Complexity and dynamics of in organello translation landscape assessed by high-resolution mitochondrial ribosome profiling
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Tsutomu Suzuki | K. Tomizawa | Haruna Yamashiro | Takeo Suzuki | Shintaro Iwasaki | Asuteka Nagao | M. Mito | Yuichi Shichino | T. Chujo | Fan-Yan Wei | Taisei Wakigawa | Kotaro Tomuro | Haruna Tani
[1] M. Doi,et al. Absolute calibration of ribosome profiling assesses the dynamics of ribosomal flux on transcripts , 2023, bioRxiv.
[2] Yoshimi Kawamura,et al. NSUN3-mediated mitochondrial tRNA 5-formylcytidine modification is essential for embryonic development and respiratory complexes in mice , 2023, Communications Biology.
[3] Tsutomu Suzuki,et al. Restoration of mitochondrial function through activation of hypomodified tRNAs with pathogenic mutations associated with mitochondrial diseases , 2023, Nucleic acids research.
[4] A. Higashibata,et al. Gravitational and mechanical forces drive mitochondrial translation through the cell adhesion–FAK axis , 2023, bioRxiv.
[5] Shintaro Iwasaki,et al. Thor-Ribo-Seq: ribosome profiling tailored for low input with RNA-dependent RNA amplification , 2023, bioRxiv.
[6] A. Firth,et al. Translation initiation of leaderless and polycistronic transcripts in mammalian mitochondria , 2023, Nucleic acids research.
[7] Shintaro Iwasaki,et al. Compounds for selective translational inhibition. , 2022, Current opinion in chemical biology.
[8] Haiwang Yang,et al. Low-input RNase footprinting for simultaneous quantification of cytosolic and mitochondrial translation , 2022, Genome research.
[9] D. Klepacki,et al. Structural basis for the context-specific action of the classic peptidyl transferase inhibitor chloramphenicol , 2022, Nature Structural & Molecular Biology.
[10] R. Green,et al. Bursting Translation on Single mRNAs in Live Cells , 2022, bioRxiv.
[11] Shintaro Iwasaki,et al. Into the matrix: current methods for mitochondrial translation studies. , 2022, Journal of biochemistry.
[12] Tatsuya Osaki,et al. Mito-FUNCAT-FACS reveals cellular heterogeneity in mitochondrial translation , 2022, bioRxiv.
[13] H. Taguchi,et al. The landscape of translational stall sites in bacteria revealed by monosome and disome profiling , 2021, RNA.
[14] P. Oefner,et al. Balancing of mitochondrial translation through METTL8-mediated m3C modification of mitochondrial tRNAs. , 2021, Molecular cell.
[15] H. Urlaub,et al. An in vitro system to silence mitochondrial gene expression , 2021, Cell.
[16] Sebastian A. Leidel,et al. Humans and other commonly used model organisms are resistant to cycloheximide-mediated biases in ribosome profiling experiments , 2021, Nature Communications.
[17] A. Mankin,et al. Structural basis for context-specific inhibition of translation by oxazolidinone antibiotics , 2021, bioRxiv.
[18] F. Weber,et al. eIF2B-capturing viral protein NSs suppresses the integrated stress response , 2021, Nature Communications.
[19] L. S. Churchman,et al. Balanced mitochondrial and cytosolic translatomes underlie the biogenesis of human respiratory complexes , 2021, bioRxiv.
[20] Sophia Hsin-Jung Li,et al. Monitoring mammalian mitochondrial translation with MitoRiboSeq , 2021, Nature Protocols.
[21] Tsutomu Suzuki. The expanding world of tRNA modifications and their disease relevance , 2021, Nature Reviews Molecular Cell Biology.
[22] E. Kim,et al. Ribosome stalling and SGS3 phase separation prime the epigenetic silencing of transposons , 2021, Nature Plants.
[23] R. Best,et al. Mechanism of membrane-tethered mitochondrial protein synthesis , 2021, Science.
[24] N. Ban,et al. Mechanisms and regulation of protein synthesis in mitochondria , 2021, Nature Reviews Molecular Cell Biology.
[25] Wenfeng Qian,et al. Disome-seq reveals widespread ribosome collisions that promote cotranslational protein folding , 2021, Genome biology.
[26] V. Gladyshev,et al. Translation elongation rate varies among organs and decreases with age , 2020, Nucleic acids research.
[27] Yuichiro Mishima,et al. Protocol for Disome Profiling to Survey Ribosome Collision in Humans and Zebrafish , 2020, STAR protocols.
[28] Angus E. McMillan,et al. Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome , 2020, Science.
[29] Tsutomu Suzuki,et al. Complete chemical structures of human mitochondrial tRNAs , 2020, Nature Communications.
[30] N. Guydosh,et al. Disome and Trisome Profiling Reveal Genome-wide Targets of Ribosome Quality Control. , 2020, Molecular cell.
[31] A. Tuck,et al. Mammalian RNA Decay Pathways Are Highly Specialized and Widely Linked to Translation , 2020, Molecular cell.
[32] Maxim N. Shokhirev,et al. Accurate annotation of human protein-coding small open reading frames , 2019, Nature Chemical Biology.
[33] Jeffrey A. Hussmann,et al. GIGYF2 and 4EHP Inhibit Translation Initiation of Defective Messenger RNAs to Assist Ribosome-Associated Quality Control , 2019, bioRxiv.
[34] Yuichiro Mishima,et al. Genome-wide survey of ribosome collision , 2019, bioRxiv.
[35] D. Gatfield,et al. Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing , 2019, bioRxiv.
[36] J. Weissman,et al. Cycloheximide can distort measurements of mRNA levels and translation efficiency , 2019, Nucleic acids research.
[37] R. Green,et al. High-Resolution Ribosome Profiling Defines Discrete Ribosome Elongation States and Translational Regulation during Cellular Stress. , 2019, Molecular cell.
[38] R. Green,et al. A systematically-revised ribosome profiling method for bacteria reveals pauses at single-codon resolution , 2019, eLife.
[39] D. Klepacki,et al. Retapamulin-assisted ribosome profiling reveals the alternative bacterial proteome , 2019, bioRxiv.
[40] J. Richter,et al. Optimization of ribosome profiling using low-input brain tissue from fragile X syndrome model mice , 2018, Nucleic acids research.
[41] T. Morisaki,et al. Quantifying Single mRNA Translation Kinetics in Living Cells. , 2018, Cold Spring Harbor perspectives in biology.
[42] Xiao He,et al. Deletion of Mtu1 (Trmu) in zebrafish revealed the essential role of tRNA modification in mitochondrial biogenesis and hearing function , 2018, Nucleic acids research.
[43] G. Dittmar,et al. Queuosine‐modified tRNAs confer nutritional control of protein translation , 2018, The EMBO journal.
[44] E. Phizicky,et al. A rationale for tRNA modification circuits in the anticodon loop , 2018, RNA.
[45] C. Fraser,et al. Toward a Kinetic Understanding of Eukaryotic Translation. , 2018, Cold Spring Harbor perspectives in biology.
[46] Tsutomu Suzuki,et al. CO2-sensitive tRNA modification associated with human mitochondrial disease , 2018, Nature Communications.
[47] Jia Gu,et al. fastp: an ultra-fast all-in-one FASTQ preprocessor , 2018, bioRxiv.
[48] Y. Okazaki,et al. Metabolic and chemical regulation of tRNA modification associated with taurine deficiency and human disease , 2018, Nucleic acids research.
[49] Sophia Hsin-Jung Li,et al. Mitochondrial translation requires folate-dependent tRNA methylation , 2018, Nature.
[50] L. Scorrano,et al. Defective Mitochondrial tRNA Taurine Modification Activates Global Proteostress and Leads to Mitochondrial Disease. , 2018, Cell reports.
[51] Anna Feldman,et al. The extent of ribosome queuing in budding yeast , 2018, PLoS Comput. Biol..
[52] J. Chao,et al. Single-Molecule Quantification of Translation-Dependent Association of mRNAs with the Endoplasmic Reticulum. , 2017, Cell reports.
[53] R. Agami,et al. Using mitoribosomal profiling to investigate human mitochondrial translation , 2017, Wellcome open research.
[54] M. Garber,et al. Transcriptome-wide Analysis of Roles for tRNA Modifications in Translational Regulation. , 2017, Molecular cell.
[55] F. Förster,et al. Structure of the Human Mitochondrial Ribosome Studied In Situ by Cryoelectron Tomography. , 2017, Structure.
[56] J. Mata,et al. Effects of cycloheximide on the interpretation of ribosome profiling experiments in Schizosaccharomyces pombe , 2017, Scientific Reports.
[57] Nicholas T Ingolia,et al. Transcriptome-wide measurement of translation by ribosome profiling. , 2017, Methods.
[58] A. Suomalainen,et al. Mitochondrial diseases: the contribution of organelle stress responses to pathology , 2017, Nature Reviews Molecular Cell Biology.
[59] Tsutomu Suzuki,et al. ALKBH1 is an RNA dioxygenase responsible for cytoplasmic and mitochondrial tRNA modifications , 2017, Nucleic acids research.
[60] R. Green,et al. eIF5A Functions Globally in Translation Elongation and Termination. , 2017, Molecular cell.
[61] K. Kannan,et al. Context-specific inhibition of translation by ribosomal antibiotics targeting the peptidyl transferase center , 2016, Proceedings of the National Academy of Sciences.
[62] S. Oeljeklaus,et al. Mitochondrial Protein Synthesis Adapts to Influx of Nuclear-Encoded Protein , 2016, Cell.
[63] Vadim N. Gladyshev,et al. Ribonuclease selection for ribosome profiling , 2016, Nucleic acids research.
[64] Tsutomu Suzuki,et al. Mtu1-Mediated Thiouridine Formation of Mitochondrial tRNAs Is Required for Mitochondrial Translation and Is Involved in Reversible Infantile Liver Injury , 2016, PLoS genetics.
[65] M. Rodnina,et al. NSUN3 and ABH1 modify the wobble position of mt‐tRNA Met to expand codon recognition in mitochondrial translation , 2016, The EMBO journal.
[66] Tsutomu Suzuki,et al. NSUN3 methylase initiates 5-formylcytidine biogenesis in human mitochondrial tRNA(Met). , 2016, Nature chemical biology.
[67] Michaela Frye,et al. Deficient methylation and formylation of mt-tRNAMet wobble cytosine in a patient carrying mutations in NSUN3 , 2016, Nature Communications.
[68] Bin Wu,et al. Translation dynamics of single mRNAs in live cells and neurons , 2016, Science.
[69] Luke D. Lavis,et al. Real-time quantification of single RNA translation dynamics in living cells , 2016, Science.
[70] A. Heger,et al. UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy , 2016, bioRxiv.
[71] X. Zhuang,et al. Real-Time Imaging of Translation on Single mRNA Transcripts in Live Cells , 2016, Cell.
[72] Ronald D. Vale,et al. Dynamics of Translation of Single mRNA Molecules In Vivo , 2016, Cell.
[73] V. de Crécy-Lagard,et al. Global translational impacts of the loss of the tRNA modification t6A in yeast , 2015, Microbial cell.
[74] Jeffrey A. Hussmann,et al. Understanding Biases in Ribosome Profiling Experiments Reveals Signatures of Translation Dynamics in Yeast , 2015, bioRxiv.
[75] Sebastian A. Leidel,et al. Optimization of Codon Translation Rates via tRNA Modifications Maintains Proteome Integrity , 2015, Cell.
[76] V. Kelly,et al. The Queuine Micronutrient: Charting a Course from Microbe to Man , 2015, Nutrients.
[77] F. Förster,et al. Organization of the mitochondrial translation machinery studied in situ by cryoelectron tomography , 2015, Nature Communications.
[78] Shu-Bing Qian,et al. Quantitative profiling of initiating ribosomes in vivo , 2014, Nature Methods.
[79] E. O’Shea,et al. An Integrated Approach Reveals Regulatory Controls on Bacterial Translation Elongation , 2014, Cell.
[80] W. Huber,et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.
[81] Vadim N. Gladyshev,et al. Translation inhibitors cause abnormalities in ribosome profiling experiments , 2014, Nucleic acids research.
[82] Neville E. Sanjana,et al. Improved vectors and genome-wide libraries for CRISPR screening , 2014, Nature Methods.
[83] P. Brown,et al. Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments , 2014, eLife.
[84] Rachel Green,et al. Dom34 Rescues Ribosomes in 3′ Untranslated Regions , 2014, Cell.
[85] Reuven Agami,et al. Ribosome profiling reveals features of normal and disease-associated mitochondrial translation , 2013, Nature Communications.
[86] W. Gilbert,et al. Loss of a Conserved tRNA Anticodon Modification Perturbs Cellular Signaling , 2013, PLoS genetics.
[87] F. Murphy,et al. Expanded use of sense codons is regulated by modified cytidines in tRNA , 2013, Proceedings of the National Academy of Sciences.
[88] Ching-Wei Chang,et al. Coordinated regulation of synthesis and stability of RNA during the acute TNF-induced proinflammatory response , 2013, Proceedings of the National Academy of Sciences.
[89] B. Shen,et al. Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution , 2012, Proceedings of the National Academy of Sciences.
[90] Jon R Lorsch,et al. A mechanistic overview of translation initiation in eukaryotes , 2012, Nature Structural &Molecular Biology.
[91] N. Nomura,et al. LRPPRC/SLIRP suppresses PNPase-mediated mRNA decay and promotes polyadenylation in human mitochondria , 2012, Nucleic acids research.
[92] A. Wakamatsu,et al. Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals , 2012, Genome research.
[93] Ji Yu,et al. Single-molecule imaging of translational output from individual RNA granules in neurons , 2012, Molecular biology of the cell.
[94] Nicholas T. Ingolia,et al. Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes , 2011, Cell.
[95] M. Haque,et al. Properties of the C-terminal Tail of Human Mitochondrial Inner Membrane Protein Oxa1L and Its Interactions with Mammalian Mitochondrial Ribosomes* , 2010, The Journal of Biological Chemistry.
[96] R. Lightowlers,et al. Human mitochondrial mRNAs—like members of all families, similar but different , 2010, Biochimica et biophysica acta.
[97] V. Kelly,et al. Characterization of the human tRNA-guanine transglycosylase: confirmation of the heterodimeric subunit structure. , 2010, RNA.
[98] M. Vinayak,et al. Queuosine modification of tRNA: its divergent role in cellular machinery. , 2009, Bioscience reports.
[99] H. True,et al. The Sua5 Protein Is Essential for Normal Translational Regulation in Yeast , 2009, Molecular and Cellular Biology.
[100] H. Mandel,et al. Acute infantile liver failure due to mutations in the TRMU gene. , 2009, American journal of human genetics.
[101] Nicholas T. Ingolia,et al. Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling , 2009, Science.
[102] L. Spremulli,et al. Unconventional decoding of the AUA codon as methionine by mitochondrial tRNAMet with the anticodon f5CAU as revealed with a mitochondrial in vitro translation system , 2009, Nucleic acids research.
[103] E. Shoubridge,et al. The A3243G tRNALeu(UUR) MELAS mutation causes amino acid misincorporation and a combined respiratory chain assembly defect partially suppressed by overexpression of EFTu and EFG2. , 2008, Human molecular genetics.
[104] Pierre Baldi,et al. An enhanced MITOMAP with a global mtDNA mutational phylogeny , 2006, Nucleic Acids Res..
[105] Martin Ott,et al. Mba1, a membrane‐associated ribosome receptor in mitochondria , 2006, The EMBO journal.
[106] Tsutomu Suzuki,et al. Specific correlation between the wobble modification deficiency in mutant tRNAs and the clinical features of a human mitochondrial disease. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[107] Y. Ohya,et al. Mitochondria-specific RNA-modifying Enzymes Responsible for the Biosynthesis of the Wobble Base in Mitochondrial tRNAs , 2005, Journal of Biological Chemistry.
[108] Takehiro Yasukawa,et al. Codon-specific translational defect caused by a wobble modification deficiency in mutant tRNA from a human mitochondrial disease. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[109] C. Florentz,et al. Recognition of human mitochondrial tRNALeu(UUR) by its cognate leucyl-tRNA synthetase. , 2004, Journal of molecular biology.
[110] R. Stuart,et al. Yeast Oxa1 interacts with mitochondrial ribosomes: the importance of the C‐terminal region of Oxa1 , 2003, The EMBO journal.
[111] W. Neupert,et al. Ribosome binding to the Oxa1 complex facilitates co‐translational protein insertion in mitochondria , 2003, The EMBO journal.
[112] C. Florentz,et al. Towards understanding human mitochondrial leucine aminoacylation identity. , 2003, Journal of molecular biology.
[113] Tsutomu Suzuki,et al. Taurine as a constituent of mitochondrial tRNAs: new insights into the functions of taurine and human mitochondrial diseases , 2002, The EMBO journal.
[114] Takehiro Yasukawa,et al. Modification Defect at Anticodon Wobble Nucleotide of Mitochondrial tRNAsLeu(UUR) with Pathogenic Mutations of Mitochondrial Myopathy, Encephalopathy, Lactic Acidosis, and Stroke-like Episodes* , 2000, The Journal of Biological Chemistry.
[115] Y. Goto,et al. A new mtDNA mutation associated with mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS). , 1991, Biochimica et biophysica acta.
[116] K. Nihei,et al. A point mutation in the mitochondrial tRNA(Leu)(UUR) gene in MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes). , 1990, Biochemical and biophysical research communications.
[117] I. Nonaka,et al. A mutation in the tRNALeu(UUR) gene associated with the MELAS subgroup of mitochondrial encephalomyopathies , 1990, Nature.
[118] A. Byström,et al. Prevention of translational frameshifting by the modified nucleoside 1-methylguanosine. , 1989, Science.
[119] F. Sanger,et al. Sequence and organization of the human mitochondrial genome , 1981, Nature.
[120] Thomas R. Gingeras,et al. STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..
[121] S. Dimauro,et al. Mitochondrial diseases. , 1989, Neurologic clinics.