Kotaro Fujii

Kotaro Fujii,

Assistant Professor

Department: Molecular Genetics & Microbiology
Business Phone: (352) 273-7279
Business Email: kotaro.fujii@ufl.edu

About Kotaro Fujii

Dr. Fujii is an Assistant Professor of Molecular Genetics & Microbiology and Center for NeuroGenetics at the University of Florida College of Medicine. He obtained Ph.D. degrees in RNA biochemistry and molecular biology. He came to the United States as a postdoctoral fellow at Stanford University and complemented his experience with developmental biology as well as state-of-the-art genome-wide sequence analyses by applying his biochemical techniques to the developing mammalian embryo. The research vision of Dr. Fujii is to molecularly understand mammalian development and homeostasis by utilizing a variety of interdisciplinary approaches from cutting edge biochemistry to in vivo animal models.

Related Links:


1st Grant: PRESTO
2020-2024 · JST
Starting Fujii laboratory
2020 · University of Florida
Poster Award 1st Place
2017 · The Bay Area RNA Club
Human Frontier Science Program (HFSP), Long Term Fellow
2013-2016 · Human Frontier Science Program (HFSP)
The Uehara Memorial Foundation, Postdoctoral fellowship
2012-2013 · The Uehara Memorial Foundation
Start postdoc at the Barna laboratory
2012 · UCSF, Stanford
Obtain Ph.D
2011 · Kyoto University
Japan Society for the Promotion of Science (JSPS), Research fellowship for young scientists
2010-2012 · Japan Society for the Promotion of Science (JSPS)
Return exemption of scholarship due to outstanding achievements
2010 · Japan Student Services Organization (JASSO)
Outstanding Young Scientist (2nd Place)
2009 · 16th East Asia Joint Conference on Biomedical Research

Teaching Profile

Courses Taught
GMS6920 Genetics Journal Colloquy

Research Profile

Dr. Fujii’s research has been centered on delineating new regulatory mechanisms of gene regulation at the step of mRNA translation by the ribosome. Given that the building blocks of our bodies are proteins, maintaining homeostasis of the proteome is critical for our health. His work has elucidated the quality control mechanism of the functional protein synthesis (Fujii et al., 2009 and 2012) and the fidelity of protein production (Fujii et al., 2018). His research also revealed spatiotemporal regulation of mRNA translation in developing mouse embryos (Fujii et al., 2017) and translational regulation by the ribosome itself (Shi et al., 2017) as well as core translation initiation factor eIF3 complex (Fujii et al., 2021). Dr. Fujii’s research program will unravel new layers of spatiotemporal specificity and fidelity of protein synthesis, to further understand the impact of mRNA translation regulation in development and diseases, particularly those caused by protein aggregation such as neurodegenerative disorders.

Open Researcher and Contributor ID (ORCID)



Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics
Nature Communications. 13(1) [DOI] 10.1038/s41467-022-28776-w.
Silver nanoparticles enhance the efficacy of aminoglycosides against antibiotic-resistant bacteria.
Frontiers in microbiology. 13 [DOI] 10.3389/fmicb.2022.1064095. [PMID] 36798870.
Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics
bioRxiv. [DOI] 10.1101/2021.03.29.437587. [PMID] 33821271.
Controlling tissue patterning by translational regulation of signaling transcripts through the core translation factor eIF3c
Developmental Cell. 56(21):2928-2937.e9 [DOI] 10.1016/j.devcel.2021.10.009. [PMID] 34752747.
VELCRO-IP RNA-seq reveals ribosome expansion segment function in translation genome-wide.
Cell reports. 34(3) [DOI] 10.1016/j.celrep.2020.108629. [PMID] 33472078.
Gene- and Species-Specific Hox mRNA Translation by Ribosome Expansion Segments.
Molecular cell. 80(6):980-995.e13 [DOI] 10.1016/j.molcel.2020.10.023. [PMID] 33202249.
Decoding the Function of Expansion Segments in Ribosomes
Molecular Cell. 72(6):1013-1020.e6 [DOI] 10.1016/j.molcel.2018.11.023. [PMID] 30576652.
Heterogeneous Ribosomes Preferentially Translate Distinct Subpools of mRNAs Genome-wide
Molecular Cell. 67(1):71-83.e7 [DOI] 10.1016/j.molcel.2017.05.021. [PMID] 28625553.
Pervasive translational regulation of the cell signalling circuitry underlies mammalian development
Nature Communications. 8(1) [DOI] 10.1038/ncomms14443. [PMID] 28195124.
Crt10 directs the cullin-E3 ligase Rtt101 to nonfunctional 25S rRNA decay
Biochemical and Biophysical Research Communications. 457(1):90-94 [DOI] 10.1016/j.bbrc.2014.12.072.
RNA regulons in Hox 5′ UTRs confer ribosome specificity to gene regulation
Nature. 517(7532):33-38 [DOI] 10.1038/nature14010. [PMID] 25409156.
40S subunit dissociation and proteasome-dependent RNA degradation in nonfunctional 25S rRNA decay
The EMBO Journal. 31(11):2579-2589 [DOI] 10.1038/emboj.2012.85. [PMID] 22505030.
[Quality control of ribosomal RNAs].
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme. 54(16 Suppl):2195-200 [PMID] 21089640.
A role for ubiquitin in the clearance of nonfunctional rRNAs
Genes & Development. 23(8):963-974 [DOI] 10.1101/gad.1775609. [PMID] 19390089.


Apr 2021 ACTIVE
The spatiotemporal landscape for the accuracy of protein synthesis in mammalian development and disease.
Role: Principal Investigator


PhD in Biochemistry
2008-2011 · Kyoto University (Japan)
MA in Biochemistry
2006-2008 · Kyoto University (Japan)
BA in Biology
2002-2006 · Tohoku University (Japan)

Contact Details

(352) 273-7279
Business Mailing:
PO Box 103610