The emerging complexity of the tRNA world: mammalian tRNAs beyond protein synthesis
暂无分享,去创建一个
[1] M. Ibba,et al. Translation quality control is critical for bacterial responses to amino acid stress , 2016, Proceedings of the National Academy of Sciences.
[2] Bianca M. Schmitt,et al. Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States , 2016, PLoS genetics.
[3] S. Perner,et al. Identification of aberrant tRNA-halves expression patterns in clear cell renal cell carcinoma , 2016, Scientific Reports.
[4] M. Voskuil,et al. The Mycobacterium tuberculosis DosR Regulon Assists in Metabolic Homeostasis and Enables Rapid Recovery from Nonrespiring Dormancy , 2009, Journal of bacteriology.
[5] Resected RNA pseudoknots and their recognition by histidyl-tRNA synthetase. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[6] Xiaoping Zhou,et al. Genome-wide analysis reveals origin of transfer RNA genes from tRNA halves. , 2013, Molecular biology and evolution.
[7] W. Schamel,et al. Molecular evolution of transfer RNA from two precursor hairpins: Implications for the origin of protein synthesis , 1995, Journal of Molecular Evolution.
[8] Todd M. Lowe,et al. ARM-Seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments , 2015, Nature Methods.
[9] K. Musier-Forsyth,et al. Formation of the tRNALys packaging complex in HIV‐1 , 2010, FEBS letters.
[10] J. L. Bethune,et al. Tumor-derived angiogenesis factors from rat Walker 256 carcinoma: an experimental investigation and review , 1985, Experientia.
[11] S Rodin,et al. The presence of codon-anticodon pairs in the acceptor stem of tRNAs. , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[12] P. Ivanov,et al. RNA biology of angiogenin: Current state and perspectives , 2017, RNA biology.
[13] Z. Ignatova,et al. Emerging roles of tRNA in adaptive translation, signalling dynamics and disease , 2014, Nature Reviews Genetics.
[14] James A. Raleigh,et al. Tuberculous Granulomas Are Hypoxic in Guinea Pigs, Rabbits, and Nonhuman Primates , 2008, Infection and Immunity.
[15] M. Bushell,et al. Translational regulation of gene expression during conditions of cell stress. , 2010, Molecular cell.
[16] T. Pan,et al. Evolutionary Gain of Alanine Mischarging to Noncognate tRNAs with a G4:U69 Base Pair. , 2016, Journal of the American Chemical Society.
[17] S. Martinis,et al. Acceptor stem and anticodon RNA hairpin helix interactions with glutamine tRNA synthetase. , 1993, Biochimie.
[18] David I. K. Martin,et al. 5′ tRNA halves are present as abundant complexes in serum, concentrated in blood cells, and modulated by aging and calorie restriction , 2013, BMC Genomics.
[19] Paul Schimmel,et al. Distinct domains of tRNA synthetase recognize the same base pair , 2008, Nature.
[20] S. Ackerman,et al. Editing-defective tRNA synthetase causes protein misfolding and neurodegeneration , 2006, Nature.
[21] J. Barciszewski,et al. Modified Nucleic Acids in Biology and Medicine , 2016, RNA Technologies.
[22] A. Weiner,et al. tRNA-like structures tag the 3' ends of genomic RNA molecules for replication: implications for the origin of protein synthesis. , 1987, Proceedings of the National Academy of Sciences of the United States of America.
[23] H. Shulha,et al. Genetic and Epigenetic Variation, but Not Diet, Shape the Sperm Methylome. , 2015, Developmental cell.
[24] J. Tyagi,et al. Appropriate DevR (DosR)-Mediated Signaling Determines Transcriptional Response, Hypoxic Viability and Virulence of Mycobacterium tuberculosis , 2012, PloS one.
[25] Tao Pan,et al. Tissue-Specific Differences in Human Transfer RNA Expression , 2006, PLoS genetics.
[26] A. Weiner,et al. Molecular Evolution: Unlocking the secrets of retroviral evolution , 1994, Current Biology.
[27] C. Florentz,et al. Efficient aminoacylation of resected RNA helices by class II aspartyl‐tRNA synthetase dependent on a single nucleotide. , 1994, The EMBO journal.
[28] Ya-Ming Hou,et al. Enzymatic aminoacylation of tRNA acceptor stem helices with cysteine is dependent on a single nucleotide. , 1995, Biochemistry.
[29] Tao Pan,et al. Genome-wide analysis of N1-methyl-adenosine modification in human tRNAs. , 2010, RNA.
[30] Margaret J. Morris,et al. Chronic high-fat diet in fathers programs β-cell dysfunction in female rat offspring , 2010, Nature.
[31] M. Hafner,et al. RNA Polymerase III Output Is Functionally Linked to tRNA Dimethyl-G26 Modification , 2015, PLoS genetics.
[32] T. Pan,et al. Diversity of human tRNA genes from the 1000-genomes project , 2013, RNA biology.
[33] Jie Wu,et al. tRF2Cancer: A web server to detect tRNA-derived small RNA fragments (tRFs) and their expression in multiple cancers , 2016, Nucleic Acids Res..
[34] Masaru Tomita,et al. Tri-split tRNA is a transfer RNA made from 3 transcripts that provides insight into the evolution of fragmented tRNAs in archaea , 2009, Proceedings of the National Academy of Sciences.
[35] Jeffrey H. Chuang,et al. Activation of GCN2 kinase by ribosome stalling links translation elongation with translation initiation , 2016, eLife.
[36] J R Sampson,et al. Contributions of discrete tRNA(Ser) domains to aminoacylation by E.coli seryl-tRNA synthetase: a kinetic analysis using model RNA substrates. , 1993, Nucleic acids research.
[37] Arne Klungland,et al. ALKBH1-Mediated tRNA Demethylation Regulates Translation , 2016, Cell.
[38] P. Gounon,et al. RNA-mediated non-mendelian inheritance of an epigenetic change in the mouse , 2006, Nature.
[39] Steven P Gygi,et al. Angiogenin-induced tRNA fragments inhibit translation initiation. , 2011, Molecular cell.
[40] D. Guallar,et al. Regulation of Mouse Retroelement MuERV-L/MERVL Expression by REX1 and Epigenetic Control of Stem Cell Potency , 2014, Front. Oncol..
[41] Jernej Ule,et al. Aberrant methylation of tRNAs links cellular stress to neuro-developmental disorders , 2014, The EMBO journal.
[42] Peng Yao,et al. Aminoacyl-tRNA synthetases in medicine and disease , 2013, EMBO molecular medicine.
[43] T. Pan,et al. Functional analysis of human tRNA isodecoders. , 2010, Journal of molecular biology.
[44] J. Yewdell,et al. Innate Immune and Chemically Triggered Oxidative Stress Modifies Translational Fidelity , 2009, Nature.
[45] Michael H. Schwartz,et al. Global tRNA misacylation induced by anaerobiosis and antibiotic exposure broadly increases stress resistance in Escherichia coli , 2016, Nucleic acids research.
[46] Gordon C. K. Roberts,et al. Encyclopedia of Biophysics , 2013, Springer Berlin Heidelberg.
[47] Chao Cheng,et al. Protein mistranslation protects bacteria against oxidative stress , 2015, Nucleic acids research.
[48] Nathan Morris,et al. Codon Optimality Is a Major Determinant of mRNA Stability , 2015, Cell.
[49] Phillipe Loher,et al. Sex hormone-dependent tRNA halves enhance cell proliferation in breast and prostate cancers , 2015, Proceedings of the National Academy of Sciences.
[50] Sunghoon Kim,et al. Secreted tryptophanyl-tRNA synthetase as a primary defence system against infection , 2016, Nature Microbiology.
[51] Huihao Zhou,et al. Ribosome stalling induced by mutation of a CNS-specific tRNA causes neurodegeneration , 2014, Science.
[52] Christopher E. Mason,et al. Single-nucleotide resolution mapping of m6A and m6Am throughout the transcriptome , 2015, Nature Methods.
[53] P. Schimmel,et al. Trbp111 selectively binds a noncovalently assembled tRNA-like structure , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[54] Thomas J. Begley,et al. A Platform for Discovery and Quantification of Modified Ribonucleosides in RNA: Application to Stress-Induced Reprogramming of tRNA Modifications. , 2015, Methods in enzymology.
[55] Lisa Fish,et al. Endogenous tRNA-Derived Fragments Suppress Breast Cancer Progression via YBX1 Displacement , 2015, Cell.
[56] Paul Schimmel,et al. Aminoacylation of RNA minihelices with alanine , 1989, Nature.
[57] W. Wong,et al. Human tRNA synthetase catalytic nulls with diverse functions , 2014, Science.
[58] R Giegé,et al. An operational RNA code for amino acids and possible relationship to genetic code. , 1993, Proceedings of the National Academy of Sciences of the United States of America.
[59] S. Martinis,et al. Non-catalytic regulation of gene expression by aminoacyl-tRNA synthetases. , 2014, Topics in current chemistry.
[60] Jef Rozenski,et al. The RNA modification database, RNAMDB: 2011 update , 2010, Nucleic Acids Res..
[61] Eva Maria Novoa,et al. Speeding with control: codon usage, tRNAs, and ribosomes. , 2012, Trends in genetics : TIG.
[62] H. Nechushtan,et al. Non-canonical roles of lysyl-tRNA synthetase in health and disease. , 2013, Trends in molecular medicine.
[63] A. Lambowitz,et al. The mauriceville plasmid reverse transcriptase can initiate cDNA synthesis de novo and may be related to reverse transcriptase and DNA polymerase progenitor , 1993, Cell.
[64] Junchao Shi,et al. Identification and characterization of an ancient class of small RNAs enriched in serum associating with active infection , 2022 .
[65] Xin Niu,et al. tRNA-Derived Small Non-Coding RNAs in Response to Ischemia Inhibit Angiogenesis , 2016, Scientific Reports.
[66] T. Lowe,et al. Small RNA Modifications: Integral to Function and Disease. , 2016, Trends in molecular medicine.
[67] D. Söll,et al. Transfer RNA genes in pieces , 2008, EMBO reports.
[68] L. Farinelli,et al. Implication of sperm RNAs in transgenerational inheritance of the effects of early trauma in mice , 2014, Nature Neuroscience.
[69] Volker A. Erdmann,et al. The Translational Apparatus , 1993, Springer US.
[70] H. Lodish. Molecular Cell Biology , 1986 .
[71] Wei Li,et al. A novel class of tRNA-derived small RNAs extremely enriched in mature mouse sperm , 2012, Cell Research.
[72] Zhiping Weng,et al. Paternally Induced Transgenerational Environmental Reprogramming of Metabolic Gene Expression in Mammals , 2010, Cell.
[73] A. Shelling,et al. YB-1, the E2F pathway, and regulation of tumor cell growth. , 2012, Journal of the National Cancer Institute.
[74] C. de Duve. Transfer RNAs: the second genetic code. , 1988, Nature.
[75] Eduard Batlle,et al. Role of tRNA modifications in human diseases. , 2014, Trends in molecular medicine.
[76] S Cusack. Aminoacyl-tRNA synthetases. , 1997, Current opinion in structural biology.
[77] A. Rich,et al. Transfer RNA: molecular structure, sequence, and properties. , 1976, Annual review of biochemistry.
[78] Paul F Agris,et al. tRNA's wobble decoding of the genome: 40 years of modification. , 2007, Journal of molecular biology.
[79] P. Ivanov,et al. Regulated tRNA Cleavage in Biology and Medicine: Roles of tRNA Modifications , 2016 .
[80] S. Yamasaki,et al. Angiogenin cleaves tRNA and promotes stress-induced translational repression , 2009, The Journal of cell biology.
[81] A. Ortiz,et al. Crystal structure of Trbp111: a structure‐specific tRNA‐binding protein , 2000, The EMBO journal.
[82] Manuel A. S. Santos,et al. A genetic code alteration generates a proteome of high diversity in the human pathogen Candida albicans , 2007, Genome Biology.
[83] J. Lieberman,et al. G-quadruplex structures contribute to the neuroprotective effects of angiogenin-induced tRNA fragments , 2014, Proceedings of the National Academy of Sciences.
[84] P. Ivanov,et al. YB-1 regulates tiRNA-induced Stress Granule formation but not translational repression , 2016, Nucleic acids research.
[85] J. Mak,et al. Primer tRNAs for reverse transcription , 1997, Journal of virology.
[86] P. Schimmel,et al. Functional defects of pathogenic human mitochondrial tRNAs related to structural fragility , 2000, Nature Structural Biology.
[87] T. Pan,et al. Genome-wide Identification and Quantitative Analysis of Cleaved tRNA Fragments Induced by Cellular Stress* , 2012, The Journal of Biological Chemistry.
[88] T. Pan,et al. tRNA base methylation identification and quantification via high-throughput sequencing , 2016, RNA.
[89] Christian de Duve,et al. The second genetic code , 1988, Nature.
[90] Michaela Frye,et al. Stem cell function and stress response are controlled by protein synthesis , 2016, Nature.
[91] Giovanni Nigita,et al. Dysregulation of a family of short noncoding RNAs, tsRNAs, in human cancer , 2016, Proceedings of the National Academy of Sciences.
[92] Modesto Orozco,et al. Saturation of recognition elements blocks evolution of new tRNA identities , 2016, Science Advances.
[93] Oliver J. Rando,et al. Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals , 2016, Science.
[94] Antonio J Giraldez,et al. Codon identity regulates mRNA stability and translation efficiency during the maternal‐to‐zygotic transition , 2016, The EMBO journal.
[95] C. Dunham,et al. Structural insights into +1 frameshifting promoted by expanded or modification-deficient anticodon stem loops , 2014, Proceedings of the National Academy of Sciences.
[96] Tao Pan,et al. Angiogenin-Cleaved tRNA Halves Interact with Cytochrome c, Protecting Cells from Apoptosis during Osmotic Stress , 2014, Molecular and Cellular Biology.
[97] Efficient mischarging of a viral tRNA-like structure and aminoacylation of a minihelix containing a pseudoknot: histidinylation of turnip yellow mosaic virus RNA. , 1992, Nucleic acids research.
[98] P. Schimmel,et al. Isolated RNA binding domain of a class I tRNA synthetase. , 1995, Biochemistry.
[99] Yves Van de Peer,et al. The Mycobacterium tuberculosis regulatory network and hypoxia , 2013, Nature.
[100] Dae Kim,et al. Promiscuous methionyl-tRNA synthetase mediates adaptive mistranslation to protect cells against oxidative stress , 2014, Journal of Cell Science.
[101] Wei Yan,et al. Epigenetic inheritance of acquired traits through sperm RNAs and sperm RNA modifications , 2016, Nature Reviews Genetics.
[102] P. Schimmel,et al. Atomic Determinants for Aminoacylation of RNA Minihelices and Relationship to Genetic Code , 1999 .
[103] E. Rubin,et al. Mycobacterial mistranslation is necessary and sufficient for rifampicin phenotypic resistance , 2014, Proceedings of the National Academy of Sciences.
[104] Demis Hassabis,et al. Mastering the game of Go with deep neural networks and tree search , 2016, Nature.
[105] T. Tsuzuki,et al. YB-1 Is Important for an Early Stage Embryonic Development , 2006, Journal of Biological Chemistry.
[106] Peter M. Schlag,et al. Identification of Y-Box Binding Protein 1 As a Core Regulator of MEK/ERK Pathway-Dependent Gene Signatures in Colorectal Cancer Cells , 2010, PLoS genetics.
[107] G. Hu,et al. Angiogenin Promotes Hematopoietic Regeneration by Dichotomously Regulating Quiescence of Stem and Progenitor Cells , 2016, Cell.
[108] J F Riordan,et al. Amino acid sequence of human tumor derived angiogenin. , 1985, Biochemistry.
[109] G. Janssen,et al. Statistical evidence for remnants of the primordial code in the acceptor stem of prokaryotic transfer RNA , 1992, Journal of Molecular Evolution.
[110] J. Yong,et al. tRNA binds to cytochrome c and inhibits caspase activation. , 2010, Molecular cell.
[111] Sharmila Anishetty,et al. In silico analysis of DosR regulon proteins of Mycobacterium tuberculosis. , 2012, Gene.
[112] Gyorgy Hutvagner,et al. tRNA-Derived Fragments (tRFs): Emerging New Roles for an Ancient RNA in the Regulation of Gene Expression , 2015, Life.
[113] Sunghoon Kim,et al. Structural switch of lysyl-tRNA synthetase between translation and transcription. , 2013, Molecular cell.
[114] Paul Schimmel,et al. Essential nontranslational functions of tRNA synthetases. , 2013, Nature chemical biology.
[115] K. Musier-Forsyth,et al. Transfer RNA recognition by aminoacyl‐tRNA synthetases , 1999, Biopolymers.
[116] Tsutomu Suzuki,et al. A complete landscape of post-transcriptional modifications in mammalian mitochondrial tRNAs , 2014, Nucleic acids research.
[117] Henrik Molina,et al. Modulated Expression of Specific tRNAs Drives Gene Expression and Cancer Progression , 2016, Cell.
[118] Alka A. Potdar,et al. EPRS is a critical mTORC1-S6K1 effector that influences adiposity in mice , 2017, Nature.
[119] P. Schimmel,et al. Fragile T-stem in Disease-associated Human Mitochondrial tRNA Sensitizes Structure to Local and Distant Mutations* , 2001, The Journal of Biological Chemistry.
[120] H. Inokuchi,et al. tRNADB-CE: tRNA gene database well-timed in the era of big sequence data , 2014, Front. Genet..
[121] Naoki Shigi. Sulfur Modifications in tRNA: Function and Implications for Human Disease , 2016 .
[122] Michael H. Schwartz,et al. Temperature dependent mistranslation in a hyperthermophile adapts proteins to lower temperatures , 2015, Nucleic acids research.
[123] R. Maraia,et al. tRNA gene copy number variation in humans. , 2014, Gene.
[124] Xudong Zhang,et al. Sperm tsRNAs contribute to intergenerational inheritance of an acquired metabolic disorder , 2016, Science.
[125] J. Sampson,et al. Variant minihelix RNAs reveal sequence‐specific recognition of the helical tRNA(Ser) acceptor stem by E.coli seryl‐tRNA synthetase. , 1996, The EMBO journal.
[126] Francesca Tuorto,et al. RNA methylation by Dnmt2 protects transfer RNAs against stress-induced cleavage. , 2010, Genes & development.
[127] T. Ohkubo,et al. Conformational change in transfer RNA is an early indicator of acute cellular damage. , 2014, Journal of the American Society of Nephrology : JASN.
[128] L. Ribas de Pouplana,et al. Regulation of RNA function by aminoacylation and editing? , 2004, Trends in genetics : TIG.
[129] M. Giulio,et al. The Presence in tRNA Molecule Sequences of the Double Hairpin, an Evolutionary Stage Through Which the Origin of this Molecule is Thought to have Passed , 2011, Journal of Molecular Evolution.
[130] Human cytoplasmic ProX edits mischarged tRNAPro with amino acid but not tRNA specificity. , 2013, The Biochemical journal.
[131] C. Florentz,et al. Anticodon-independent aminoacylation of an RNA minihelix with valine. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[132] Takeo Suzuki,et al. Human mitochondrial tRNAs: biogenesis, function, structural aspects, and diseases. , 2011, Annual review of genetics.
[133] Y. Sasaguri,et al. Strong YB‐1 expression is associated with liver metastasis progression and predicts shorter disease‐free survival in advanced gastric cancer , 2012, Journal of surgical oncology.
[134] Canan Kuscu,et al. Biogenesis and Function of Transfer RNA-Related Fragments (tRFs). , 2016, Trends in biochemical sciences.
[135] P. Schimmel,et al. Structure‐specific tRNA‐binding protein from the extreme thermophile Aquifex aeolicus , 1999, The EMBO journal.
[136] Jacob D. Jaffe,et al. Naturally occurring aminoacyl-tRNA synthetases editing-domain mutations that cause mistranslation in Mycoplasma parasites , 2011, Proceedings of the National Academy of Sciences.
[137] J. Nichols,et al. The RNA–Methyltransferase Misu (NSun2) Poises Epidermal Stem Cells to Differentiate , 2011, PLoS genetics.
[138] J. Bujnicki,et al. MODOMICS: a database of RNA modification pathways—2013 update , 2012, Nucleic Acids Res..
[139] P. Agris,et al. Post-Transcriptional Modifications of RNA: Impact on RNA Function and Human Health , 2016 .
[140] F. Tuorto,et al. RNA cytosine methylation by Dnmt2 and NSun2 promotes tRNA stability and protein synthesis , 2012, Nature Structural &Molecular Biology.
[141] Thomas J. Begley,et al. tRNA-mediated codon-biased translation in mycobacterial hypoxic persistence , 2016, Nature Communications.
[142] J. L. Bethune,et al. Isolation and characterization of angiogenin, an angiogenic protein from human carcinoma cells. , 1985, Biochemistry.