Ryuya Fukunaga - Related publications

2013- Biological Chemistry Johns Hopkins University School of Medicine, Baltimore, MD, United States 
RNA silencing mechanism
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Yang WQ, Xiong QP, Ge JY, Li H, Zhu WY, Nie Y, Lin X, Lv D, Li J, Lin H, Liu RJ. THUMPD3-TRMT112 is a m2G methyltransferase working on a broad range of tRNA substrates. Nucleic Acids Research. PMID 34669960 DOI: 10.1093/nar/gkab927   
2021 Wang N, Dong WL, Zhang XJ, Zhou T, Huang XJ, Li BG, Liu JN, Ma XF, Li ZH. Evolutionary characteristics and phylogeny of cotton chloroplast tRNAs. Planta. 254: 116. PMID 34750674 DOI: 10.1007/s00425-021-03775-1   
2021 Thomas NK, Poodari VC, Jain M, Olsen HE, Akeson M, Abu-Shumays RL. Direct Nanopore Sequencing of Individual Full Length tRNA Strands. Acs Nano. PMID 34618430 DOI: 10.1021/acsnano.1c06488   
2021 Ravel JM, Dreumont N, Mosca P, Smith DEC, Mendes MI, Wiedemann A, Coelho D, Schmitt E, Rivière JB, Tran Mau-Them F, Thevenon J, Kuentz P, Polivka M, Fuchs SA, Kok G, et al. A bi-allelic loss-of-function SARS1 variant in children with neurodevelopmental delay, deafness, cardiomyopathy, and decompensation during fever. Human Mutation. 42: 1576-1583. PMID 34570399 DOI: 10.1002/humu.24285   
2021 Shen L, Su Z, Yang K, Wu C, Becker T, Bell-Pedersen D, Zhang J, Sachs MS. Structure of the translating ribosome arrested by cycloheximide. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34815343 DOI: 10.1073/pnas.2111862118   
2021 Lee JO, Lee M, Chung YJ. DBtRend: A Web-Server of tRNA Expression Profiles from Small RNA Sequencing Data in Humans. Genes. 12. PMID 34680971 DOI: 10.3390/genes12101576   
2021 Schöller E, Marks J, Marchand V, Bruckmann A, Powell CA, Reichold M, Mutti CD, Dettmer K, Feederle R, Hüttelmaier S, Helm M, Oefner P, Minczuk M, Motorin Y, Hafner M, et al. Balancing of mitochondrial translation through METTL8-mediated mC modification of mitochondrial tRNAs. Molecular Cell. PMID 34774131 DOI: 10.1016/j.molcel.2021.10.018   
2021 Joon S, Singal B, Grüber A, Wong DMK, Ragunathan P, Grüber G. Atomic structure of the regulatory TGS domain of Rel protein from Mycobacterium tuberculosis and its interaction with deacylated tRNA. Febs Letters. PMID 34808002 DOI: 10.1002/1873-3468.14236   
2021 Lee BS, Choi WJ, Lee SW, Ko BJ, Yoo TH. Towards Engineering an Orthogonal Protein Translation Initiation System. Frontiers in Chemistry. 9: 772648. PMID 34765589 DOI: 10.3389/fchem.2021.772648   
2021 Kouvela A, Zaravinos A, Stamatopoulou V. Adaptor Molecules Epitranscriptome Reprograms Bacterial Pathogenicity. International Journal of Molecular Sciences. 22. PMID 34445114 DOI: 10.3390/ijms22168409   
2021 Li H, Dong H, Xu B, Xiong QP, Li CT, Yang WQ, Li J, Huang ZX, Zeng QY, Wang ED, Liu RJ. A dual role of human tRNA methyltransferase hTrmt13 in regulating translation and transcription. The Embo Journal. e108544. PMID 34850409 DOI: 10.15252/embj.2021108544   
2021 Chen M, Long Q, Borrie MS, Sun H, Zhang C, Yang H, Shi D, Gartenberg MR, Deng W. Nucleoporin TPR promotes tRNA nuclear export and protein synthesis in lung cancer cells. Plos Genetics. 17: e1009899. PMID 34793452 DOI: 10.1371/journal.pgen.1009899   
2021 Guegueniat J, Halabelian L, Zeng H, Dong A, Li Y, Wu H, Arrowsmith CH, Kothe U. The human pseudouridine synthase PUS7 recognizes RNA with an extended multi-domain binding surface. Nucleic Acids Research. PMID 34718722 DOI: 10.1093/nar/gkab934   
2021 Zeng F, Li X, Pires-Alves M, Chen X, Hawk CW, Jin H. Conserved heterodimeric GTPase Rbg1/Tma46 promotes efficient translation in eukaryotic cells. Cell Reports. 37: 109877. PMID 34706231 DOI: 10.1016/j.celrep.2021.109877   
2021 Liu C, Yuan J, Zhang X, Jin S, Li F, Xiang J. tRNA copy number and codon usage in the sea cucumber genome provide insights into adaptive translation for saponin biosynthesis. Open Biology. 11: 210190. PMID 34753322 DOI: 10.1098/rsob.210190   
2021 Fradejas-Villar N, Bohleber S, Zhao W, Reuter U, Kotter A, Helm M, Knoll R, McFarland R, Taylor RW, Mo Y, Miyauchi K, Sakaguchi Y, Suzuki T, Schweizer U. The Effect of tRNA Isopentenylation on Selenoprotein Expression. International Journal of Molecular Sciences. 22. PMID 34768885 DOI: 10.3390/ijms222111454   
2021 Gu H, Lian B, Yuan Y, Kong C, Li Y, Liu C, Qi Y. A 5' tRNA-Ala-derived small RNA regulates anti-fungal defense in plants. Science China. Life Sciences. PMID 34705222 DOI: 10.1007/s11427-021-2017-1   
2021 Zahra S, Singh A, Poddar N, Kumar S. Transfer RNA-derived non-coding RNAs (tncRNAs): Hidden regulation of plants' transcriptional regulatory circuits. Computational and Structural Biotechnology Journal. 19: 5278-5291. PMID 34630945 DOI: 10.1016/j.csbj.2021.09.021   
2021 Daniels PN, Lee H, Splain RA, Ting CP, Zhu L, Zhao X, Moore BS, van der Donk WA. A biosynthetic pathway to aromatic amines that uses glycyl-tRNA as nitrogen donor. Nature Chemistry. PMID 34725492 DOI: 10.1038/s41557-021-00802-2   
2021 Yamasaki S, Nakashima M, Ida H. Possible Roles of tRNA Fragments, as New Regulatory ncRNAs, in the Pathogenesis of Rheumatoid Arthritis. International Journal of Molecular Sciences. 22. PMID 34502386 DOI: 10.3390/ijms22179481   
2021 Hu XP, Lercher MJ. An optimal growth law for RNA composition and its partial implementation through ribosomal and tRNA gene locations in bacterial genomes. Plos Genetics. 17: e1009939. PMID 34843465 DOI: 10.1371/journal.pgen.1009939   
2021 Das R, Watkins AM. RiboDraw: semiautomated two-dimensional drawing of RNA tertiary structure diagrams. Nar Genomics and Bioinformatics. 3: lqab091. PMID 34661102 DOI: 10.1093/nargab/lqab091   
2021 Sekulovski S, Devant P, Panizza S, Gogakos T, Pitiriciu A, Heitmeier K, Ramsay EP, Barth M, Schmidt C, Tuschl T, Baas F, Weitzer S, Martinez J, Trowitzsch S. Assembly defects of human tRNA splicing endonuclease contribute to impaired pre-tRNA processing in pontocerebellar hypoplasia. Nature Communications. 12: 5610. PMID 34584079 DOI: 10.1038/s41467-021-25870-3   
2021 Flores ME, McNamara-Bordewick NK, Lovinger NL, Snow JW. Halofuginone triggers a transcriptional program centered on ribosome biogenesis and function in honey bees. Insect Biochemistry and Molecular Biology. 139: 103667. PMID 34626768 DOI: 10.1016/j.ibmb.2021.103667   
2021 Chan DL, Rudinger-Thirion J, Frugier M, Riley LG, Ho G, Kothur K, Mohammad SS. A case of QARS1 associated epileptic encephalopathy and review of epilepsy in aminoacyl-tRNA synthetase disorders. Brain & Development. PMID 34774383 DOI: 10.1016/j.braindev.2021.10.009   
2021 Ficaretta ED, Wrobel CJJ, Roy SJS, Erickson SB, Italia JS, Chatterjee A. A Robust Platform for Unnatural Amino Acid Mutagenesis in E. coli Using the Bacterial Tryptophanyl-tRNA synthetase/tRNA pair. Journal of Molecular Biology. 167304. PMID 34655653 DOI: 10.1016/j.jmb.2021.167304   
2021 Wang MQ, Yao R, Jiang F, Zhan XD. Determination of the complete mitochondrial genome of (Acari: Astigmata). Mitochondrial Dna. Part B, Resources. 6: 3222-3223. PMID 34676294 DOI: 10.1080/23802359.2021.1990147   
2021 Zhang G, Yang C, Chen L, Chen G, Wang J. Complete mitochondrial genome of the spectacled parrotbill David, 1871 (Aves: Passeriformes: Sylviidae). Mitochondrial Dna. Part B, Resources. 6: 3244-3245. PMID 34746398 DOI: 10.1080/23802359.2021.1991241   
2021 Kato Y. Plasmid Curing and Exchange Using a Novel Counter-Selectable Marker Based on Unnatural Amino Acid Incorporation at a Sense Codon. International Journal of Molecular Sciences. 22. PMID 34768910 DOI: 10.3390/ijms222111482   
2021 Zhao H, Qin Y, Xiao Z, Liang K, Gong D, Sun Q, Qiu F. Knockdown NRPC2, 3, 8, NRPABC1 and NRPABC2 Affects RNAPIII Activity and Disrupts Seed Development in Arabidopsis. International Journal of Molecular Sciences. 22. PMID 34768744 DOI: 10.3390/ijms222111314   
2021 Dong Y, Tong H, Hu Q, Dong X. RNase Z Oxidative Degradation Impedes tRNA Maturation and is Involved in Streptococcal Translation Regulation in Response to Oxidative Stress. Microbiology Spectrum. e0116721. PMID 34704809 DOI: 10.1128/Spectrum.01167-21   
2021 Chandrasekaran V, Desai N, Burton NO, Yang H, Price J, Miska EA, Ramakrishnan V. Visualizing formation of the active site in the mitochondrial ribosome. Elife. 10. PMID 34609277 DOI: 10.7554/eLife.68806   
2021 Kim KQ, Zaher HS. Canary in a coal mine: collided ribosomes as sensors of cellular conditions. Trends in Biochemical Sciences. PMID 34607755 DOI: 10.1016/j.tibs.2021.09.001   
2021 Ding X, Zhang C, Gao Y, Bei Z, Yan X. Characterization of the complete chloroplast genome of (Fabaceae). Mitochondrial Dna. Part B, Resources. 6: 3278-3279. PMID 34712811 DOI: 10.1080/23802359.2021.1993105   
2021 Cassaignau AME, Włodarski T, Chan SHS, Woodburn LF, Bukvin IV, Streit JO, Cabrita LD, Waudby CA, Christodoulou J. Interactions between nascent proteins and the ribosome surface inhibit co-translational folding. Nature Chemistry. PMID 34650236 DOI: 10.1038/s41557-021-00796-x   
2021 Srinivas P, Steiner RE, Pavelich IJ, Guerrero-Ferreira R, Juneja P, Ibba M, Dunham CM. Oxidation alters the architecture of the phenylalanyl-tRNA synthetase editing domain to confer hyperaccuracy. Nucleic Acids Research. PMID 34581811 DOI: 10.1093/nar/gkab856   
2021 Zou Q, Yang L, Shi R, Qi Y, Zhang X, Qi H. Proteostasis regulated by testis-specific ribosomal protein RPL39L maintains mouse spermatogenesis. Iscience. 24: 103396. PMID 34825148 DOI: 10.1016/j.isci.2021.103396   
2021 Ohkubo A, Van Haute L, Rudler DL, Stentenbach M, Steiner FA, Rackham O, Minczuk M, Filipovska A, Martinou JC. The FASTK family proteins fine-tune mitochondrial RNA processing. Plos Genetics. 17: e1009873. PMID 34748562 DOI: 10.1371/journal.pgen.1009873   
2021 Gu Y, Mao Y, Jia L, Dong L, Qian SB. Bi-directional ribosome scanning controls the stringency of start codon selection. Nature Communications. 12: 6604. PMID 34782646 DOI: 10.1038/s41467-021-26923-3   
2021 Jaafar M, Contreras J, Dominique C, Martín-Villanueva S, Capeyrou R, Vitali P, Rodríguez-Galán O, Velasco C, Humbert O, Watkins NJ, Villalobo E, Bohnsack KE, Bohnsack MT, Henry Y, Merhi RA, et al. Association of snR190 snoRNA chaperone with early pre-60S particles is regulated by the RNA helicase Dbp7 in yeast. Nature Communications. 12: 6153. PMID 34686656 DOI: 10.1038/s41467-021-26207-w   
2021 Liu C, Huang H, Duan X, Chen Y. Integrated Metagenomic and Metaproteomic Analyses Unravel Ammonia Toxicity to Active Methanogens and Syntrophs, Enzyme Synthesis, and Key Enzymes in Anaerobic Digestion. Environmental Science & Technology. 55: 14817-14827. PMID 34657430 DOI: 10.1021/acs.est.1c00797   
2021 Leininger SE, Rodriguez J, Vu QV, Jiang Y, Li MS, Deutsch C, O'Brien EP. Ribosome Elongation Kinetics of Consecutively Charged Residues Are Coupled to Electrostatic Force. Biochemistry. PMID 34652913 DOI: 10.1021/acs.biochem.1c00507   
2021 Luo Y, Shi DQ, Jia PF, Bao Y, Li HJ, Yang WC. Nucleolar histone deacetylases HDT1, HDT2 and HDT3 regulate plant reproductive development. Journal of Genetics and Genomics = Yi Chuan Xue Bao. PMID 34699991 DOI: 10.1016/j.jgg.2021.10.002   
2021 Zhu L, Che X, Liu X, Wang X, Wang J, Cheng G, Chen X, Chen X. Complete mitochondrial genome of Bleekers (Cypriniformes: Cyprinidae) in China's Dianshan Lake. Mitochondrial Dna. Part B, Resources. 6: 3367-3368. PMID 34778555 DOI: 10.1080/23802359.2021.1997109   
2021 Aquino GRR, Hackert P, Krogh N, Pan KT, Jaafar M, Henras AK, Nielsen H, Urlaub H, Bohnsack KE, Bohnsack MT. The RNA helicase Dbp7 promotes domain V/VI compaction and stabilization of inter-domain interactions during early 60S assembly. Nature Communications. 12: 6152. PMID 34686661 DOI: 10.1038/s41467-021-26208-9   
2021 Tandon S, Muthuswami R, Madhubala R. Role of two aminoacyl-tRNA synthetase associated proteins (Endothelial Monocyte Activating Polypeptides 1 and 2) of Leishmania donovani in chemotaxis of human monocytes. Acta Tropica. 224: 106128. PMID 34509454 DOI: 10.1016/j.actatropica.2021.106128   
2021 Yi X, He S, Wang S, Zhao H, Wu M, Liu S, Pan Y, Zhang Y, Sun X. Expression of different genotypes of bovine TRDMT1 gene and its polymorphisms association with body measures in Qinchuan cattle (Bos Taurus). Animal Biotechnology. 1-11. PMID 34629027 DOI: 10.1080/10495398.2021.1984248   
2021 Mo C, Xie C, Wang G, Tian T, Liu J, Zhu C, Xiao X, Xiao Y. Cyclophilin acts as a ribosome biogenesis factor by chaperoning the ribosomal protein (PlRPS15) in filamentous fungi. Nucleic Acids Research. PMID 34792171 DOI: 10.1093/nar/gkab1102   
2021 Guzman-Luna V, Fuchs AM, Allen AJ, Staikos A, Cavagnero S. An intrinsically disordered nascent protein interacts with specific regions of the ribosomal surface near the exit tunnel. Communications Biology. 4: 1236. PMID 34716402 DOI: 10.1038/s42003-021-02752-4   
2021 Zhu L, Zhu Z, Zhu L, Wang D, Wang J, Lin Q. The complete mitogenome of Lysmata vittata (Crustacea: Decapoda: Hippolytidae) with implication of phylogenomics and population genetics. Plos One. 16: e0255547. PMID 34735446 DOI: 10.1371/journal.pone.0255547