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Publication

2021-

  • Bayer KV, Taeb M, Koch B, Yoshimura SH, and Wombacher R. (2025) "Dual SLIPT-A lipid mimic to enable spatiotemporally defined, sequential protein dimerization" ACS Chem. Biol., in press

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  • Kumeta M, Otani M, Toyoda M, Yoshimura SH. (2025) "Acoustic modulation of mechanosensitive genes and adipocyte differentiation" Commun. Biol., 595(8)

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  • Fujiwara K, Inoue T, Kimoto A, Zixian J, Tokuhiro K, Yasukochi Y, Akama TO, Cai CL, Shiojima I, Kimura H, Yoshimura SH, Nakamura T, Hirai M. (2024) "Spatial organizations of heterochromatin underpin nuclear structural integrity of ventricular cardiomyocytes against mechanical stress" Cell Reports, 43(12): 115048

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  • Ju H, Skibbe H, Fukui M, Yoshimura SH, Honda N. (2024) "Machine learning-guided reconstruction of cytoskeleton network from Live-cell AFM Images." iScience, 27(10): 110907

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  • Yi B, Tanaka YL, Cornish D, Kosako H, Butlertanaka EP, Sengupta P, Lippincott-Schwartz J, Hultquist JF, Saito A, Yoshimura SH. (2024) "Host ZCCHC3 blocks HIV-1 infection and production through a dual mechanism" iScience, vol. 7, 109107

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  • Zhang Y, Kitagawa T, Furutani-Seiki M, Yoshimura SH. (2023) "Yes-associated protein regulates cortical actin architecture and dynamics through intracellular translocation of Rho GTPase-activating protein 18" FASEB J., 37(9): e23161

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  • Yu Y, Yoshimura SH. (2023) "Self-assembly of CIP4 drives actin-mediated asymmetric pit-closing in clathrin-mediated endocytosis" Nat. Commun., 14: 4602

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  • Im JH, Duic I, Yoshimura SH, Onomoto K, Yoneyama M, Kato H, Fujita T. (2023) "Mechanisms of length-dependent recognition of viral double-stranded RNA by RIG-I" Sci. Rep., 13(1): 6318

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  • Ju H, Honda N, Yoshimura SH, Kaneko M, Shigematsu T, Kiyono K. (2023) "Multidimensional fractal scaling analysis using higher order moving average polynomials and its fast algorithm" J. Signal Processing, in press

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  • Khalil B, Chhangani D, Wren MC, Smith CL, Lee JH, Li X, Puttinger C, Tsai C, Fortin G, Morderer D, Gao J, Liu F, Lim CK, Chen J, Chou C, Croft CL, Gleixner AM, Donnelly CJ, Golde TE, Petrucelli L, Oskarsson B, Dickson DW, Zhang K, Shorter J, Yoshimura SH, Barmada SJ, Rincon-Limas DE, Rossoll W. (2022) "Nuclear import receptors are recruited by FG-nucleoporins to rescue hallmarks of TDP-43 proteinopathy" Mol. Neurodeg., 17(1): 80

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  • Yamazaki H, Takagi M, Kosako H, Hirano T, Yoshimura SH. (2022) "Cell cycle-specific phase separation regulated by protein charge blockiness" Nat. Cell Biol., 24(5): 625-632

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  • Maarof ND, Kumeta M, Yoshimura SH. (2021) "Modulation of actin-binding and -bundling activities of MISP/Caprice by multiple phosphorylation" B. B. R. C., 561: 128-135

2016-2020

  • Zhang W, Watanabe R, Konishi HA, Fujiwara T, Yoshimura SH, Kumeta M. (2020) "Redox-sensitive cysteines confer proximal control of the molecular crowding barrier in the nuclear pore" Cell Rep., 33(11): 108484

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  • Yamaguchi I, Yoshimura SH, Katoh H. (2020) "High cell density increases glioblastoma cell viability under glucose deprivation via degradation of the cystine/glutamate transporter xCT (SLC7A11)" J. Biol. Chem., 295(20): 6936-6945

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  • Konishi HA, Yoshimura SH. (2019) "Interactions between non-structured domains of FG- and non-FG-nucleoporins coordinate the ordered assembly of the nuclear pore complex in mitosis" FASEB Journal, 34(1): 1532-1545

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  • Fumoto K, Takigawa-Imamura H, Sumiyama K, Yoshimura SH, Maehara N, Kikuchi A. (2019) "Mark1 regulates distal airspace expansion through type I pneumocyte flattening in lung development" J. Cell Sci., 132(24): jcs235556

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  • Yamazaki H, Kosako H, Yoshimura SH. (2019) "Quantitative proteomics indicate a strong correlation of mitotic phospho-/dephosphorylation with non-structured regions of substrates" B. B. A. Proteins Proteom., 1868(1): 140295

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  • Nishimura K, Johmura Y, Deguchi K, Jiang Z, Uchida K, Suzuki N, Shimada M, Chiba Y, Hirota T, Yoshimura SH, Kono K, Nakanishi M. (2019) "Cdk1-mediated DIAPH1 phosphorylation maintains metaphase cortical tension and inactivates the spindle assembly checkpoint at anaphase" Nat. Commun., 10(1): 981

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  • Yoshida A, Sakai N, Uekusa Y, Imaoka Y, Itagaki Y, Suzuki Y, Yoshimura SH. (2018) "Morphological changes of plasma membrane and protein assembly during clathrin-mediated endocytosis" PLOS Biology, 16(5): e2004786

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  • Kumeta M, Panina Y, Yamazaki H, Takeyasu K, Yoshimura SH. (2018) "N-terminal dual lipidation-coupled molecular targeting into the primary cilium" Genes Cells, 23(8): 715-723

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  • Kumeta M, Takahashi D, Takeyasu K, Yoshimura SH. (2018) "Cell type-specific suppression of mechanosensitive genes by audible sound stimulation" PLOS ONE, 13(1): e0188764

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  • Kumeta M, Konishi HA, Zhang W, Sakagami S, Yoshimura SH. (2017) "Prolines in the α-helix confer the structural flexibility and functional integrity of importin β" J. Cell Sci., 131(1): jcs.206326

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  • Konishi HA, Asai S, Watanabe TM, and Yoshimura SH. (2017) "In vivo analysis of protein crowding within the nuclear pore complex in interphase and mitosis" Sci. Rep., 7: 5709 [Top 100 Scientific Reports cell biology papers in 2017]

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  • Zhang Y, Yoshida A, Sakai N, Uekusa Y, Kumeta M, Yoshimura SH. (2017) "In vivo dynamics of the cortical actin network revealed by fast-scanning atomic force microscopy" Microscopy, 20: 1-11 [Editor's Choice] [The Japanese Society of Microscopy Award for the Scientific Paper 2019]

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  • Yoshimura SH, Hirano T. (2016) "HEAT repeats – versatile arrays of amphiphilic helices working in crowded environments?" J. Cell Sci., 129(21): 3963-3970

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  • Shrivastava G, Hyodo M, Yoshimura SH, Akita H, Harashima H. (2016) "Identification of a Nucleoporin358-Specific RNA Aptamer for Use as a Nucleus-Targeting Liposomal Delivery System" Nucleic Acid Therapeutics, 26(5): 286-298

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  • Lolodi O, Yamazaki H, Otsuka S, Kumeta M, Yoshimura SH. (2016) "Dissecting in vivo steady-state dynamics of karyopherin-dependent nuclear transport" Mol. Biol. Cell, 27(1): 167-176

2011-2015

  • Yoshimura SH, Kumeta M, Takeyasu K. (2014) "Structural mechanism of nuclear transport mediated by importin β and flexible amphiphilic proteins" Structure, 22(12): 1699-1710

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  • Sotoma S, Yoshinari Y, Igarashi R, Yamazaki A, Yoshimura SH, Tochio H, Shirakawa M, Harada Y. (2014) "Effective production of fluorescent nanodiamonds containing negatively-charged nitrogen-vacancy centers by ion irradiation" Diam. Relat. Mater., 49: 33-38

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  • Kumeta M, Hirai Y, Yoshimura SH, Horigome T, Takeyasu K. (2013) "Antibody-based analysis reveals 'filamentous vs. non-filamentous' and 'cytoplasmic vs. nuclear' crosstalk of cytoskeletal proteins" Exp. Cell Res., 319(20): 3226-3237

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  • Yoshimura SH, Otsuka S, Kumeta M, Taga M, Takeyasu K. (2013) "Intermolecular disulfide bonds among nucleoporins regulate karyopherin-dependent nuclear transport" J. Cell Sci., 126(Pt 14): 3141-3150

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  • Suzuki Y, Goetze TA, Stroebel D, Balasuriya D, Yoshimura SH, Henderson RM, Paoletti P, Takeyasu K, Edwardson JM. (2013) "Visualization of structural changes accompanying activation of N-methyl-D-aspartate (NMDA) receptors using fast-scan atomic force microscopy imaging" J. Biol. Chem., 288(2): 778-784

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  • Prieto E, Hizume K, Kobori T, Yoshimura SH, Takeyasu K. (2012) "Core histone charge and linker histone H1 effects on the chromatin structure of Schizosaccharomyces pombe" Biosci. Biotechnol. Biochem., 76(12): 2261-2266

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  • Kumeta M, Yamaguchi H, Yoshimura SH, Takeyasu K. (2012) "Karyopherin-independent spontaneous transport of amphiphilic proteins through the nuclear pore" J. Cell Sci., 125(Pt 21): 4979-4984

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  • Suzuki Y, Shin M, Yoshida A, Yoshimura SH, Takeyasu K. (2012) "Fast microscopical dissection of action scenes played by Escherichia coli RNA polymerase" FEBS Lett., 586(19): 3187-3192

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  • Yoshimura SH, Khan S, Ohno S, Yokogawa T, Nishikawa K, Hosoya T, Maruyama H, Nakayama Y, Takeyasu K. (2012) "Site-specific attachment of a protein to a carbon nanotube end without loss of protein function" Bioconjug. Chem., 23(7): 1488-1493

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  • Kumeta M, Yoshimura SH, Hejna J, Takeyasu K. (2012) "Nucleocytoplasmic shuttling of cytoskeletal proteins: molecular mechanism and biological significance" Int. J. Cell Biol., 2012: 494902

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  • Akai Y, Kurokawa Y, Nakazawa N, Tonami-Murakami Y, Suzuki Y, Yoshimura SH, Iwasaki H, Shiroiwa Y, Nakamura T, Shibata E, Yanagida M. (2011) "Opposing role of condensin hinge against replication protein A in mitosis and interphase through promoting DNA annealing" Open Biol., 1(4): 110023

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  • Yoshimura SH, Khan S, Maruyama H, Nakayama Y, Takeyasu K. (2011) "Fluorescence labeling of carbon nanotubes and visualization of a nanotube-protein hybrid under fluorescence microscope" Biomacromolecules, 12(4): 1200-1204

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  • Ohno H, Kobayashi T, Kabata R, Endo K, Iwasa T, Yoshimura SH, Takeyasu K, Inoue T, Saito H. (2011) "Synthetic RNA-protein complex shaped like an equilateral triangle" Nat. Nanotechnol., 6(2): 116-120

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  • Asally M, Yasuda Y, Oka M, Otsuka S, Yoshimura SH, Takeyasu K, Yoneda Y. (2011) "Nup358, a nucleoporin, functions as a key determinant of the nuclear pore complex structure remodeling during skeletal myogenesis" FEBS J., 278(4): 610-621

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  • Maruyama H, Shin M, Oda T, Matsumi R, Ohniwa RL, Itoh T, Shirahige K, Imanaka T, Atomi H, Yoshimura SH, Takeyasu K. (2011) "Histone and TK0471/TrmBL2 form a novel heterogeneous genome architecture in the hyperthermophilic archaeon Thermococcus kodakarensis" Mol. Biol. Cell, 22(3): 386-398

2006-2010

  • Teramoto J, Yoshimura SH, Takeyasu K, Ishihama A. (2010) "A novel nucleoid protein of Escherichia coli induced under anaerobiotic growth conditions" Nucleic Acids Res., 38(11): 3605-3618

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  • Suzuki Y, Higuchi Y, Hizume K, Yokokawa M, Yoshimura SH, Yoshikawa K, Takeyasu K. (2010) "Molecular Dynamics of DNA and Nucleosomes in Solution Studied by Fast-scanning Atomic Force Microscopy" Ultramicroscopy, 110(6): 682-688

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  • Kumeta M, Yoshimura SH, Harata M, Takeyasu K. (2010) "Molecular mechanisms underlying nucleocytoplasmic shuttling of actinin-4" J. Cell Sci., 123(Pt 7): 1020-1030

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  • Otsuka S, Iwasaka S, Yoneda Y, Takahashi H, Takeyasu K, Yoshimura SH. (2008) "Individual binding pockets of importin beta for FG-nucleoporins have different binding properties and different sensitivities to RanGTP" Proc. Natl. Acad. Sci. USA, 105: 16101-16106

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  • Yokokawa M, Takeyasu K, Yoshimura SH. (2008) "Mechanical properties of plasma membrane and nuclear envelope measured by scanning probe microscope" J. Microscopy, 232: 82-90

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  • Yoshimura SH, Iwasaka S, Schwarz W, Takeyasu K. (2008) "Fast degradation of the auxiliary subunits of Na/K-ATPase in the plasma membrane of HeLa cells" J. Cell Sci., 121: 2159-2168

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  • Wen J, Lancaster L, Hodges C, Zeri A, Yoshimura SH, Noller HF, Bustamante C, Tinoco I. (2008) "Following translation by single ribosomes one codon at a time" Nature, 452: 598-603

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  • Hirano Y, Takahashi H, Kumeta M, Hizume K, Hirai Y, Otsuka S, Yoshimura SH, Takeyasu K. (2008) "Nuclear Architectures and Chromatin Dynamics Revealed by Atomic Force Microscopy in Combination with Biochemistry and Cell Biology" Eur. J. Physiol., 456: 139-153

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  • Sanchez H, Cardenas PP, Yoshimura SH, Takeyasu K, Alonso JC. (2008) "Dynamic structures of Bacillus subtilis RecN-DNA complexes" Nucleic Acids Res., 36(1): 110-120

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  • Crampton N, Yokokawa M, Dryden DT, Edwardson JM, Rao DN, Takeyasu K, Yoshimura SH, Henderson RM. (2007) "Fast-scan atomic force microscopy reveals that the type III restriction enzyme EcoP15I is capable of DNA translocation and looping" Proc. Natl. Acad. Sci. USA, 104: 12755-12760

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  • Liu D, Ge L, Wang F, Takahashi H, Wang D, Guo A, Yoshimura SH, Ward T, Ding X, Takeyasu K, Yao X. (2007) "Single-molecule detection of phosphorylation-induced plasticity changes during ezrin activation" FEBS Lett., 581: 3563-3571

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  • Ohniwa RL, Morikawa K, Kim J, Kobori T, Hizume K, Matsumi R, Atomi H, Imanaka T, Ohta T, Yoshimura SH, Takeyasu K. (2007) "Atomic force microscopy dissects the hierarchy of genome architectures in eukaryote, prokaryote and chloroplast" Microscopy and Microanalysis, 13: 3-12

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  • Maruyama H, Yoshimura SH, Akita S, Nagataki A, Nakayama Y. (2007) "Covalent attachment of protein to the tip of a multiwalled carbon nanotube without sidewall decoration" J. Appl. Phys., 102: 094701

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  • Hirano Y, Ohniwa RL, Wada C, Yoshimura SH, Takeyasu K. (2006) "Human small G proteins, ObgH1 and ObgH2, participate in the maintenance of mitochondria and nucleolar architectures" Genes Cells, 11: 1295-1304

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  • Yokokawa M, Yoshimura SH, Naito Y, Ando T, Yagi A, Sakai N, Takeyasu K. (2006) "Fast-scanning atomic force microscopy revealed the molecular mechanism of DNA cleavage by ApaI endonuclease" IEE Proc. Nanobiotechnology, 153: 60-66

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  • Yoshimura SH, Takahashi H, Ohtsuka S, Takeyasu K. (2006) "Development of glutathione-coupled cantilever for the single-molecule force measurement by scanning force microscopy" FEBS Lett., 580: 3961-3965

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  • Kobori T, Kodama M, Hizume K, Yoshimura SH, Ohtani T, Takeyasu K. (2006) "Comparative structural biology of the genome: Nano-scale imaging of single nucleus from different kingdoms reveals the chromatin built up on a 40 nm structural unit" J. Electron Microscopy, 55: 31-40

2001-2005

  • Nakai T, Hizume K, Yoshimura SH, Takeyasu K, Yoshikawa K. (2005) "Phase transition in reconstituted chromatin" Europhysics Lett., 69(6): 1024-1030

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  • Hizume K, Yoshimura SH, Takeyasu K. (2005) "Linker histone H1 per se can induce three-dimensional folding of chromatin fiber" Biochemistry, 44: 12978-12989

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  • Kim J, Yoshimura SH, Hizume K, Ishihama A, Takeyasu K. (2004) "Fundamental structural unit of the Escherichia coli nucleoid revealed by atomic force microscopy" Nucleic Acid Res., 32: 1982-1992

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  • Yoshimura SH, Maruyama H, Ishikawa F, Ohki R, Takeyasu K. (2004) "Molecular mechanisms of DNA end-loop formation by TRF2" Genes Cells, 9: 205-218

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  • Hizume K, Yoshimura SH, Takeyasu K. (2004) "Atomic force microscopy demonstrates a critical role of DNA superhelicity in the nucleosome dynamics" Cell Biochem. Biophy., 40: 249-262

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  • Takeyasu K, Kim J, Ohniwa RL, Kobori T, Inose Y, Morikawa K, Ohta T, Ishihama A, Yoshimura SH. (2004) "Genome architecture studied by nano-scale imaging: Analyses among bacterial phyla and their implication to eukaryotic genome folding" Cytogenet Genomes Res, 107: 38-48

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  • Ito K, Toyoda I, Higashiyama M, Uemura D, Sato M, Yoshimura SH, Ishii T, Takeyasu K. (2003) "Channel induction by palytoxin in yeast cells expressing Na+,K+-ATPase or its chimera with sarco/endoplasmic reticulum Ca2+-ATPase" FEBS Lett., 543: 108-112

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  • Yoshimura SH, Kim J, Takeyasu K. (2003) "On-substrate lysis treatment combined with the scanning probe microscopy revealed chromosome structures in eukaryotes and prokaryotes" J. Electron Microscopy, 52: 415-423

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  • Hizume K, Yoshimura SH, Maruyama H, Kim J, Wada H, Takeyasu K. (2002) "Chromatin reconstitution: development of a salt-dialysis method monitored by nano-technology" Arch. Histol. Cytol., 65: 405-413

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  • Uemura T, Yoshimura SH, Takeyasu K, Sato MH. (2002) "Vacuolar Membrane Dynamics Revealed by GFP-AtVam3 Fusion Protein" Genes Cells, 7: 743-753

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  • Yoshimura SH, Hizume K, Murakami A, Sutani T, Takeyasu K, Yanagida M. (2002) "Condensin Architecture and Interaction with DNA: Regulatory Non-SMC Subunits Bind to the Head of SMC Heterodimer" Curr. Bio., 12: 508-512

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  • Sakaue S, Yoshikawa K, Yoshimura SH, Takeyasu K. (2001) "Histone Core Slips along DNA and Prefers Positioning at the Chain End" Phys. Rev. Lett., 87: 078105-1 – 4

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  • Takeyasu K, Okamura H, Ogita Y, Yoshimura SH. (2001) "P-type ATPase Diversity and Evolution: The origins of ouabain-sensitivity and subunit assembly" Cell. Mol. Biol., 47: 325-333

1995-2000

  • Yoshimura SH, Ohniwa RL, Sato MH, Matsunaga F, Kobayashi G, Uga H, Wada C, Takeyasu K. (2000) "DNA phase transition promoted by replication initiator" Biochemistry, 39: 9139-9145

     

  • Hohmura KI, Itokazu Y, Yoshimura SH, Mizuguchi G, Masamura Y, Takeyasu K, Shiomi Y, Tsurimoto T, Nishijima H, Akita S, Nakayama Y. (2000) "AFM with carbon nanotube resolve the subunit organization of protein complexes" J. Electron Microscopy, 49: 415-421

     

  • Yoshimura SH, Yoshida C, Igarashi K, Takeyasu K. (2000) "AFM proposes a 'Kiss and Pull' mechanism for enhancer function" J. Electron Microscopy, 49: 407-413

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