BDR researchers coming from diverse research fields are working together to achieve higher goals.

Seminars & Symposia

Seminars & Symposia

BDR hosts annual symposium and regular seminars inviting international scientists in life science.

Careers & Study

Careers & Study

BDR embraces people from diverse backgrounds, and strives to create an open and supportive setting for research.



BDR communicates the appeal and significance of our research to society through the use of various media and activities.



From research, events, people and everything in between, find out what’s going on at RIKEN BDR.

About Us

About Us

Exploring the scientific foundations of life through interdisciplinary approaches to address society’s problems.

Photo of Team leder, Shun-ichi Sekine

Team Leader
Shun-ichi Sekine Ph.D.

Laboratory for Transcription Structural Biology



Please replace [at] with @.

Recruiting graduate students

Shedding light on molecular mechanisms underlying biological functions

Life activities are supported by numerous biomolecules, which communicate with each other and constitute huge assemblies to fulfill diverse cellular needs. In order to visualize their architecture and elucidate their action mechanisms, our team analyzes their 3D structures by cryo-electron microscopy and X-ray crystallography. Our main focus is on huge complexes such as complexes of RNA polymerase and transcription factors, and we unravel molecular mechanisms behind various important biological phenomena. Furthermore, viral or bacterial proteins involved in replication and/or transcription are one of the major drug targets, and our team provides the structural foundations for the drug discovery research.

Research Theme

  • Structural bases of transcription and its-related phenomena
  • Advancement of technologies for the structural analyses of supramolecular complexes
  • Structural basis of viral and bacterial replication/transcription toward drug discovery

Selected Publications

Sekine S, Ehara H, Kujirai T, et al.
Structural perspectives on transcription in chromatin
Trends in Cell Biology (2023) doi: 10.1016/j.tcb.2023.07.011

Osawa T, Aoki M, Ehara H, et al.
Structures of dengue virus RNA replicase complexes
Molecular Cell (2023) doi: 10.1016/j.molcel.2023.06.023

Murayama Y, Ehara H, Aoki M, et al.
Structural basis of the transcription termination factor Rho engagement with transcribing RNA polymerase from Thermus thermophilus
Science Advances 9(6), eade7093 (2023) doi: 10.1126/sciadv.ade7093

Hirano R, Ehara H, Kujirai T, et al.
Structural basis of RNA polymerase II transcription on the chromatosome containing linker histone H1
Nature Communications 13, 7287 (2022) doi: 10.1038/s41467-022-35003-z

Ehara H, Kujirai T, et al.
Structural basis of nucleosome disassembly and reassembly by RNAPII elongation complex with FACT
Science 377(6611), abp9466 (2022) doi: 10.1126/science.abp9466

Sekine S, Uejima T, Ehara H.
RNA Polymerase-associated Transcription Elongation Factors
RNA Polymerases as Molecular Motors 2nd ed, Chapter 4 (2021) doi: 10.1039/9781839160561-00072

Ehara H, Kujirai T, et al.
Structural insight into nucleosome transcription by RNA polymerase II with elongation factors.
Science 363(6428), 744-747 (2019) doi: 10.1126/science.aav8912

Shimizu H, Saito A, Mikuni J, et al.
Discovery of a small molecule inhibitor targeting dengue virus NS5 RNA-dependent RNA polymerase.
Plos Neglected Tropical Diseases 13(11), e0007894 (2019) doi: 10.1371/journal.pntd.0007894

Kujirai T, Ehara H, et al.
Structural basis of the nucleosome transition during RNA polymerase II passage.
Science 362(6414), 595-598 (2018) doi: 10.1126/science.aau9904

Ooi WY, Murayama Y, Mekler V, et al.
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 (2017) doi: 10.1093/nar/gkx1162

Ehara H, Yokoyama T, Shigematsu H, et al.
Structure of the complete elongation complex of RNA polymerase II with basal factors.
Science 357(6354), 921-924 (2017) doi: 10.1126/science.aan8552

Sekine S, Murayama Y, Svetlov V, et al.
Ratcheting of RNA polymerase toward structural principles of RNA polymerase operations.
Transcription 6(3), 56-60 (2015) doi: 10.1080/21541264.2015.1059922

Sekine S, Murayama Y, Svetlov V, et al.
The ratcheted and ratchetable structural states of RNA polymerase underlie multiple transcriptional functions.
Molecular Cell 57(3), 408-421 (2015) doi: 10.1016/j.molcel.2014.12.014

Tagami S, Sekine S, Minakhin L, et al.
Structural basis for promoter specificity switching of RNA polymerase by a phage factor.
Genes & Development 28(5), 521-531 (2014) doi: 10.1101/gad.233916.113

Tagami S, Sekine S, Kumarevel T, et al.
Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein.
Nature 468(7326), 978-982 (2010) doi: 10.1038/nature09573


Photo of team leader, Shun-ichi Sekine

Team LeaderShun-ichi Sekine

Shun-ichi Sekine

Team Leader

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