Ryuya Fukunaga

Associate Professor

20042019
If you made any changes in Pure, your changes will be visible here soon.

Research Output 2004 2019

Filter
Article
2019

DEAD-box RNA helicase Belle posttranscriptionally promotes gene expression in an ATPase activity-dependent manner

Liao, S. E., Kandasamy, S. K., Zhu, L. & Fukunaga, R., Jan 1 2019, In : RNA. 27, 5, p. 825-839 15 p.

Research output: Contribution to journalArticle

Open Access
DEAD-box RNA Helicases
Adenosine Triphosphatases
Cyclin B
Gene Expression
Messenger RNA

Drosophila Regnase-1 RNase is required for mRNA and miRNA profile remodelling during larva-to-adult metamorphosis

Zhu, L., Liao, S. E. & Fukunaga, R., Jan 1 2019, In : RNA Biology.

Research output: Contribution to journalArticle

Pupa
Ribonucleases
MicroRNAs
Drosophila
Larva

RNA methyltransferase BCDIN3D is crucial for female fertility and miRNA and mRNA profiles in Drosophila ovaries

Zhu, L., Liao, S. E., Ai, Y. & Fukunaga, R., May 1 2019, In : PloS one. 14, 5, e0217603.

Research output: Contribution to journalArticle

Open Access
female fertility
methyltransferases
Methyltransferases
MicroRNAs
microRNA
2018

Allele-specific differences in transcriptome, miRNome, and mitochondrial function in two hypertrophic cardiomyopathy mouse models

Vakrou, S., Fukunaga, R., Foster, D. B., Sorensen, L., Liu, Y., Guan, Y., Woldemichael, K., Pineda-Reyes, R., Liu, T., Tardiff, J. C., Leinwand, L. A., Tocchetti, C. G., Abraham, T. P., O'Rourke, B., Aon, M. A. & Abraham, M. R., Mar 22 2018, In : JCI insight. 3, 6

Research output: Contribution to journalArticle

Open Access
Hypertrophic Cardiomyopathy
Transcriptome
Alleles
Mutation
Antioxidants

An RNA-binding protein Blanks plays important roles in defining small RNA and mRNA profiles in Drosophila testes

Liao, S. E., Ai, Y. & Fukunaga, R., Jul 1 2018, In : Heliyon. 4, 7, e00706.

Research output: Contribution to journalArticle

RNA-Binding Proteins
Drosophila
Testis
RNA
Messenger RNA

Dicer partner protein tunes the length of miRNAs using base-mismatch in the pre-miRNA stem

Zhu, L., Kandasamy, S. K. & Fukunaga, R., Apr 20 2018, In : Nucleic Acids Research. 46, 7, p. 3726-3741 16 p.

Research output: Contribution to journalArticle

MicroRNAs
Proteins
Nucleotides
Base Pairing
Drosophila
Small Interfering RNA
Phosphates
RNA
Processing
Substrates

LOTUS domain protein MARF1 binds CCR4-NOT deadenylase complex to post-transcriptionally regulate gene expression in oocytes

Zhu, L., Kandasamy, S. K., Liao, S. E. & Fukunaga, R., Dec 1 2018, In : Nature Communications. 9, 1, 4031.

Research output: Contribution to journalArticle

gametocytes
gene expression
Gene expression
Oocytes
proteins
2017

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

Kandasamy, S. K., Zhu, L. & Fukunaga, R., Jul 1 2017, In : RNA. 23, 7, p. 1139-1153 15 p.

Research output: Contribution to journalArticle

Small Interfering RNA
Drosophila
Nucleotides
RNA Interference
Ribonuclease III
2016

Common miR-590 variant rs6971711 present only in African Americans reduces miR-590 biogenesis

Lin, X., Steinberg, S., Kandasamy, S. K., Afzal, J., Mbiyangandu, B., Liao, S. E., Guan, Y., Corona Villalobos, C., Matkovich, S. J., Epstein, N., Tripodi, D., Huo, Z., Cutting, G. R., Abraham, T. P., Fukunaga, R. & Abraham, M. R., May 1 2016, In : PLoS One. 11, 5, e0156065.

Research output: Contribution to journalArticle

African Americans
MicroRNAs
microRNA
Single Nucleotide Polymorphism
Hypertrophic Cardiomyopathy

Phosphate-binding pocket in Dicer-2 PAZ domain for high-fidelity siRNA production

Kandasamy, S. K. & Fukunaga, R., Dec 6 2016, In : Proceedings of the National Academy of Sciences of the United States of America. 113, 49, p. 14031-14036 6 p.

Research output: Contribution to journalArticle

Small Interfering RNA
Phosphates
RNA Interference
MicroRNAs
Ribonuclease III
2015

A SelB/EF-Tu/aIF2γ-like protein from Methanosarcina mazei in the GTP-bound form binds cysteinyl-tRNACys

Yanagisawa, T., Ishii, R., Hikida, Y., Fukunaga, R., Sengoku, T., Sekine, S. I. & Yokoyama, S., 2015, In : Journal of Structural and Functional Genomics. 16, 1, p. 25-41 17 p.

Research output: Contribution to journalArticle

RNA, Transfer, Cys
Methanosarcina
Peptide Elongation Factor Tu
Guanosine Triphosphate
Hydrolysis
2014

A universal small molecule, inorganic phosphate, restricts the substrate specificity of Dicer-2 in small RNA biogenesis

Fukunaga, R. & Zamore, P. D., Jun 1 2014, In : Cell cycle (Georgetown, Tex.). 13, 11, p. 1671-1676 6 p.

Research output: Contribution to journalArticle

Substrate Specificity
MicroRNAs
Phosphates
RNA
Double-Stranded RNA

Inorganic phosphate blocks binding of pre-miRNA to Dicer-2 via its PAZ domain

Fukunaga, R., Colpan, C., Han, B. W. & Zamore, P. D., Feb 18 2014, In : The EMBO journal. 33, 4, p. 371-384 14 p.

Research output: Contribution to journalArticle

MicroRNAs
Double-Stranded RNA
Phosphates
Substrates
Adenosine Triphosphate
2012

Dicer partner proteins tune the length of mature miRNAs in flies and mammals

Fukunaga, R., Han, B. W., Hung, J. H., Xu, J., Weng, Z. & Zamore, P. D., Oct 26 2012, In : Cell. 151, 3, p. 533-546 14 p.

Research output: Contribution to journalArticle

Mammals
MicroRNAs
Diptera
Small Interfering RNA
Proteins

Erratum: Dicer partner proteins tune the length of mature miRNAs in flies and mammals (Cell (2012) 151 (533-546))

Fukunaga, R., Han, B. W., Hung, J. H., Xu, J., Weng, Z. & Zamore, P. D., Nov 9 2012, In : Cell. 151, 4, p. 912 1 p.

Research output: Contribution to journalArticle

Mammals
MicroRNAs
Proteins

Loquacious, a Dicer Partner Protein, Functions in Both the MicroRNA and siRNA Pathways

Fukunaga, R. & Zamore, P. D., 2012, In : Enzymes. 32, p. 37-68 32 p.

Research output: Contribution to journalArticle

MicroRNAs
Small Interfering RNA
Ribonuclease III
Substrates
Proteins
2011

Phosphate and R2D2 Restrict the Substrate Specificity of Dicer-2, an ATP-Driven Ribonuclease

Cenik, E. S., Fukunaga, R., Lu, G., Dutcher, R., Wang, Y., Tanaka Hall, T. M. & Zamore, P. D., Apr 22 2011, In : Molecular Cell. 42, 2, p. 172-184 13 p.

Research output: Contribution to journalArticle

Double-Stranded RNA
Ribonucleases
Substrate Specificity
MicroRNAs
Adenosine Triphosphate
2010

Riding in silence: A little snowboarding, a lot of small RNAs

Ameres, S. L. & Fukunaga, R., Mar 15 2010, In : Silence. 1, 1, 8.

Research output: Contribution to journalArticle

Skiing
RNA Interference
RNA
Regulator Genes
MicroRNAs
2009

dsRNA with 5′ overhangs contributes to endogenous and antiviral RNA silencing pathways in plants

Fukunaga, R. & Doudna, J. A., Mar 4 2009, In : The EMBO journal. 28, 5, p. 545-555 11 p.

Research output: Contribution to journalArticle

Double-Stranded RNA
RNA Interference
Antiviral Agents
RNA
RNA Replicase

Unique protein architecture of alanyl-tRNA synthetase for aminoacylation, editing, and dimerization

Naganuma, M., Sekine, S. I., Fukunaga, R. & Yokoyama, S., May 26 2009, In : Proceedings of the National Academy of Sciences of the United States of America. 106, 21, p. 8489-8494 6 p.

Research output: Contribution to journalArticle

Alanine-tRNA Ligase
Transfer RNA Aminoacylation
Dimerization
Transfer RNA
Aminoacylation
2008

Crystallographic Studies on Multiple Conformational States of Active-site Loops in Pyrrolysyl-tRNA Synthetase

Yanagisawa, T., Ishii, R., Fukunaga, R., Kobayashi, T., Sakamoto, K. & Yokoyama, S., May 2 2008, In : Journal of Molecular Biology. 378, 3, p. 634-652 19 p.

Research output: Contribution to journalArticle

Amino Acyl-tRNA Synthetases
Catalytic Domain
Adenylyl Imidodiphosphate
Transfer RNA
Aspartate-tRNA Ligase

Multistep Engineering of Pyrrolysyl-tRNA Synthetase to Genetically Encode Nε-(o-Azidobenzyloxycarbonyl) lysine for Site-Specific Protein Modification

Yanagisawa, T., Ishii, R., Fukunaga, R., Kobayashi, T., Sakamoto, K. & Yokoyama, S., Nov 24 2008, In : Chemistry and Biology. 15, 11, p. 1187-1197 11 p.

Research output: Contribution to journalArticle

Amino Acyl-tRNA Synthetases
Lysine
Proteins
Aminoacylation
Bearings (structural)

Phosphoserine aminoacylation of tRNA bearing an unnatural base anticodon

Fukunaga, R., Harada, Y., Hirao, I. & Yokoyama, S., Aug 1 2008, In : Biochemical and Biophysical Research Communications. 372, 3, p. 480-485 6 p.

Research output: Contribution to journalArticle

Bearings (structural)
Transfer RNA Aminoacylation
Anticodon
Phosphoserine
Transfer RNA
2007
Alanine-tRNA Ligase
Archaeoglobus fulgidus
Dimerization
Archaea
Crystallization

Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea

Fukunaga, R. & Yokoyama, S., Apr 2007, In : Nature structural & molecular biology. 14, 4, p. 272-279 8 p.

Research output: Contribution to journalArticle

RNA, Transfer, Cys
Archaea
Cysteine
Phosphoserine
cysteinyl-tRNA synthetase
RNA, Transfer, Cys
Archaeoglobus fulgidus
Archaea
Transfer RNA
Cysteine

Structure of the AlaX-M trans-editing enzyme from Pyrococcus horikoshii

Fukunaga, R. & Yokoyama, S., Feb 21 2007, In : Acta Crystallographica Section D: Biological Crystallography. 63, 3, p. 390-400 11 p.

Research output: Contribution to journalArticle

Pyrococcus horikoshii
RNA, Transfer, Ala
editing
Glycine
Alanine-tRNA Ligase

The C-terminal domain of the archaeal leucyl-tRNA synthetase prevents misediting of isoleucyl-tRNAIle

Fukunaga, R. & Yokoyama, S., May 1 2007, In : Biochemistry®. 46, 17, p. 4985-4996 12 p.

Research output: Contribution to journalArticle

RNA, Transfer, Ile
Amino Acyl-tRNA Synthetases
RNA, Transfer, Val
Aminoacylation
Isoleucine-tRNA Ligase
2006
Methanosarcina
Amino Acyl-tRNA Synthetases
Archaea
Crystallization
Catalytic Domain

Structural and mutational studies of the amino acid-editing domain from archaeal/eukaryal phenylalanyl-tRNA synthetase

Sasaki, H. M., Sekine, S. I., Sengoku, T., Fukunaga, R., Hattori, M., Utsunomiya, Y., Kuroishi, C., Kuramitsu, S., Shirouzu, M. & Yokoyama, S., Oct 3 2006, In : Proceedings of the National Academy of Sciences of the United States of America. 103, 40, p. 14744-14749 6 p.

Research output: Contribution to journalArticle

Phenylalanine-tRNA Ligase
Archaea
RNA, Transfer, Phe
Amino Acids
Pyrococcus horikoshii

Structural Basis for Substrate Recognition by the Editing Domain of Isoleucyl-tRNA Synthetase

Fukunaga, R. & Yokoyama, S., Jun 16 2006, In : Journal of Molecular Biology. 359, 4, p. 901-912 12 p.

Research output: Contribution to journalArticle

Isoleucine-tRNA Ligase
Valine
Thermus thermophilus
Isoleucine
Catalytic Domain
2005
RNA, Transfer, Leu
Aminoacylation
Amino Acyl-tRNA Synthetases
Transfer RNA
Pyrococcus horikoshii
Pyrococcus horikoshii
RNA, Transfer, Leu
Amino Acyl-tRNA Synthetases
Archaea
Crystallization
Pyrococcus horikoshii
Amino Acyl-tRNA Synthetases
Archaea
Aminoacylation
Valine-tRNA Ligase

Crystal structure of tRNA adenosine deaminase (TadA) from Aquifex aeolicus

Kuratani, M., Ishii, R., Bessho, Y., Fukunaga, R., Sengoku, T., Shirouzu, M., Sekine, S. I. & Yokoyama, S., Apr 22 2005, In : Journal of Biological Chemistry. 280, 16, p. 16002-16008 7 p.

Research output: Contribution to journalArticle

Adenosine Deaminase
Transfer RNA
Crystal structure
Cytosine Deaminase
Yeast

Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain

Fukunaga, R. & Yokoyama, S., Aug 19 2005, In : Journal of Biological Chemistry. 280, 33, p. 29937-29945 9 p.

Research output: Contribution to journalArticle

Valine-tRNA Ligase
RNA, Transfer, Val
Amino Acids
Transfer RNA
Substitution reactions

The crystal structure of leucyl-tRNA synthetase complexed with tRNA Leu in the post-transfer-editing conformation

Tukalo, M., Yaremchuk, A., Fukunaga, R., Yokoyama, S. & Cusack, S., Oct 2005, In : Nature structural & molecular biology. 12, 10, p. 923-930 8 p.

Research output: Contribution to journalArticle

RNA, Transfer, Leu
Amino Acyl-tRNA Synthetases
Transfer RNA
Thermus thermophilus
Aminoacylation
2004
Pyrococcus horikoshii
Amino Acyl-tRNA Synthetases
Archaea
Crystallization
X-Rays
Isoleucine-tRNA Ligase
RNA, Transfer, Ile
Thermus thermophilus
editing
Adenosine Monophosphate

Crystal Structures of the CP1 Domain from Thermus thermophilus Isoleucyl-tRNA Synthetase and Its Complex with L-Valine

Fukunaga, R., Fukai, S., Ishitani, R., Nureki, O. & Yokoyama, S., Feb 27 2004, In : Journal of Biological Chemistry. 279, 9, p. 8396-8402 7 p.

Research output: Contribution to journalArticle

Isoleucine-tRNA Ligase
RNA, Transfer, Ile
Thermus thermophilus
Valine
Crystal structure