenient assay for release factor activity and has provided some novel views of the mechanism of antizyme frameshifting...
  75. ncbi request reprint Ribosomal protein L11 mutations in two functional domains equally affect release factors 1 and 2 activity
    Hanae Sato
    Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Mol Microbiol 60:108-20. 2006
    ..These L11 mutations were located on the surface of two domains of L11, and interpreted to affect the interaction between L11 and rRNA or the RFs thereby leading to the altered translation termination...
  76. doi request reprint Antagonistic RNA aptamer specific to a heterodimeric form of human interleukin-17A/F
    Hironori Adachi
    Department of Basic Medical Sciences, Institute of Medical Science, The University of Tokyo, Minato ku, Tokyo, Japan
    Biochimie 93:1081-8. 2011
    ..These results suggest that the selected aptamer recognizes a global conformation specified by the heterodimeric surface of IL-17A/F...
  77. ncbi request reprint Novel mutations and genotype-phenotype relationships in 107 families with Fukuyama-type congenital muscular dystrophy (FCMD)
    E Kondo-Iida
    Laboratory of Genome Medicine, Human Genome Center, Institute of Medical Science, University of Tokyo, Japan
    Hum Mol Genet 8:2303-9. 1999
    ..Our results provided strong evidence that loss of function of fukutin is the major cause of FCMD, and appeared to shed some light on the mechanism responsible for the broad clinical spectrum seen in this disease...
  78. ncbi request reprint Cloning of P2XM, a novel human P2X receptor gene regulated by p53
    T Urano
    Laboratory of Molecular Medicine, The Institute of Medical Science, The University of Tokyo, Minato ku, Japan
    Cancer Res 57:3281-7. 1997
    ..The results suggest that P2XM may play a significant role in the proliferation and/or differentiation of skeletal muscle cells and that its altered expression may be involved in the development of some sarcomas...
  79. ncbi request reprint Isolation and mutational analysis of a novel human cDNA, DEC1 (deleted in esophageal cancer 1), derived from the tumor suppressor locus in 9q32
    T Nishiwaki
    Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
    Genes Chromosomes Cancer 27:169-76. 2000
    ..Genes Chromosomes Cancer 27:169-176, 2000...
  80. ncbi request reprint Characterization of a 1200-kb genomic segment of chromosome 3p22-p21.3
    Y Daigo
    Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Japan
    DNA Res 6:37-44. 1999
    ..The other gene F56 revealed no significant homology to any known genes. These results disclosed complete physical and transcriptional maps of the 1200-kb region of 3p present in YAC 936c1...
  81. ncbi request reprint Significant differences in the frequency of transcriptional units, types and numbers of repetitive elements, GC content, and the number of CpG islands between a 1010-kb G-band genomic segment on chromosome 9q31.3 and a 1200-kb R-band genomic segment on ch
    Y Daigo
    Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Minato, Japan
    DNA Res 6:227-33. 1999
    ....
  82. ncbi request reprint Intronic U50 small-nucleolar-RNA (snoRNA) host gene of no protein-coding potential is mapped at the chromosome breakpoint t(3;6)(q27;q15) of human B-cell lymphoma
    R Tanaka
    Departments of Pathology Tumor Biology, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Genes Cells 5:277-87. 2000
    ..Most snoRNAs so far characterized are encoded and processed from introns of premRNAs...
  83. ncbi request reprint High-density single-nucleotide polymorphism (SNP) map of the 150-kb region corresponding to the human ATP-binding cassette transporter A1 (ABCA1) gene
    A Iida
    Laboratory for Genotyping, RIKEN SNP Research Center, Tokyo, Japan
    J Hum Genet 46:522-8. 2001
    ..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...
  84. pmc Crystal structure combined with genetic analysis of the Thermus thermophilus ribosome recycling factor shows that a flexible hinge may act as a functional switch
    T Toyoda
    Department of Tumor Biology, The Institute of Medical Science, The University of Tokyo, Japan
    RNA 6:1432-44. 2000
    ..These properties will add a new insight into RRF, suggesting that RRF is more than a simple tRNA mimic...
  85. ncbi request reprint Molecular cloning of a human cDNA encoding putative cysteine protease (PRSC1) and its chromosome assignment to 14q32.1
    T Tanaka
    Laboratory of Molecular Medicine, University of Tokyo, Japan
    Cytogenet Cell Genet 74:120-3. 1996
    ..Northern-blot analysis revealed the strongest expression of this gene in kidney, among the human tissues examined. By fluorescence in situ hybridization, we determined its chromosome location at 14q32.1...
  86. ncbi request reprint Isolation of novel mouse genes associated with ectopic ossification by differential display method using ttw, a mouse model for ectopic ossification
    Y Koshizuka
    Laboratory of Genome Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Japan
    Cytogenet Cell Genet 94:163-8. 2001
    ..Our identification of the novel genes would give novel insight into the mechanism of ectopic ossification and etiology of OPLL...
  87. ncbi request reprint Isolation and characterization of human NBL4, a gene involved in the beta-catenin/tcf signaling pathway
    H Ishiguro
    Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Minato ku, Tokyo 108 8639, Japan
    Jpn J Cancer Res 91:597-603. 2000
    ..The results support the view that NBL4 is an important component of the beta-catenin / Tcf pathway and is probably related to determination of cell polarity or proliferation...
  88. ncbi request reprint Cloning and mapping of a human novel cDNA (NHP2L1) that encodes a protein highly homologous to yeast nuclear protein NHP2
    H Saito
    Department of Biochemistry, Cancer Institute, Tokyo, Japan
    Cytogenet Cell Genet 72:191-3. 1996
    ..The 1,493-bp cDNA sequence includes an open reading frame of 384 bp. This gene (NHP2L1) was expressed in all human tissues examined, and was localized to chromosome hand 12q24.3 by fluorescence in situ hybridization...
  89. ncbi request reprint Isolation and characterization of a novel gene encoding a putative seven-span transmembrane protein, TM7SF3
    H Akashi
    Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Japan
    Cytogenet Cell Genet 88:305-9. 2000
    ..We determined the chromosome location of TM7SF3 as 12q11.2-->q12 by a combination of fluorescence in situ hybridization and radiation hybrid mapping...
  90. ncbi request reprint Molecular cloning and expression of a novel human gene that is highly homologous to human FK506-binding protein 12kDa (hFKBP-12) and characterization of two alternatively spliced transcripts
    H Arakawa
    Department of Biochemistry, Cancer Institute, Tokyo, Japan
    Biochem Biophys Res Commun 200:836-43. 1994
    ..Although the biological function of the truncated version of OTK4 is unknown, both transcripts were ubiquitously expressed in human tissues examined by the reverse-transcriptase PCR (RT-PCR) method...
  91. ncbi request reprint Cloning and mapping of a novel human cDNA homologous to DROER, the enhancer of the Drosophila melanogaster rudimentary gene
    M Isomura
    Laboratory of Molecular Medicine, Institute of Medical Science, University of Tokyo, Japan
    Genomics 32:125-7. 1996
    ..The ERH gene was expressed in all normal human tissues examined. We assigned the ERH gene locus to chromosomal band 7q34 by fluorescence in situ hybridization...
  92. ncbi request reprint Molecular cloning of a novel gene similar to myeloid antigen CD33 and its specific expression in placenta
    Y Takei
    Laboratory of Molecular Medicine, University of Tokyo, Japan
    Cytogenet Cell Genet 78:295-300. 1997
    ..We mapped CD33L by fluorescence in situ hybridization (FISH) to human chromosome 19q13.3, where the CD33 gene is also located...
  93. ncbi request reprint Identification of Rad51 alteration in patients with bilateral breast cancer
    M Kato
    Department of Molecular Diagnosis, Cancer Institute, Tokyo, Japan
    J Hum Genet 45:133-7. 2000
    ..As this alteration was not present in any patients with breast or colon cancer examined, we assume that this missense alteration is likely to be a disease-causing mutation...
  94. pmc Isolation of a novel human gene, MARKL1, homologous to MARK3 and its involvement in hepatocellular carcinogenesis
    T Kato
    Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
    Neoplasia 3:4-9. 2001
    ..Expression levels of MARKL1 were markedly elevated in eight of nine HCCs in which nuclear accumulation of beta-catenin were observed, which may suggest that MARKL1 plays some role in hepatocellular carcinogenesis...
  95. pmc RNA aptamers to initiation factor 4A helicase hinder cap-dependent translation by blocking ATP hydrolysis
    Akihiro Oguro
    Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, Minato ku, Tokyo 108 8639, Japan
    RNA 9:394-407. 2003
    ....
  96. doi request reprint HEXIM1-binding elements on mRNAs identified through transcriptomic SELEX and computational screening
    Yuki Fujimoto
    Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Biochimie 94:1900-9. 2012
    ..Our findings suggest a possible role for HEXIM1 in the regulation of specific gene expressions...
  97. doi request reprint RNA aptamers to translational components
    Yoshikazu Nakamura
    Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, Tokyo, Japan
    Prog Mol Biol Transl Sci 90:369-95. 2009
    ..This provides us with a solid and promising basis to take steps to create novel RNA molecules of therapeutic potential with distinct structures, which should be equivalent or superior to antibodies...
  98. doi request reprint tRNA mimicry in translation termination and beyond
    Yoshikazu Nakamura
    Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, Japan
    Wiley Interdiscip Rev RNA 2:647-68. 2011
    ..WIREs RNA 2011 2 647-668 DOI: 10.1002/wrna.81 For further resources related to this article, please visit the WIREs website...
  99. pmc Omnipotent decoding potential resides in eukaryotic translation termination factor eRF1 of variant-code organisms and is modulated by the interactions of amino acid sequences within domain 1
    Koichi Ito
    Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Proc Natl Acad Sci U S A 99:8494-9. 2002
    ....
  100. pmc Genetic defect in phospholipase Cδ1 protects mice from obesity by regulating thermogenesis and adipogenesis
    Masayuki Hirata
    Laboratory of Genome and Biosignal, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
    Diabetes 60:1926-37. 2011
    ..Gene-disrupted mice of phospholipase Cδ1 (PLCδ1), a key enzyme of phosphoinositide turnover, seemed to show leanness. Here we examined whether and how PLCδ1 is involved in obesity...
  101. doi request reprint Phosphatidylinositol 4,5-bisphosphate and PIP5-kinase Ialpha are required for invadopodia formation in human breast cancer cells
    Hideki Yamaguchi
    Laboratory of Genome and Biosignal, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
    Cancer Sci 101:1632-8. 2010
    ..These results indicate that localized production of PI(4,5)P(2) by PIP5KIalpha is required for invadopodia formation and ECM degradation by human breast cancer cells...