Team Director
Shun-ichi Sekine Ph.D.

Laboratory for Transcription Structural Biology

[Affiliation has changed to RIKEN Center for Integrated Medical Sciences (IMS) as of April 2025]

E-mailshunichi.sekine@riken.jp

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.

https://doi.org/10.1126/science.abp9466

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

Naganuma M, Kujirai T, Ehara H, et al.
Structural insights into promoter-proximal pausing of RNA polymerase II at +1 nucleosome.
Science Advances 11(10), eadu0577 (2025) doi: 10.1126/sciadv.adu0577

Yanagisawa T, Murayama Y, Ehara H, et al.
Structural basis of eukaryotic transcription termination by the Rat1 exonuclease complex
Nature Communications 15, 7854 (2024) doi: 10.1038/s41467-024-52157-0

Akatsu M, Ehara H, Kujirai T, et al.
Cryo-EM structures of RNA polymerase II-nucleosome complexes rewrapping transcribed DNA
J Biol Chem 299(12), 105477 (2023) doi: 10.1016/j.jbc.2023.105477

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

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.
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