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RIKEN Center for Biosystems Dynamics Research Laboratory for Transcription Structural Biology

Team Leader: Shun-ichi Sekine (Ph.D.)

Research Summary

Shun-ichi  Sekine(Ph.D.)

We conduct structural biology studies to unravel action mechanisms of cellular macromolecular systems comprising cellular macromolecules, including transcription complexes of RNA polymerases bound with cellular components. To this end, we will develop a technology platform for the supramolecular structure analysis, with methods for preparation of biologically significant macromolecular complexes and structure analyses by taking advantage of SPring-8/SACLA, cryo-electronmicroscopy, etc.

Related Research Fields

  • Biology


  • Transcription
  • RNA polymerase
  • Virus
  • Cryo-electron microscopy
  • X-ray crystallography

Selected Publications

  • 1.Ehara, H., Kujirai, T., Fujino, Y., Shirouzu, M., Kurumizaka, H., and Sekine, S.:
    “Structural insight into nucleosome transcription by RNA polymerase II with elongation factors.”
    Science 363(6428), 744-747. (2019)
  • 2.Kujirai, T., Ehara, H., Fujino, Y., Shirouzu, M., Sekine, S., and Kurumizaka, H.;
    “Structural basis of the nucleosome transition during RNA polymerase II passage.”
    Science 362(6414), 595-598. (2018)
  • 3.Ooi, WY., Murayama, Y., Mekler, V., Minakhin, L., Severinov, K., Yokoyama, S., and Sekine, S.:
    “A Thermus phage protein inhibits host RNA polymerase by preventing template DNA strand loading during open promoter complex formation.”
    Nucleic Acids Research 46(1), 431-441. (2018)
  • 4.Ehara, H., Yokoyama, T., Shigematsu, H., Yokoyama, S., Shirouzu, M., and Sekine, S.:
    “Structure of the complete elongation complex of RNA polymerase II with basal factors.”
    Science 357(6354), 921-924. (2017)
  • 5.Shimizu, H., Miyazaki, H., Ohsawa, N., Shoji, S., Ishizuka-Katsura, Y., Tosaki, A., Oyama, F., Terada, T., Sakamoto, K., Shirouzu, M., Sekine, S., Nukina, N., and Yokoyama, S.:
    “Structure-based site-directed photo-crosslinking analyses of multimeric cell-adhesive interactions of voltage-gated sodium channel β subunits.”
    Scientific Reports 6, 26618. (2016)
  • 6.Sekine, S., Murayama, Y., Svetlov, V., Nudler, E., and Yokoyama, S.:
    “The ratcheted and ratchetable structural states of RNA polymerase underlie multiple transcriptional functions.”
    Molecular Cell 57(3), 408-421. (2015)
  • 7.Naganuma, M., Sekine, S., Chong, Y.E., Guo, M., Yang, X.L., Gamper, H., Hou, Y.M., Schimmel, P., and Yokoyama, S.:
    “The selective tRNA aminoacylation mechanism based on a single G·U pair.”
    Nature 510(7506), 507-511. (2014)
  • 8.Tagami, S., Sekine, S., Minakhin, L., Esyunina, D., Akasaka, R., Shirouzu, M., Kulbachinskiy, A., Severinov, K., and Yokoyama, S.:
    “Structural basis for promoter specificity switching of RNA polymerase by a phage factor.”
    Genes & Development 28(5), 521-531. (2014)
  • 9.Itoh, Y, Brocker, MJ, Sekine, S, Hammond, G., Suetsugu, S., Sol,l D., and Yokoyama, S.:
    “Decameric SelA·tRNASec Ring Structure Reveals Mechanism of Bacterial Selenocysteine Formation.”
    Science 340(6128), 75-78. (2013)
  • 10.Tagami, S., Sekine, S., Kumarevel, T., Hino, N., Murayama, Y., Kamegamori, S., Yamamoto, M., Sakamoto, K., and Yokoyama, S.:
    “Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein.”
    Nature 468(7326), 978-982. (2010)

Recent Research Results

Related Links

Lab Members

Principal investigator

Shun-ichi Sekine
Team Leader

Core members

Kumarevel Thirumananseri
Senior Research Scientist
Haruhiko Ehara
Senior Scientist
Takuo Osawa
Research Scientist
Tatsuo Yanagisawa
Research Scientist
Masahiro Naganuma
Research Scientist
Yuko Murayama
Senior Technical Staff
Mie Goto
Technical Staff I
Mari Aoki
Technical Staff I
Masami Henmi
Technical Staff II
Tomoko Kudo

Contact Information

1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
Tel: +81-(0)45-503-9257
Fax: +81-(0)45-503-9201
Email: shunichi.sekine [at] riken.jp