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Ryuya Fukunaga - Publications

Affiliations: 
2013- Biological Chemistry Johns Hopkins University School of Medicine, Baltimore, MD, United States 
Area:
RNA silencing mechanism
Website:
https://www.hopkinsmedicine.org/profiles/results/directory/profile/3173205/ryuya-fukunaga
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38 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Zhu L, Liao SE, Fukunaga R. Regnase-1 RNase is required for mRNA and miRNA profile remodeling during larva-to-adult metamorphosis. Rna Biology. PMID 31195914 DOI: 10.1080/15476286.2019.1630799  0.471
2019 Zhu L, Liao SE, Ai Y, Fukunaga R. RNA methyltransferase BCDIN3D is crucial for female fertility and miRNA and mRNA profiles in Drosophila ovaries. Plos One. 14: e0217603. PMID 31145769 DOI: 10.1371/Journal.Pone.0217603  0.51
2019 Liao SE, Kandasamy SK, Zhu L, Fukunaga R. DEAD-box RNA helicase Belle post-transcriptionally promotes gene expression in an ATPase activity-dependent manner. Rna (New York, N.Y.). PMID 30979781 DOI: 10.1261/Rna.070268.118  0.407
2018 Zhu L, Kandasamy SK, Liao SE, Fukunaga R. LOTUS domain protein MARF1 binds CCR4-NOT deadenylase complex to post-transcriptionally regulate gene expression in oocytes. Nature Communications. 9: 4031. PMID 30279526 DOI: 10.1038/S41467-018-06404-W  0.384
2018 Liao SE, Ai Y, Fukunaga R. An RNA-binding protein Blanks plays important roles in defining small RNA and mRNA profiles in testes. Heliyon. 4: e00706. PMID 30094376 DOI: 10.1016/J.Heliyon.2018.E00706  0.473
2018 Fukunaga R. Loquacious-PD removes phosphate inhibition of Dicer-2 processing of hairpin RNAs into siRNAs. Biochemical and Biophysical Research Communications. 498: 1022-1027. PMID 29550490 DOI: 10.1016/J.Bbrc.2018.03.108  0.443
2018 Zhu L, Kandasamy SK, Fukunaga R. Dicer partner protein tunes the length of miRNAs using base-mismatch in the pre-miRNA stem. Nucleic Acids Research. PMID 29373753 DOI: 10.1093/Nar/Gky043  0.457
2018 Liao SE, Fukunaga R. Kinetic Analysis of Small Silencing RNA Production by Human and Drosophila Dicer Enzymes In Vitro. Methods in Molecular Biology (Clifton, N.J.). 1680: 101-121. PMID 29030844 DOI: 10.1007/978-1-4939-7339-2_7  0.508
2017 Kandasamy SK, Zhu L, Fukunaga R. 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. Rna (New York, N.Y.). PMID 28416567 DOI: 10.1261/Rna.059915.116  0.481
2016 Kandasamy SK, Fukunaga R. Phosphate-binding pocket in Dicer-2 PAZ domain for high-fidelity siRNA production. Proceedings of the National Academy of Sciences of the United States of America. 113: 14031-14036. PMID 27872309 DOI: 10.1073/Pnas.1612393113  0.575
2016 Lin X, Steinberg S, Kandasamy SK, Afzal J, Mbiyangandu B, Liao SE, Guan Y, Corona-Villalobos CP, Matkovich SJ, Epstein N, Tripodi D, Huo Z, Cutting G, Abraham TP, Fukunaga R, et al. Common miR-590 Variant rs6971711 Present Only in African Americans Reduces miR-590 Biogenesis. Plos One. 11: e0156065. PMID 27196440 DOI: 10.1371/Journal.Pone.0156065  0.307
2015 Yanagisawa T, Ishii R, Hikida Y, Fukunaga R, Sengoku T, Sekine S, Yokoyama S. A SelB/EF-Tu/aIF2γ-like protein from Methanosarcina mazei in the GTP-bound form binds cysteinyl-tRNA(Cys.). Journal of Structural and Functional Genomics. 16: 25-41. PMID 25618148 DOI: 10.1007/S10969-015-9193-6  0.382
2014 Fukunaga R, Zamore PD. A universal small molecule, inorganic phosphate, restricts the substrate specificity of Dicer-2 in small RNA biogenesis. Cell Cycle (Georgetown, Tex.). 13: 1671-6. PMID 24787225 DOI: 10.4161/Cc.29066  0.685
2014 Fukunaga R, Colpan C, Han BW, Zamore PD. Inorganic phosphate blocks binding of pre-miRNA to Dicer-2 via its PAZ domain. The Embo Journal. 33: 371-84. PMID 24488111 DOI: 10.1002/Embj.201387176  0.676
2012 Fukunaga R, Han BW, Hung JH, Xu J, Weng Z, Zamore PD. Dicer Partner Proteins Tune the Length of Mature miRNAs in Flies and Mammals. Cell. 151: 912. PMID 30360291 DOI: 10.1016/J.Cell.2012.10.029  0.609
2012 Fukunaga R, Han BW, Hung JH, Xu J, Weng Z, Zamore PD. Dicer partner proteins tune the length of mature miRNAs in flies and mammals. Cell. 151: 533-46. PMID 23063653 DOI: 10.1016/J.Cell.2012.09.027  0.639
2012 Fukunaga R, Zamore PD. Loquacious, a Dicer Partner Protein, Functions in Both the MicroRNA and siRNA Pathways Enzymes. 32: 37-68. DOI: 10.1016/B978-0-12-404741-9.00002-7  0.678
2011 Cenik ES, Fukunaga R, Lu G, Dutcher R, Wang Y, Tanaka Hall TM, Zamore PD. Phosphate and R2D2 restrict the substrate specificity of Dicer-2, an ATP-driven ribonuclease. Molecular Cell. 42: 172-84. PMID 21419681 DOI: 10.1016/J.Molcel.2011.03.002  0.686
2010 Ameres SL, Fukunaga R. Riding in silence: a little snowboarding, a lot of small RNAs. Silence. 1: 8. PMID 20230614 DOI: 10.1186/1758-907X-1-8  0.64
2009 Naganuma M, Sekine S, Fukunaga R, Yokoyama S. Unique protein architecture of alanyl-tRNA synthetase for aminoacylation, editing, and dimerization. Proceedings of the National Academy of Sciences of the United States of America. 106: 8489-94. PMID 19423669 DOI: 10.1073/Pnas.0901572106  0.375
2009 Fukunaga R, Doudna JA. dsRNA with 5' overhangs contributes to endogenous and antiviral RNA silencing pathways in plants. The Embo Journal. 28: 545-55. PMID 19165150 DOI: 10.1038/Emboj.2009.2  0.586
2008 Yanagisawa T, Ishii R, Fukunaga R, Kobayashi T, Sakamoto K, Yokoyama S. Multistep engineering of pyrrolysyl-tRNA synthetase to genetically encode N(epsilon)-(o-azidobenzyloxycarbonyl) lysine for site-specific protein modification. Chemistry & Biology. 15: 1187-97. PMID 19022179 DOI: 10.1016/J.Chembiol.2008.10.004  0.301
2008 Fukunaga R, Harada Y, Hirao I, Yokoyama S. Phosphoserine aminoacylation of tRNA bearing an unnatural base anticodon. Biochemical and Biophysical Research Communications. 372: 480-5. PMID 18503748 DOI: 10.1016/J.Bbrc.2008.05.078  0.322
2008 Yanagisawa T, Ishii R, Fukunaga R, Kobayashi T, Sakamoto K, Yokoyama S. Crystallographic studies on multiple conformational states of active-site loops in pyrrolysyl-tRNA synthetase. Journal of Molecular Biology. 378: 634-52. PMID 18387634 DOI: 10.1016/J.Jmb.2008.02.045  0.31
2007 Fukunaga R, Yokoyama S. Structural insights into the second step of RNA-dependent cysteine biosynthesis in archaea: crystal structure of Sep-tRNA:Cys-tRNA synthase from Archaeoglobus fulgidus. Journal of Molecular Biology. 370: 128-41. PMID 17512006 DOI: 10.1016/J.Jmb.2007.04.050  0.413
2007 Fukunaga R, Yokoyama S. The C-terminal domain of the archaeal leucyl-tRNA synthetase prevents misediting of isoleucyl-tRNA(Ile). Biochemistry. 46: 4985-96. PMID 17407269 DOI: 10.1021/Bi6024935  0.305
2007 Fukunaga R, Yokoyama S. Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea. Nature Structural & Molecular Biology. 14: 272-9. PMID 17351629 DOI: 10.1038/Nsmb1219  0.378
2007 Fukunaga R, Yokoyama S. Structure of the AlaX-M trans-editing enzyme from Pyrococcus horikoshii. Acta Crystallographica. Section D, Biological Crystallography. 63: 390-400. PMID 17327676 DOI: 10.1107/S090744490605640X  0.36
2006 Yanagisawa T, Ishii R, Fukunaga R, Nureki O, Yokoyama S. Crystallization and preliminary X-ray crystallographic analysis of the catalytic domain of pyrrolysyl-tRNA synthetase from the methanogenic archaeon Methanosarcina mazei. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 62: 1031-3. PMID 17012805 DOI: 10.1107/S1744309106036700  0.309
2006 Sasaki HM, Sekine S, Sengoku T, Fukunaga R, Hattori M, Utsunomiya Y, Kuroishi C, Kuramitsu S, Shirouzu M, Yokoyama S. Structural and mutational studies of the amino acid-editing domain from archaeal/eukaryal phenylalanyl-tRNA synthetase. Proceedings of the National Academy of Sciences of the United States of America. 103: 14744-9. PMID 17003130 DOI: 10.1073/Pnas.0603182103  0.364
2006 Fukunaga R, Yokoyama S. Structural basis for substrate recognition by the editing domain of isoleucyl-tRNA synthetase. Journal of Molecular Biology. 359: 901-12. PMID 16697013 DOI: 10.1016/J.Jmb.2006.04.025  0.329
2005 Fukunaga R, Yokoyama S. Aminoacylation complex structures of leucyl-tRNA synthetase and tRNALeu reveal two modes of discriminator-base recognition. Nature Structural & Molecular Biology. 12: 915-22. PMID 16155584 DOI: 10.1038/Nsmb985  0.38
2005 Tukalo M, Yaremchuk A, Fukunaga R, Yokoyama S, Cusack S. The crystal structure of leucyl-tRNA synthetase complexed with tRNALeu in the post-transfer-editing conformation. Nature Structural & Molecular Biology. 12: 923-30. PMID 16155583 DOI: 10.1038/Nsmb986  0.391
2005 Fukunaga R, Yokoyama S. Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain. The Journal of Biological Chemistry. 280: 29937-45. PMID 15970591 DOI: 10.1074/Jbc.M502668200  0.368
2005 Kuratani M, Ishii R, Bessho Y, Fukunaga R, Sengoku T, Shirouzu M, Sekine S, Yokoyama S. Crystal structure of tRNA adenosine deaminase (TadA) from Aquifex aeolicus. The Journal of Biological Chemistry. 280: 16002-8. PMID 15677468 DOI: 10.1074/Jbc.M414541200  0.341
2005 Fukunaga R, Yokoyama S. Crystal structure of leucyl-tRNA synthetase from the archaeon Pyrococcus horikoshii reveals a novel editing domain orientation. Journal of Molecular Biology. 346: 57-71. PMID 15663927 DOI: 10.1016/J.Jmb.2004.11.060  0.354
2004 Fukunaga R, Yokoyama S. Crystallization and preliminary X-ray crystallographic study of the editing domain of Thermus thermophilus isoleucyl-tRNA synthetase complexed with pre- and post-transfer editing-substrate analogues. Acta Crystallographica. Section D, Biological Crystallography. 60: 1900-2. PMID 15388946 DOI: 10.1107/S0907444904019511  0.343
2004 Fukunaga R, Fukai S, Ishitani R, Nureki O, Yokoyama S. Crystal structures of the CP1 domain from Thermus thermophilus isoleucyl-tRNA synthetase and its complex with L-valine. The Journal of Biological Chemistry. 279: 8396-402. PMID 14672940 DOI: 10.1074/Jbc.M312830200  0.314
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