RIKEN Center for Integrative Medical Sciences Laboratory for Transcription Structural Biology

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

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Research Summary

Transcription is a fundamental process that underpins virtually all biological activities. In cells, transcription machinery interacts with numerous biomolecules, forming various high-order complexes, which not only facilitate transcription, but also serve as hubs for a wide range of cellular functions. To visualize these complexes and elucidate their action mechanisms, our team employs structural biology approach, in particular cryo-electron microscopy. Our research focus is on transcription regulation in chromatin and its crosstalk with various essential biological phenomena. In parallel, we also investigate the mechanisms of viral replication/transcription and viral-host interactions to provide structural foundations for drug discovery research.

Related Research Fields

Biology

Keywords

Transcription
RNA polymerase
Chromatin
Virus
Cryo-electron microscopy

Selected Publications

1. Kujirai, T., Ehara, H., Ito, T., Henmi, M., Oya, E., Kobayashi, T., Sekine, S. and Kurumizaka, H.
"Structural basis of transcription-coupled H3K36 trimethylation by Set2 in coordination with FACT."
Sci. Adv. 12, eaed1952. (2026). doi: 10.1126/sciadv.aed1952
2. Sekine, S.
"Toward structural understanding of eukaryotic transcription elongation."
Proc. Jpn Acad. Ser. B Phys. Biol. Sci. 101, 414-430. (2025). doi: 10.2183/pjab.101.024
3. Naganuma, M., Kujirai, T., Ehara, H., Uejima, T., Ito, T., Goto, M., Aoki, M., Henmi, M., Miyamoto-Kohno, S., Shirouzu, M., Kurumizaka, H. and Sekine, S.
"Structural insights into promoter-proximal pausing of RNA polymerase II at +1 nucleosome."
Sci Adv. 11, adu0577. (2025). doi: 10.1126/sciadv.adu0577
4. Yanagisawa, T., Murayama, Y., Ehara, H., Goto, M., Aoki, M. and Sekine, S.
"Structural basis of eukaryotic transcription termination by the Rat1 exonuclease complex."
Nat. Commun. 15, 7854. (2024). doi: 10.1038/s41467-024-52157-0
5. Osawa, T., Aoki, M., Ehara, H. and Sekine, S.
"Structures of dengue virus RNA replicase complexes."
Mol. Cell 83, 2781-2791. (2023). doi: 10.1016/j.molcel.2023.06.023
6. Murayama, Y., Ehara, H., Aoki, M., Goto, M., Yokoyama, T. and Sekine, S.
"Structural basis of the transcription termination factor Rho engagement with transcribing RNA polymerase from Thermus thermophilus."
Sci. Adv. 9, eade7093. (2023). doi: 10.1126/sciadv.ade7093
7. Ehara, H., Kujirai, T., Shirouzu, M., Kurumizaka, H. and Sekine, S.
"Structural basis of nucleosome disassembly and reassembly by RNAPII elongation complex with FACT."
Science 377, eabp9466. (2022). doi: 10.1126/science.abp9466
8. 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, 744-747. (2019). doi: 10.1126/science.aav8912
9. 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, 595-598. (2018). doi: 10.1126/science.aau9904
10. 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, 921-924. (2017). doi: 10.1126/science.aan8552