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2010 Fiscal Year Final Research Report

Higher-order genomic structure and subcellular organization

Research Project

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Project/Area Number 19207001
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Genetics/Genome dynamics
Research InstitutionKyoto University

Principal Investigator

TAKEYASU Kunio  Kyoto University, 大学院・生命科学研究科, 教授 (40135695)

Co-Investigator(Kenkyū-buntansha) YOSHIMURA Shigehiro  京都大学, 大学院・生命科学研究科, 准教授 (90346106)
HIDUME Kouji  京都大学, 大学院・生命科学研究科, 助教 (10378846)
ATOMI Haruyuki  京都大学, 大学院・工学科学研究科, 准教授 (90243047)
Project Period (FY) 2007 – 2010
Keywordsゲノム構築 / 機能 / 再編 / 発現 / 維持
Research Abstract

(1) In Archaea, TK0471 is a structural protein as well as a transcription factor. (2) Nucleolar proteins (MAk16, WD46, MAGEFF, FAM27E1, etc.) with unknown function move very slowly compared to the well-known nucleolar proteins. They behave also very differently in the presence of transcription inhibitor, actinomycin D. (3) A cytoskeletal protein, actinin-4, shuttles between cytoplasm and nuclelar plasm, dependent of cell cycle and independent on importin-β.

  • Research Products

    (35 results)

All 2011 2010 2009 2008 2007

All Journal Article (26 results) Presentation (3 results) Book (6 results)

  • [Journal Article] Motion of Ca-pump captured.2011

    • Author(s)
      M.Yokokawa, K.Takeyasu
    • Journal Title

      FEBS J. In Press

  • [Journal Article] Unusual structures are present in DNA fragments containing super-long Huntingtin CAG repeats.2011

    • Author(s)
      Daniel Duzdevich, Jinliang Li, Jhoon Whang, H.Takahashi, K.Takeyasu, David T.F. Dryden, A.Jennifer Morton, J.Michael Edwardson
    • Journal Title

      PloS ONE 6

      Pages: e17119

  • [Journal Article] Nup358, a nucleoporin, functions as a key determinant of the nuclear pore complex structure remodeling during skeletal myogenesise.2011

    • Author(s)
      Muehiro Asally, Y.Yasuda, M.Oka, S.Otsuka S.H.Y oshimura, Ktakeyasu, Y.Yoneda
    • Journal Title

      The FASEB J. 278

      Pages: 610-621

  • [Journal Article] Histone and TK0471/TrmBL2 form a novel heterogeneous genome architecture in the hyperthermophilic archaeon Thermococcus kodakarensis.2010

    • Author(s)
      H.Maruyama, Minsang Shin , T.Oda , Rie Matsumi , R.L.Ohniwa , T.Itoh , K.Shirahige , T.Imanaka , H.Atomi , Shige H.Yoshimura , K.Takeyasu
    • Journal Title

      Mol.Biol.Cell 22

      Pages: 386-398

  • [Journal Article] Formation of equilateral-triangular shaped RNA-protein complex with kink-turn-L7Ae interacting motifs.2010

    • Author(s)
      H.Ohno, T.Kobayashi, R.Kabata, T.Iwasa, S.H.Yoshimura, K.Takeyasu, T.Inoue, H.Saito
    • Journal Title

      Nature Nanotechnology

      Pages: DOI : 10.1038/NNANO.2010.268.

  • [Journal Article] Molecular Dynamics of DNA and Nucleosomes in Solution Studied by Fast-scanning Atomic Force Microscopy.2010

    • Author(s)
      Y.Suzuki, Y.Higuchi, K.Hizume, M.Yokokawa, S.H.Yoshimura, K.Yoshikawa, K.Takeyasu
    • Journal Title

      Ultramicroscopy 110

      Pages: 682-688

  • [Journal Article] RecO-mediated DNA homology search and annealing is facilitated by SsbA.2010

    • Author(s)
      C.Manfredi, Y.Suzuki, T.Yadav, K.Takeyasu, J.C.Alonso.
    • Journal Title

      Nucleic Acids Res. 38

      Pages: 6920-6929

  • [Journal Article] Molecular mechanisms underlying nucleocytoplasmic shuttling of actinin-4.2010

    • Author(s)
      M.Kumeta, S.H.Yoshimura, M.Harata, K.Takeyasu
    • Journal Title

      J.Cell Sci. 123

      Pages: 1020-1030

  • [Journal Article] Interaction of synaptotagmin with lipid bilayers, analyzed by single-molecule force spectroscopy.2010

    • Author(s)
      H.Takahashi, Victor Shahin, Robert M.Henderson, K.Takeyasu, J.Michael Edwardson
    • Journal Title

      Biophysical J. 99

      Pages: 2550-2558

  • [Journal Article] Acid-sensing ion channel (ASIC) 1a undergoes a height transition in response to acidification.2010

    • Author(s)
      M.Yokokawa, K.Takeyasu, J.M.Edwardson
    • Journal Title

      FEBS Lett. 584

      Pages: 3107-3110

  • [Journal Article] Adaptation beyond the Stress Response : Cell Structure Dynamics and Population Heterogeneity in Staphylococcus aureus2010

    • Author(s)
      K.Morikawa, R.L.Ohniwa, T.Ohta, Y.Tanaka, K.Takeyasu, T.Msadek
    • Journal Title

      Microbes and Environments 25

      Pages: 75-82

  • [Journal Article] Single-molecule Anatomy by Atomic Force Microscopy and Recognition Imaging.2009

    • Author(s)
      H.Takahashi, K.Hizume, M.Kumeta, S.H.Yoshimura, K.Takeyasu
    • Journal Title

      Arch.Histology and Cytology 72

      Pages: 17-225

  • [Journal Article] Cell Cycle-Dependent Phosphorylation of MAN-1.2009

    • Author(s)
      Y.Hirano, Y.Iwase, K.Ishii, M.Kumeta, T.Horigome, K.Takeyasu
    • Journal Title

      Biochemistry 48

      Pages: 1636-1643

  • [Journal Article] Removal of histone tails from nucleosome dissects the physical mechanisms of salt-induced aggregation, linker histone H1-induced compaction and 30-nm fiber formation of the nucleosome array.2009

    • Author(s)
      K.Hizume, T.Nakai, S.Araki, E.Prieto, K.Yoshikawa, K.Takeyasu
    • Journal Title

      Ultramicroscopy 109

      Pages: 868-873

  • [Journal Article] Single-Molecule Dynamics of the DNA-EcoRII Protein Complexes Revealed with High-Speed Atomic Force Microscopy.2009

    • Author(s)
      J.L.Gilmore, Y.Suzuki, G.Tamulaitis, V.Siksnys, K.Takeyasu, Y.L.Lyubchenko
    • Journal Title

      Biochemistry. 48(44)

      Pages: 10492-10498

  • [Journal Article] Nucleosomal arrays reconstituted from ring and linear DNA.2009

    • Author(s)
      S.Araki, K.Hizume, T.Iwaki, Y.Suzuki, K.Takeyasu, K.Yoshikawa
    • Journal Title

      Chem.Phys.Lett. 479

      Pages: 284-289

  • [Journal Article] Single-molecule analysis of protein-DNA complexes formed during partition of newly replicated plasmid molecules in Streptococcus pyogenes.2009

    • Author(s)
      F.Pratto, Y.Suzuki, K.Takeyasu, J.C.Alonso
    • Journal Title

      J Biol Chem. 284(44)

      Pages: 30298-30306

  • [Journal Article] Proteomic and targeted analytical identification of BXDC1 and EBNA1BP2 as dynamic scaffold proteins in the nucleous.2008

    • Author(s)
      Y.Hirano, K.Ishii, M.Kumeta, K.Furukawa, K.Takeyasu, T.Horigome.
    • Journal Title

      Genes Cell 14

      Pages: 155-166

  • [Journal Article] Nuclear matrix contains novel WD-repeat and disordered-regin-rich proteins.2008

    • Author(s)
      K.Ishii, Y.Hirano, N.Araki, T.Oda, M.Kumeta, K.Takeyasu, K.Furukawa, T.Horigome
    • Journal Title

      FEBS Lett. 582

      Pages: 3515-3519

  • [Journal Article] Individual binding pockets of importin beta for FG-nucleoporins have different binding properties and different sensitivities to RanGTP.2008

    • Author(s)
      S.Otsuka, S.Iwasaka, Y.Yoneda, H.Takahashi, K.Takeyasu, S.H.Yoshimura
    • Journal Title

      Proc Natl Acad Sci USA 105

      Pages: 16101-16106

  • [Journal Article] Scanning probe microscope revealed mechanical properties of plasma membrane and nuclear envelope in living cells.2008

    • Author(s)
      M.Yokokawa, K.Takeyasu, S.H.Yoshimura
    • Journal Title

      J.Microscopy 232

      Pages: 82-90

  • [Journal Article] Nuclear Architectures and Chromatin Dynamics Revealed by Atomic Force Microscopy in Combination with Biochemistry and Cell Biology.2008

    • Author(s)
      Y.Hirano, H.Takahashi, M.Kumeta, K,Hizume, Y.Hirai, S.Otsuka, S.H.Yoshimura, K.Takeyasu
    • Journal Title

      Eur.J.Physiol. 456

      Pages: 139-153

  • [Journal Article] Transcription-coupled uncleoid architecture in bacteria.2007

    • Author(s)
      R.L.Ohniwa, K.Morikawa, S.L.Takeshita, J.Kim, T.Ohta, C.Wada, K.Takeyasu
    • Journal Title

      Gene to Cells 12

      Pages: 1141-1152

  • [Journal Article] Fast-scan atomic force microscopy reveals that the type III restriction enzyme EcoP15I is capable of DNA translocation and looping.2007

    • Author(s)
      N.Crampton, M.Yokokawa, D.T.Dryden, J.M.Edwardson, D.N.Rao, K.Takeyasu, S.H.Yoshimura, R.M.Henderson
    • Journal Title

      Proc Natl Acad Sci USA 104

      Pages: 12755-12760

  • [Journal Article] Topoisomerase II, a scaffold component, promotes chromatin-compaction in vitro in a linker-histone H1-dependent manner.2007

    • Author(s)
      K.Hizume, S.Araki, K.Yoshikawa, K.Takeyasu
    • Journal Title

      Nucleic Asid Res. 35

      Pages: 2787-2799

  • [Journal Article] Chromatin dynamics of unfolding and refolding controlled by the nucleosome repeat length and the linker and core histones.2007

    • Author(s)
      T.Kobori, S.Iwamoto, K.Takeyasu, T.Ohtani
    • Journal Title

      Biopolymers 85

      Pages: 295-307

  • [Presentation] Karyopherin-independent nuclear Transport of spectrin for superfamily proteins2010

    • Author(s)
      M.Kumeta, S.Otsuka, S.H.Yoshimura, K.Takeyasu
    • Organizer
      The American Society for Cell Biology-50^<th> annual meeting
    • Place of Presentation
      Philadelphia, USA
    • Year and Date
      2010-12-14
  • [Presentation] Nucleosome and Chromatin Dynamics Revealed by Atomic Force Microscopy2009

    • Author(s)
      K.Takeyasu
    • Organizer
      The 7th European Biophysical Society Association meeting
    • Place of Presentation
      Genoa, Italy
    • Year and Date
      2009-07-15
  • [Presentation] Genome/Chromatin Dynamics Revealed by Atomic force Microscopy2008

    • Author(s)
      K.Takeyasu
    • Organizer
      International Scanning Probe Microscopy conference
    • Place of Presentation
      Seattle, USA
    • Year and Date
      2008-06-22
  • [Book] Scanning Probe Microscopy in Nanoscience and Nanotechnology, Vol 2(Biological Application of Fast-Scanning Atomic Force Microscopy)(ed.B.Bhushan.)2011

    • Author(s)
      Yu-ki Suzuki, Masatoshi Yokokawa, S.H.Yoshimura, Kunio Takeyasu
    • Total Pages
      217-246
    • Publisher
      Springer-Verlag, Heidelberg
  • [Book] Microscopy : Science, Technology, Applications and Education(Force spectroscopy addresses fundamental problems in cell physiology.)(ed.A.Mendez-Vilas)2010

    • Author(s)
      Hirohide Takahashi, Yaron R.Silberberg, Masahiro Kumeta, J.Michael Edwardson, Kunio Takeyasu
    • Total Pages
      478-488
    • Publisher
      Formatex Research Center, Badajoz, Spain pp.
  • [Book] Applied Scanning Probe Methods, Vol.14(Modern Atomic Force Microscopy and Its Application to the Study of Genome Architecture.)(ed.B.Bhushan.)2009

    • Author(s)
      K.Takeyasu, H.Maruyama, Y.Suzuki, K.Hizume, S.H.Yoshimura
    • Publisher
      Springer-Verlag, Heidelberg.
  • [Book] Bacterial DNA Research Progress(Nucleoid Architecture and Dynamics in Bacteria.)(eds.Frank Columbus and Lauren Perl.)2009

    • Author(s)
      Ohniwa R.L., K.Morikawa, Ohta T., Wada C., Takeyasu K.
    • Publisher
      NOVA Publishers.
  • [Book] )Chromatin and Disease(Structural organization of dynamic chromatin.)(eds.T.K.Kundu.D.Dipak )(Subsellular Biochemistry series Vol. 41)2007

    • Author(s)
      Hizume K, Yoshimura S.H, Kumeta M, Takeyasu K.
    • Total Pages
      3-28
    • Publisher
      SpringerVerlag.
  • [Book] Biopolymer Research Trends(Biochemical and biophysical basis of genome folding mechanisms.)(ed.Pablo C.Sanchez.)2007

    • Author(s)
      Kobori T, Hizume K, Ohniwa R.L, Yoshimura S.H, Takeyasu K.
    • Total Pages
      107-135
    • Publisher
      Nova Science Publishers.

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Published: 2012-01-26   Modified: 2016-04-21  

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