Makio Tokunaga
Makio Tokunaga

Makio Tokunaga

Professor, Department of Biological Information
PhD 1987, Tokyo University
E-mail: mtoku(at)bio.titech.ac.jp
Office: Room 511, B1 building, Suzukakedai campus

Areas of Research: Biophysics, Microscopy, Cell biology

Keywords: Single-molecule imaging, Transcription, Chromatin-remodeling, Super-resolution microscopy

Research interest:

Based on emerging techniques in molecular imaging, our long-term goal is the understanding of transcriptional regulation related to cell signaling. To achieve this goal we quantify the interactions of signaling molecules, transcriptional regulators and chromatin.

Integrated quantitative analysis of molecular dynamics and interactions

Many research programs focus on the molecular dynamics of living cells. This research requires not only visualizing indivicual molecules but also quantifing molecular dynamics and interacions. Thanks to development of better fluorescent labeling techniques of bio-molecules in living cells, the target of imaging analysis is being expanded in its spatio-temporal resolution. For example, photo-activatable GFP variants enable labeling of a limited number of the proteins, an approach that yields super-resolution images of two different protein molecules. We are developing an integrated method for quantitative analysis of molecular dynamics and interactions, combining multiple methods of microscopy. Integrated use of multi-color single-molecule imaging, single molecule tracking, super-resolution microscopy, fluorescence recovery after photobleaching (FRAP) and/or fluorescence cross-correlation spectroscopy (FCCS) provides a means to obtain new kind of spatio-temporal or kinetic parameters on molecular dynamics and interactions.

Dynamic chromatin structure and function to understand fundamentals of life

Why a great variety of functions and structures is accomplished using the same genes is one of the most important subjects in the life science. Chromatin, a molecular structure storing genetic information composed of DNA and proteins, plays a vital role in not only genetic activities and biological functions. Recent studies revealed that its structure is not invariable but spatio-temporally varying in response to functions. This dynamic structural change of the chromatin is the very thing that is the basis of the biological functions and activities.

We are now focusing on elucidating this subject on the relation with signal transduction, transcription regulation, chromatin remodeling using molecular imaging and quantitative analysis.

Selected publications

  1. Ito Y, Sakata-Sogawa K, Tokunaga M.: A Facile Preparation of Glass-supported Lipid Bilayers for Analyzing Molecular Dynamics.: Anal Sci, 30 (12), 1103-1106, 2014. PMID: 25492457 selected as Hot Article Award
  2. Stasevich TJ, Hayashi-Takanaka Y, Sato Y, Maehara K, Ohkawa Y, Sakata-Sogawa K, Tokunaga M, Nagase T, Nozaki N, McNally JG, Kimura H:: Regulation of RNA polymerase II activation by histone acetylation in single living cells. Nature 516 (7530), 272-275, 2014.
  3. Yokosuka T., Kobayashi W., Takamatsu M., Sakata-Sogawa K., Zeng H., Hashimoto-Tane A., Yagita H., Tokunaga M., Saito T.: Spatiotemporal basis of ctla-4 costimulatory molecule-mediated negative regulation of T cell activation. Immunity 33, (3) 326-339, 2010. PMID: 20870175
  4. Shiina N, Yamaguchi K, Tokunaga M.: RNG105 Deficiency Impairs the Dendritic Localization of mRNAs for Na+/K+ ATPase Subunit Isoforms and Leads to the Degeneration of Neuronal Networks. J. Neuroscience, 30 (38), 12816-12830, 2010. PMID: 20861386
  5. Fukagawa A., Hiroshima M., Sakane I., Tokunaga M.: Stochastic emergence of multiple intermediates detected by single-molecule quasi-static mechanical unfolding of protein., BIOPHISICS 5, 25-35, 2009.
  6. Yokosuka T., Kobayashi W., Sakata-Sogawa K., Takamatsu M., Hashimoto-Tane A., Dustin ML., Tokunaga M., Saito T.: Spatiotemporal regulation of T cell costimulation by TCR-CD28 microclusters and protein kinase C theta translocation. Immunity, 29(4), 589-601, 2008. PMID:18848472
  7. Tokunaga M., Imamoto N., Sakata-Sogawa K.: Highly inclined thin illumination enables clear single-molecule imaging in cells. Nat Methods, 5(2), 159-161, 2008. PMID:18176568
  8. Yamasaki S., Sakata-Sogawa K., Hasegawa A., Suzuki T., Kabu K., Sato E., Kurosaki T., Yamashita S., Tokunaga M., Nishida K., Hirano T.: Zinc is a novel intracellular second messenger. J. Cell. Biol., 177(4), 637-645, 2007. PMID:17502426
  9. Yamasaki S., Ishikawa E., Sakuma M., Ogata K., Sakata-Sogawa K., Hiroshima M., Wiest DL., Tokunaga M., Saito T.: Mechanistic basis of pre-T cell receptor-mediated autonomous signaling critical for thymocyte development. Nat. Immunol., 7(1), 67-75, 2006. PMID:16327787
  10. Shiina N., Shinkura K., Tokunaga M.: A novel RNA-binding protein in neuronal RNA granules: Regulatory machinery for local translation. J.Neuroscience, 25 (17), 4420-4434, 2005.
  11. Yanagida T., Esaki S., Iwane A.H., Inoue Y., Ishijima A., Kitamura K., Tanaka H., Tokunaga M.: Single-motor mechanics and models of the myosin motor. Philos. Trans. R. Soc. Lond. B Biol Sci, 355, 441-447, 2000.
  12. Kitamura K., Tokunaga M., Iwane A. H. & Yanagida T.: A single myosin head moves along an actin filament with regular steps of 5.3 nanometres. Nature, 397, 129-134, 1999.

Kumiko Sakata-Sogawa
Kumiko Sakata-Sogawa

Kumiko Sakata-Sogawa

Associate professor, Department of Biological Information
PhD 2000, Tohoku University
E-mail: ksogawa(at)bio.titech.ac.jp
Office: Room 510, B1 building, Suzukakedai campus

Areas of Research: Biophysics, Immunology, Molecular biology

Keywords: Single-molecule imaging, Transcription, Chromatin-remodeling, Immune response

Research interest:

When cells are subjected to an extracellular signal, a specific receptor on the cell surface is activated. This activation triggers signaling cascades and results in modulation of gene expression in the nucleus, causing a response to the environment. Gene expression is strictly controlled to ensure the cells produce the correct amount of proteins when needed. Transcription is a first step of gene expression, and orchestrated by various protein factors, such as transcription machinery proteins and transcription factors, Chromatin-remodeling is also an important process to regulate transcription by the dynamic modification of chromatin architecture.

Aiming to understand how the transcription factors regulate the function of transcription machinery proteins, we develop single molecule imaging system and observe the events in the nucleus of living cells. We are also interested in the regulation of immune response by transcription factors.

Selected publications

  1. Stasevich TJ, Hayashi-Takanaka Y, Sato Y, Maehara K, Ohkawa Y, Sakata-Sogawa K, Tokunaga M, Nagase T, Nozaki N, McNally JG, and *Kimura H.: Regulation of RNA polymerase II activation by histone acetylation in single living cells. Nature 516, 272–275 (2014)
  2. Ito Y., *Sakata-Sogawa K., *Tokunaga M.: A facile preparation of glass-supported lipid bilayers for analyzing molecular dynamics. Analytical Sciences 30 (12), 1103-1106 (2014)
  3. Yamazaki S., Yamamoto K., Tokunaga M., Sakata-Sogawa K., * Harata M.: Nuclear actin activates human transcription factor genes including the eOCT4 g. Biosci Biotechnol Biochem 2014. Ct 30 1-5. DOI:10.1080/09168451.2014.972332
  4. Asakawa H, Yang HJ, Yamamoto TG, Ohtsuki C, Chikashige Y, Sakata-Sogawa K, Tokunaga M, Iwamoto M, Hiraoka Y, *Haraguchi T: Characterization of nuclear pore complex components in fission yeast Schizosaccharomyces pombe. Nucleus 5 (2) 1-14 (2014)
  5. Hotta K, Nashimoto A., Yasumura E., Suzuki M., Azuma M., Iizumi Y., Shima D., Nabeshima R., Hiramoto M., Okada A., Sakata-Sogawa K., Tokunaga M., Ito T., Ando H., Sakamoto S., Kabe Y., Aizawa S., Imai T., Yamaguchi Y., Watanabe H., *Handa H.: Vesnarinone Suppresses TNFa mRNA Expression by Inhibiting Valosin-containing Protein. Mol Pharmacol, 83, (5) 930-938 (2013)
  6. Hashimoto-Tane A. ,Yokosuka T., Sakata-Sogawa K., Sakuma M., Ishihara C., Tokunaga M., *Saito T.: Dynein-driven transport of T cell receptor microclusters regulates immune synapse formation and T cell activation. Immunity, 34, 919-931 (2011)
  7. Yokosuka T., Kobayashi W., Takamatsu M., Sakata-Sogawa K., Zeng H., Hashimoto-Tane A., Yagita H., Tokunaga M., *Saito T.: Spatiotemporal basis of ctla-4 costimulatory molecule-mediated negative regulation of T cell activation. Immunity 33, (3) 326-339 (2010)
  8. Yokosuka T., Kobayashi W., Sakata-Sogawa K., Takamatsu M., Hashimoto-Tane A., Dustin ML., Tokunaga M., and *Saito T.: Spatiotemporal Regulation of T Cell Costimulation by TCR-CD28 Microclusters and Protein Kinase CθTranslocation. Immunity 29, 589-601 (2008)
  9. *Tokunaga, M., Imamoto, N., Sakata-Sogawa, K.: Highly inclined thin illumination enables clear single-molecule imaging in cells. Nature Methods. 5, (2) 159-161 (2008)
  10. Yamasaki, S., Sakata-Sogawa, K., Hasegawa, A., Suzuki, T., Kabu, K., Sato, E., Kurosaki, T., Yamashita, S., Tokunaga, M., Nishida, K., *Hirano, T.: Zinc is a novel second messenger. J. Cell Biol. 177, 637-645 (2007)
  11. Yamasaki S., Ishikawa, E., Sakuma, M., Ogata, K., Sakata-Sogawa K., Hiroshima, M., Wiest, D. L., Tokunaga M., *Saito, T.: Mechanistic basis of pre-T cell receptor-mediated autonomous signaling critical for thymocyte development. Nature Immunol. 7, 67-75 (2006)
  12. Yokosuka T., Sakata-Sogawa K., Kobayashi, W., Hiroshima, M., Hashimoto-Tane, A., Tokunaga M., Dustin, M. L., *Saito, T.: Newly generated T cell receptor microclusters initiate and sustain T cell activation by recruitment of Zap70 and SLP-76. Nature Immunol. 6, 1253-1262 (2005)
  13. Sakata-Sogawa, K., *Shimamoto, N.: RNA polymerase can track a DNA groove during promoter search. Proc. Natl. Acad. Sci. USA 101(41), 14731-14735 (2004)
  14. *Sakata-Sogawa K, Kurachi M, Sogawa K, Fujii-Kuriyama Y, Tashiro H.: Direct measurement of DNA molecular length in solution using optical tweezers: detection of looping due to binding protein interactions. Eur Biophys J. 27(1):55-61.(1998)


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