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Studying RNA-binding proteins and small silencing RNAs
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Welcome to the Fukunaga Lab.
Welcome to the Fukunaga Lab.
We are in the Department of Cell Biology at Johns Hopkins University School of Medicine.
We are in the Department of Cell Biology at Johns Hopkins University School of Medicine.
We are studying RNA biology, focusing on post-transcriptional gene regulation by RNA-binding proteins and small silencing RNAs such as miRNAs and siRNAs. We are particularly interested in elucidating the mechanism in small RNA biogenesis and finding novel RNA-binding proteins that have crucial functions in post-transcriptional gene regulation. We use multi-disciplinary approaches including biochemistry, Drosophila genetics, tissue culture system and high-throughput sequencing.
We are studying RNA biology, focusing on post-transcriptional gene regulation by RNA-binding proteins and small silencing RNAs such as miRNAs and siRNAs. We are particularly interested in elucidating the mechanism in small RNA biogenesis and finding novel RNA-binding proteins that have crucial functions in post-transcriptional gene regulation. We use multi-disciplinary approaches including biochemistry, Drosophila genetics, tissue culture system and high-throughput sequencing.
Postdoc and student positions are available in our lab.
Postdoc and student positions are available in our lab.
Please contact Dr. Ryuya Fukunaga (fukunaga@jhmi.edu) if you are interested.
Please contact Dr. Ryuya Fukunaga (fukunaga@jhmi.edu) if you are interested.
Recent news
Recent news
2026-09-29
2026-09-29
Ryuya received Research Resilience Fund ($250,000 for two years) from Johns Hopkins University School of Medicine.
Ryuya received Research Resilience Fund ($250,000 for two years) from Johns Hopkins University School of Medicine.
2026-09-15
2026-09-15
Azali received Hay Fellowship Award. Congratulations!
Azali received Hay Fellowship Award. Congratulations!
2026-09-14
2026-09-14
Azali presented an oral presentation of her project in our departmental Lewis Talk.
Azali presented an oral presentation of her project in our departmental Lewis Talk.
2026-05-13
2026-05-13
Tanae received JKTG (Jayne Koskinas Ted Giovanis) Fellowship, which will provide her stipend and health support for a year and registration and travel funds to the 2026 Annual ASCB/EMBO Meeting in San Diego in December 2026. Congratulations!
Tanae received JKTG (Jayne Koskinas Ted Giovanis) Fellowship, which will provide her stipend and health support for a year and registration and travel funds to the 2026 Annual ASCB/EMBO Meeting in San Diego in December 2026. Congratulations!
2026-05-04
2026-05-04
Tanae presented an oral presentation of her project in our departmental Lewis Talk.
Tanae presented an oral presentation of her project in our departmental Lewis Talk.
2026-04-09
2026-04-09
Ryuya presented a research seminar in our departmental seminar series.
Ryuya presented a research seminar in our departmental seminar series.
2026-03-02
2026-03-02
Ryuya presented an invited research seminar at Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine.
Ryuya presented an invited research seminar at Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine.
2025-12-02
2025-12-02
Azali's paper "MYCBP interacts with Sakura and Otu and is essential for germline stem cell renewal and differentiation and oogenesis" was published in PLOS Genetics. Congratulations!
Azali's paper "MYCBP interacts with Sakura and Otu and is essential for germline stem cell renewal and differentiation and oogenesis" was published in PLOS Genetics. Congratulations!
2025-09-22
2025-09-22
Azali presented an oral presentation of her project in our departmental Lewis Talk.
Azali presented an oral presentation of her project in our departmental Lewis Talk.
2025-07-01
2025-07-01
Ryuya and the lab transferred from the Department of Biological Chemistry to the Department of Cell Biology, since the former was closed.
Ryuya and the lab transferred from the Department of Biological Chemistry to the Department of Cell Biology, since the former was closed.
2025-04-02
2025-04-02
Yuki's paper "RNA-binding protein Miso/CG44249 is crucial for minor splicing during oogenesis in Drosophila" was published in RNA. Congratulations!
Yuki's paper "RNA-binding protein Miso/CG44249 is crucial for minor splicing during oogenesis in Drosophila" was published in RNA. Congratulations!
2024-10-04
2024-10-04
Azali's paper "Female-germline specific protein Sakura interacts with Otu and is crucial for germline stem cell renewal and differentiation and oogenesis" was published in BioRxiv and eLife. Congratulations!
Azali's paper "Female-germline specific protein Sakura interacts with Otu and is crucial for germline stem cell renewal and differentiation and oogenesis" was published in BioRxiv and eLife. Congratulations!
2024-06-03
2024-06-03
The first year BC program graduate student Tanae officially joined our lab as a PhD student to pursue her thesis work. Welcome to the lab, Tanae!
The first year BC program graduate student Tanae officially joined our lab as a PhD student to pursue her thesis work. Welcome to the lab, Tanae!
2024-04-27
2024-04-27
The first year BC program graduate student Tanae joined our lab as a rotation student. Welcome to the lab, Tanae!
The first year BC program graduate student Tanae joined our lab as a rotation student. Welcome to the lab, Tanae!
2023-08-28
2023-08-28
The first year BC program graduate student Wihib joined our lab as a rotation student. Welcome to the school, department, and lab, Wihib!
The first year BC program graduate student Wihib joined our lab as a rotation student. Welcome to the school, department, and lab, Wihib!
2022-06-01
2022-06-01
Ryuya received a Maximizing Investigators’ Research Award from NIGMS (R35GM145352. 'Investigating the molecular functions and mechanisms of RNA-binding proteins crucial for gametogenesis'). It will fund our lab for the next 5 years. Thanks for support!
Ryuya received a Maximizing Investigators’ Research Award from NIGMS (R35GM145352. 'Investigating the molecular functions and mechanisms of RNA-binding proteins crucial for gametogenesis'). It will fund our lab for the next 5 years. Thanks for support!
2022-03-31
2022-03-31
Today was Licky's last day in the lab. He will start to work in Hansoh Bio as a Scientist. Congratulations Licky and Best luck!
Today was Licky's last day in the lab. He will start to work in Hansoh Bio as a Scientist. Congratulations Licky and Best luck!
2022-01-10
2022-01-10
Yuki joined our lab as a new postdoc. Welcome Yuki!
Yuki joined our lab as a new postdoc. Welcome Yuki!
2021-11-15
2021-11-15
Azali joined our lab as a new postdoc. Welcome Azali!
Azali joined our lab as a new postdoc. Welcome Azali!
2021-06-28
2021-06-28
Licky's paper "RNA-binding protein Maca is crucial for gigantic male fertility factor gene expression, spermatogenesis, and male fertility, in Drosophila" was published in PLoS Genetics. Congratulations!
Licky's paper "RNA-binding protein Maca is crucial for gigantic male fertility factor gene expression, spermatogenesis, and male fertility, in Drosophila" was published in PLoS Genetics. Congratulations!
2021-06-23
2021-06-23
Collaboration paper with Dr. Roselle Abraham at UCSF "Differences inmolecular phenotype inmouse andhuman hypertrophic cardiomyopathy" was published in Scientific Reports.
Collaboration paper with Dr. Roselle Abraham at UCSF "Differences inmolecular phenotype inmouse andhuman hypertrophic cardiomyopathy" was published in Scientific Reports.
2019-12-17
2019-12-17
Collaboration paper with Dr. Roselle Abraham at UCSF "Differences in microRNA-29 and Pro-fibrotic Gene Expression in Mouse and Human Hypertrophic Cardiomyopathy" was published in Frontiers in Cardiovascular Medicine.
Collaboration paper with Dr. Roselle Abraham at UCSF "Differences in microRNA-29 and Pro-fibrotic Gene Expression in Mouse and Human Hypertrophic Cardiomyopathy" was published in Frontiers in Cardiovascular Medicine.
2019-07-19
2019-07-19
Ryuya presented an invited talk at RNA 2019 in Japan.
Ryuya presented an invited talk at RNA 2019 in Japan.
2019-06-15
2019-06-15
2019-06-14
2019-06-14
Licky's paper "Drosophila Regnase-1 RNase is required for mRNA and miRNA profile remodeling during larva-to-adult metamorphosis" was published in RNA Biology. Congratulations!
Licky's paper "Drosophila Regnase-1 RNase is required for mRNA and miRNA profile remodeling during larva-to-adult metamorphosis" was published in RNA Biology. Congratulations!
2019-05-30
2019-05-30
Licky and Susan's paper "RNA methyltransferase BCDIN3D is crucial for female fertility and miRNA and mRNA profiles in Drosophila ovaries" was published in PLOS ONE. Congratulations!
Licky and Susan's paper "RNA methyltransferase BCDIN3D is crucial for female fertility and miRNA and mRNA profiles in Drosophila ovaries" was published in PLOS ONE. Congratulations!
2019-05-23
2019-05-23
Susan gave a thesis seminar and graduated. Congratulations, Dr. Liao!
Susan gave a thesis seminar and graduated. Congratulations, Dr. Liao!
2019-05-21
2019-05-21
Ryuya gave a talk at Biological Chemistry seminar.
Ryuya gave a talk at Biological Chemistry seminar.
2019-04-15
2019-04-15
Susan's paper "DEAD-box RNA helicase Belle post-transcriptionally promotes gene expression in an ATPase activity-dependent manner" was published in RNA. Congratulations!
Susan's paper "DEAD-box RNA helicase Belle post-transcriptionally promotes gene expression in an ATPase activity-dependent manner" was published in RNA. Congratulations!
2019-01-01
2019-01-01
Ryuya was promoted to Associate Professor.
Ryuya was promoted to Associate Professor.
2018-11-26
2018-11-26
Ryuya presented an invited seminar at Tokyo University of Agriculture and Technology.
Ryuya presented an invited seminar at Tokyo University of Agriculture and Technology.
2018-11-22
2018-11-22
Ryuya presented an invited seminar at Tokyo University of Science.
Ryuya presented an invited seminar at Tokyo University of Science.
2018-11-21
2018-11-21
Ryuya presented an invited seminar at RIKEN WAKO Institute .
Ryuya presented an invited seminar at RIKEN WAKO Institute .
2018-11-13
2018-11-13
Ryuya presented an invited seminar at Ohio State University.
Ryuya presented an invited seminar at Ohio State University.
2018-10-02
2018-10-02
Licky's paper "LOTUS domain protein MARF1 binds CCR4-NOT deadenylase complex to post-transcriptionally regulate gene expression in oocytes" was published in Nature Communications. Congratulations!
Licky's paper "LOTUS domain protein MARF1 binds CCR4-NOT deadenylase complex to post-transcriptionally regulate gene expression in oocytes" was published in Nature Communications. Congratulations!
2018-09-14
2018-09-14
Fukunaga lab attended the Biological Chemistry Retreat @ Mt. Washington and Susan presented a poster.
Fukunaga lab attended the Biological Chemistry Retreat @ Mt. Washington and Susan presented a poster.
2018-07-25
2018-07-25
Susan's paper "An RNA-binding protein Blanks plays important roles in defining small RNA and mRNA profiles in Drosophila testes" was published in Heliyon. Congratulations!
Susan's paper "An RNA-binding protein Blanks plays important roles in defining small RNA and mRNA profiles in Drosophila testes" was published in Heliyon. Congratulations!
2018-07-17
2018-07-17
Susan presented a poster at the Gordon research conference on Post-Transcriptional Gene Regulation.
Susan presented a poster at the Gordon research conference on Post-Transcriptional Gene Regulation.
2018-07-02
2018-07-02
Yiwei Ai, a new Biological Chemistry PhD student, started a rotation in our lab. Welcome to Fukunaga lab!
Yiwei Ai, a new Biological Chemistry PhD student, started a rotation in our lab. Welcome to Fukunaga lab!
2018-07-01
2018-07-01
Susan received Amgen Scholar Alumni Travel Award to attend the Gordon conference and present a poster on July 16-19. Congratulations!
Susan received Amgen Scholar Alumni Travel Award to attend the Gordon conference and present a poster on July 16-19. Congratulations!
2018-06-27
2018-06-27
Ryuya presented an invited seminar at University of Rochester.
Ryuya presented an invited seminar at University of Rochester.
2018-05-31
2018-05-31
Fukunaga lab made TEDD (Thursday Evening Dinner Discussion) presentation in the department.
Fukunaga lab made TEDD (Thursday Evening Dinner Discussion) presentation in the department.
2018-05-16
2018-05-16
Ryuya made a poster presentation at the Cold Spring Harbor Meeting on Regulatory & Non-Coding RNAs.
Ryuya made a poster presentation at the Cold Spring Harbor Meeting on Regulatory & Non-Coding RNAs.
2018-03-22
2018-03-22
Ryuya's paper "Allele-specific differencesin transcriptome, miRNome,and mitochondrial function in twohypertrophic cardiomyopathy mousemodels" was published in JCI Insight. This was collaboration with Dr. Roselle Abraham at UCSF. Congratulations!
Ryuya's paper "Allele-specific differencesin transcriptome, miRNome,and mitochondrial function in twohypertrophic cardiomyopathy mousemodels" was published in JCI Insight. This was collaboration with Dr. Roselle Abraham at UCSF. Congratulations!
2018-03-21
2018-03-21
Ryuya's paper "Loquacious-PD removes phosphate inhibition of Dicer-2 processing of hairpin RNAs into siRNAs" was published in Biochemical and Biophysical Research Communications. Congratulations!
Ryuya's paper "Loquacious-PD removes phosphate inhibition of Dicer-2 processing of hairpin RNAs into siRNAs" was published in Biochemical and Biophysical Research Communications. Congratulations!
2018-01-24
2018-01-24
Licky and Suresh's paper "Dicer partner protein tunes the length of miRNAs using base-mismatch in the pre-miRNA stem" was published in Nucleic Acid Research. Congratulations!
Licky and Suresh's paper "Dicer partner protein tunes the length of miRNAs using base-mismatch in the pre-miRNA stem" was published in Nucleic Acid Research. Congratulations!
2017-12-28
2017-12-28
Ryuya presented an invited seminar at the University of Tokyo.
Ryuya presented an invited seminar at the University of Tokyo.
2017-12-26
2017-12-26
Ryuya presented an invited seminar at RIKEN Yokoyama in Japan.
Ryuya presented an invited seminar at RIKEN Yokoyama in Japan.
2017-10-26
2017-10-26
Ryuya presented an invited seminar at University of Virginia School of Medicine.
Ryuya presented an invited seminar at University of Virginia School of Medicine.
2017-10-01
2017-10-01
Susan's method paper "Kinetic Analysis of Small Silencing RNA Production by Human and Drosophila Dicer Enzymes In Vitro" was published in Methods in Molecular Biology. Congratulations!
Susan's method paper "Kinetic Analysis of Small Silencing RNA Production by Human and Drosophila Dicer Enzymes In Vitro" was published in Methods in Molecular Biology. Congratulations!
2017-09-15
2017-09-15
Susan made an oral presentation in the Biological Chemistry retreat at Mt. Washington conference center.
Susan made an oral presentation in the Biological Chemistry retreat at Mt. Washington conference center.
2017-09-08
2017-09-08
Five-year grant support by NIH to our lab (R01GM116841) was started. Thanks for supporting our research.
Five-year grant support by NIH to our lab (R01GM116841) was started. Thanks for supporting our research.
2017-05-23
2017-05-23
Ryuya presented a faculty seminar at the Department of Biological Chemistry.
Ryuya presented a faculty seminar at the Department of Biological Chemistry.
2017-05-17
2017-05-17
Suresh's and Licky's paper "The C-terminal dsRNA-binding domain of Drosophila Dicer-2 is crucial for efficient and high-fidelity production of siRNA and loading of siRNA to Argonaute2" was published in RNA. Congratulations!
Suresh's and Licky's paper "The C-terminal dsRNA-binding domain of Drosophila Dicer-2 is crucial for efficient and high-fidelity production of siRNA and loading of siRNA to Argonaute2" was published in RNA. Congratulations!
2016-11-21
2016-11-21
Suresh's paper "Phosphate-binding pocket in Dicer-2 PAZ domain for high-fidelity siRNA production" was published in PNAS. Congratulations!
Suresh's paper "Phosphate-binding pocket in Dicer-2 PAZ domain for high-fidelity siRNA production" was published in PNAS. Congratulations!
2016-05-19
2016-05-19
Our paper "Common miR-590 Variant rs6971711 Present Only in African Americans Reduces miR-590 Biogenesis", in which Suresh and Susan are co-authors, was published in PLoS One. This was collaboration with Dr. Roselle Abraham. Congratulations!
Our paper "Common miR-590 Variant rs6971711 Present Only in African Americans Reduces miR-590 Biogenesis", in which Suresh and Susan are co-authors, was published in PLoS One. This was collaboration with Dr. Roselle Abraham. Congratulations!
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