Research Topics
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(1) tRNA modification
To date, over 170 modified nucleosides have been identified across various RNA species. tRNA is one of the most heavily modified RNA. On average, each tRNA molecule contains around 13 modifications. These chemical modifications serve diverse functions, including the regulation of transcription and translation, stabilization of tRNA structure, and responses to cellular stress. Understanding how these modifications are introduced into tRNA molecules and how they contribute to tRNA function is therefore essential. To address these questions, we employ a multidisciplinary approach that includes biochemistry, enzymology, high-throughput techniques, RNA mass spectrometry, and bioinformatics.
Projects:
Identification of novel tRNA modifications and their corresponding enzymes
High-throughput detection of RNA modifications using Next-gen sequencing
Elucidation of substrate specificity in tRNAmodification enzymes
Representative publications:
Hedetaka et al, J. Mol. Biol., 2025
Matsuda et al, Nucleic Acids Res., 2025
Yamagami et al, RNA, 2025
Fujita et al, J. Biol. Chem., 2024
Multiple manuscripts in preparation
(2) Quality control of tRNA
It is well known that the quality of cellular RNA is tightly regulated to adapt to changing environmental conditions. For example, RNA expression patterns change dramatically during cellular differentiation. However, how the quality of tRNA is regulated remains unclear. In 2023, we developed a novel method to detect newly synthesized tRNAs by combining metabolic labeling with next-generation sequencing. Using this technique, we aim to understand how tRNA expression is regulated and how tRNA modifications and a cognate amino acid are introduced/charged into newly synthesized tRNAs.
Projects:
Detection of newly synthesized tRNA
Detection of newly installed tRNA modification
Representative publications:
Sugio et al, RNA, 2023
Multiple manuscripts in preparation
(3) RNA structure
RNA is a structurally flexible molecule that can fold into multiple conformations. The dynamic nature of RNA structure plays an important role in regulating RNA maturation processes, such as splicing. Chemical reagents like dimethyl sulfate (DMS) and SHAPE reagents are used to probe RNA structures both in vivo and in vitro. The positions of reactive sites can be identified using next-generation sequencing, allowing for genome-wide RNA structure prediction based on DMS reactivities. In 2022, we developed a novel method to predict in vivo tRNA structures and discovered that even tRNAs—typically considered tightly folded and structurally stable—exhibit structural dynamics under certain conditions, such as heat stress. We are currently investigating how in vivo tRNA structures are regulated and how these structural changes impact protein synthesis.
Projects:
In vivo tRNA structure
Representative publications:
Yamagami et al, PNAS, 2022
Multiple manuscripts in preparation
Who I am
Ryota Yamagami, Ph.D.
I am an assistant professor at Ehime University.
In 2015, I completed my Ph.D. program at the Graduate School of Science and Engineering, Ehime University, under the supervision of Professor Hiroyuki Hori where I studied tRNA modification and tRNA modification enzymes.
After working for one year as a JSPS Postdoctoral Fellow (PD), I joined the Bevilacqua Lab at Pennsylvania State University in the United States in 2016 as a postdoctoral researcher where I studied RNA folding.
After five years of postdoc fellow in the Bevilacqua Lab, I returned to Ehime University in 2021 as a faculty member. In April 2025, our group merged with the Takai Lab in the Graduate School of Science and Engineering, launching the newly established Lab of Biomolecular Engineering.
I have expertises in the analysis of both proteins and RNA. I actively learn and incorporate cutting-edge technologies such as next-generation sequencing and RNA mass spectrometry, aiming to conduct internationally competitive research on the RNA fields. I am interested in how RNA regulates gene expression.
Lab News!
(This website introduces the Yamagami Group, part of the Laboratory of Biomolecular Engineering. For Professor Takai’s lab, please click here.)
Biological Molecular Engineering Lab – NEWS!!
Biological Molecular Engineering Lab – NEWS!!
We’ve launched an Instagram account!
2025
2025
Aug 1 Teppei gave a poster presentation at JCompMS 2025 and won best presentation award! Big congratulations!
July17-18 Shu and Teppei gave oral presentations at Archaea Conference in Gifu!
July08-10 Futa, Soichiro, Sota, and Ryota gave presentations at RNAJ2025 in Sendai!
July 02 Soichiro's paper was accepted in J. Mol. Biol! Big congratulations!!
June 20 Furukawa-san's paper was accepted in Biochimie! Ryota contributed to the paper by conducting tRNA-seq analysis using wheat samples. Congratulations, Furukawa-san!
June 16 Futa conducted experiments in Otsuki lab at Okayama Univ.!
June 9 Futa was selected for a Travel Fellowship for the Annual Meeting of the RNA Society of Japan. Congratulations!
May 20 Teppei's paper was accepted in Nucleic Acids Research! Congratulations!!
April 22 Teppei and Ryota conducted experiments at Tokushima University.
April 4 We’ve updated our lab members page!
April 1 A new academic year has begun! The former Lab of Applied Biochemistry (Hori Lab) has merged with the Laboratory of Chemical Engineering (Takai Lab).
March 25 Shu and Teppei were accepted for the JST SPRING Next Generation Researcher Development Program! Congratulations!
March 24 Shu received the Branch Director’s Award from the Chugoku-Shikoku Branch of the Chemical Society of Japan. Congratulations!
March 24 Graduation ceremony and celebration were held. Congratulations!
March 21 Our paper on TruD substrate specificity was accepted in RNA! Congratulations!
March 14 Teppei was awarded a Sasakawa Scientific Research Grant! Congratulations!
March 7 Prof. Hori gave his final lecture. A retirement celebration was held the following day!
Feb 21 Undergraduate thesis presentations were held—great work, everyone!
Feb 19 Our research proposal was awarded from Nakatani Foundation Research Grant!
Feb 18 Master’s thesis presentations were held. Well-done!
Jan 27 Ryota’s paper was featured on Ehime University’s website as part of the Frontline Research INFINITY series.
Jan 1 Happy New Year! We look forward to 2025!
2024
2024
Dec 13 Our grant proposal was awarded for a Research Grant from the Uehara Memorial Foundation!
Dec 5 Teppei conducted experiments at the Hirata Lab, Tokushima University.
Nov 27–29 At the Annual Meeting of the Molecular Biology Society of Japan, Futa, Soichiro, Sota, Mone, and Kyosuke gave presentations!
Nov 18 We received a Basic Science Research Grant from the Sumitomo Foundation!
Nov 18–22 The 2024 tRNA Conference was held in Kanazawa. Prof. Hori, Teppei, Shu, and Ryota presented their work.
Prof. Hori gave an invited lecture on TrmTS.
Oct 1 Our research proposal was awarded for a Research Grant from the Naito Foundation!
Oct 1 Four third-year undergraduates joined our lab. Let’s do great research together!
Sept 2 Shu’s senryu (comic haiku) won a ThermoFisher Senryu Contest award! Congratulations! His pen name was “Thermococcus Okaneganendesu.”
Aug 9 We hosted hands-on experiments at Ehime University’s Open Campus.
Aug 6 Futa and Ryota conducted experiments at the Otsuki Lab, Okayama University.
July 19 Prof. Kozo Tomita from the University of Tokyo gave a guest lecture at our Applied Chemistry Seminar Mini-Symposium.
Thank you, Tomita-sensei!
July 8– Teppei conducted experiments at the University of the Ryukyus.
July 4–5 At the 36th Annual Meeting of the Archaea Research Society of Japan, Teppei and Prof. Hori presented their work.
June 26–28 Shu, Sota, and Prof. Hori gave presentations at the 25th Annual Meeting of the RNA Society of Japan. Sota received a Travel Fellowship—congratulations!
June 20 Shu's paper was accepted in Journal of Biological Chemistry! This paper was featured on Ehime University’s research site.
May Ryota's paper was accepted in Frontiers in RNA Research! Congratulations!
April 14 Teppei and Ryota conducted experiments at the University of the Ryukyus.
April 4 We updated the lab members page.
April 1 A new academic year has begun. Three students have graduated, and six new fourth-year undergraduates joined the lab!
Feb 29 Teppei’s paper was published in RNA! Congratulations!
February Master’s and bachelor’s thesis presentations were held—great work, everyone!
Jan 4 Wishing you a great year ahead!
About Group Logo
The group logo was designed in April 2025 by our group (primarily leaded by Teppei). It inherits the concept of the green tRNA, which was the symbol of the former Hori Lab, and additionally incorporates an illustration representing molecular engineering.
The copyright belongs to our research group.
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