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  • Abbasi-Moheb L, Mertel S, Gonsior M, Nouri-Vahid L, Kahrizi K, Cirak S, Wieczorek D, Motazacker MM, Esmaeeli-Nieh S, Cremer K, Weissmann R, Tzschach A, Garshasbi M, Abedini SS, Najmabadi H, Ropers HH, Sigrist SJ, Kuss AW (2012) Mutations in NSUN2 cause autosomal-recessive intellectual disability. Am J Hum Genet 90: 847855
  • Alexandrov A, Chernyakov I, Gu W, Hiley SL, Hughes TR, Grayhack EJ, Phizicky EM (2006) Rapid tRNA decay can result from lack of nonessential modifications. Mol Cell 21: 8796
  • Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11: R106
  • Anderson P, Kedersha N (2006) RNA granules. J Cell Biol 172: 803808
  • Anderson P, Kedersha N (2008) Stress granules: the Tao of RNA triage. Trends Biochem Sci 33: 141150
  • Beaudoin GM 3rd, Lee SH, Singh D, Yuan Y, Ng YG, Reichardt LF, Arikkath J (2012) Culturing pyramidal neurons from the early postnatal mouse hippocampus and cortex. Nat Protoc 7: 17411754
  • Begley U, Dyavaiah M, Patil A, Rooney JP, DiRenzo D, Young CM, Conklin DS, Zitomer RS, Begley TJ (2007) Trm9-catalyzed tRNA modifications link translation to the DNA damage response. Mol Cell 28: 860870
  • Blanco S, Kurowski A, Nichols J, Watt FM, Benitah SA, Frye M (2011) The RNA-methyltransferase Misu (NSun2) poises epidermal stem cells to differentiate. PLoS Genet 7: e1002403
  • Brzezicha B, Schmidt M, Makalowska I, Jarmolowski A, Pienkowska J, Szweykowska-Kulinska Z (2006) Identification of human tRNA:m5C methyltransferase catalysing intron-dependent m5C formation in the first position of the anticodon of the pre-tRNA Leu (CAA). Nucleic Acids Res 34: 60346043
  • Castello A, Fischer B, Eichelbaum K, Horos R, Beckmann BM, Strein C, Davey NE, Humphreys DT, Preiss T, Steinmetz LM, Krijgsveld J, Hentze MW (2012) Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell 149: 13931406
  • Chan CT, Dyavaiah M, DeMott MS, Taghizadeh K, Dedon PC, Begley TJ (2010) A quantitative systems approach reveals dynamic control of tRNA modifications during cellular stress. PLoS Genet 6: e1001247
  • Chan CT, Pang YL, Deng W, Babu IR, Dyavaiah M, Begley TJ, Dedon PC (2012) Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins. Nat Commun 3: 937
  • Chen Y, Sierzputowska-Gracz H, Guenther R, Everett K, Agris PF (1993) 5-Methylcytidine is required for cooperative binding of Mg2+ and a conformational transition at the anticodon stem-loop of yeast phenylalanine tRNA. Biochemistry 32: 1024910253
  • Chernyakov I, Whipple JM, Kotelawala L, Grayhack EJ, Phizicky EM (2008) Degradation of several hypomodified mature tRNA species in Saccharomyces cerevisiae is mediated by Met22 and the 5′-3′ exonucleases Rat1 and Xrn1. Genes Dev 22: 13691380
  • Cole C, Sobala A, Lu C, Thatcher SR, Bowman A, Brown JW, Green PJ, Barton GJ, Hutvagner G (2009) Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. RNA 15: 21472160
  • Colonna A, Kerr SJ (1980) The nucleus as the site of tRNA methylation. J Cell Physiol 103: 2933
  • Couillard-Despres S, Winner B, Schaubeck S, Aigner R, Vroemen M, Weidner N, Bogdahn U, Winkler J, Kuhn HG, Aigner L (2005) Doublecortin expression levels in adult brain reflect neurogenesis. Eur J Neurosci 21: 114
  • Darnell JC (2011) Defects in translational regulation contributing to human cognitive and behavioral disease. Curr Opin Genet Dev 21: 465473
  • De Felice C, Signorini C, Leoncini S, Pecorelli A, Durand T, Valacchi G, Ciccoli L, Hayek J (2012) The role of oxidative stress in Rett syndrome: an overview. Ann N Y Acad Sci 1259: 121135
  • Dubowitz V (1965) Familial low birthweight dwarfism with an unusual facies and a skin eruption. J Med Genet 2: 1217
  • Emara MM, Ivanov P, Hickman T, Dawra N, Tisdale S, Kedersha N, Hu GF, Anderson P (2010) Angiogenin-induced tRNA-derived stress-induced RNAs promote stress-induced stress granule assembly. J Biol Chem 285: 1095910968
  • van Es MA, Schelhaas HJ, van Vught PW, Ticozzi N, Andersen PM, Groen EJ, Schulte C, Blauw HM, Koppers M, Diekstra FP, Fumoto K, LeClerc AL, Keagle P, Bloem BR, Scheffer H, van Nuenen BF, van Blitterswijk M, van Rheenen W, Wills AM, Lowe PP et al (2011) Angiogenin variants in Parkinson disease and amyotrophic lateral sclerosis. Ann Neurol 70: 964973
  • Essa MM, Braidy N, Vijayan KR, Subash S, Guillemin GJ (2013) Excitotoxicity in the pathogenesis of autism. Neurotox Res 23: 393400
  • Findeiss S, Langenberger D, Stadler PF, Hoffmann S (2011) Traces of post-transcriptional RNA modifications in deep sequencing data. Biol Chem 392: 305313
  • Frye M, Watt FM (2006) The RNA methyltransferase Misu (NSun2) mediates Myc-induced proliferation and is upregulated in tumors. Curr Biol 16: 971981
  • Fu H, Feng J, Liu Q, Sun F, Tie Y, Zhu J, Xing R, Sun Z, Zheng X (2009) Stress induces tRNA cleavage by angiogenin in mammalian cells. FEBS Lett 583: 437442
  • Garcia-Silva MR, Frugier M, Tosar JP, Correa-Dominguez A, Ronalte-Alves L, Parodi-Talice A, Rovira C, Robello C, Goldenberg S, Cayota A (2010) A population of tRNA-derived small RNAs is actively produced in Trypanosoma cruzi and recruited to specific cytoplasmic granules. Mol Biochem Parasitol 171: 6473
  • Gebetsberger J, Zywicki M, Kunzi A, Polacek N (2012) tRNA-derived fragments target the ribosome and function as regulatory non-coding RNA in Haloferax volcanii. Archaea 2012: 260909
  • Gold M, Hurwitz J, Anders M (1963) The enzymatic methylation of RNA and DNA, II. On the species specificity of the methylation enzymes. Proc Natl Acad Sci USA 50: 164169
  • Goll MG, Kirpekar F, Maggert KA, Yoder JA, Hsieh CL, Zhang X, Golic KG, Jacobsen SE, Bestor TH (2006) Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2. Science 311: 395398
  • Greenway MJ, Andersen PM, Russ C, Ennis S, Cashman S, Donaghy C, Patterson V, Swingler R, Kieran D, Prehn J, Morrison KE, Green A, Acharya KR, Brown RH Jr, Hardiman O (2006) ANG mutations segregate with familial and ‘sporadic’ amyotrophic lateral sclerosis. Nat Genet 38: 411413
  • Gupta R, Kasturi P, Bracher A, Loew C, Zheng M, Villella A, Garza D, Hartl FU, Raychaudhuri S (2011) Firefly luciferase mutants as sensors of proteome stress. Nat Methods 8: 879884
  • Haiser HJ, Karginov FV, Hannon GJ, Elliot MA (2008) Developmentally regulated cleavage of tRNAs in the bacterium Streptomyces coelicolor. Nucleic Acids Res 36: 732741
  • Hanada T, Weitzer S, Mair B, Bernreuther C, Wainger BJ, Ichida J, Hanada R, Orthofer M, Cronin SJ, Komnenovic V, Minis A, Sato F, Mimata H, Yoshimura A, Tamir I, Rainer J, Kofler R, Yaron A, Eggan KC, Woolf CJ et al (2013) CLP1 links tRNA metabolism to progressive motor-neuron loss. Nature 495: 474480
  • Haussecker D, Huang Y, Lau A, Parameswaran P, Fire AZ, Kay MA (2010) Human tRNA-derived small RNAs in the global regulation of RNA silencing. RNA 16: 673695
  • Huber RS, Houlihan D, Filter K (2011) Dubowitz syndrome: a review and implications for cognitive, behavioral, and psychological features. J Clin Med Res 3: 147155
  • Hussain S, Benavente SB, Nascimento E, Dragoni I, Kurowski A, Gillich A, Humphreys P, Frye M (2009) The nucleolar RNA methyltransferase Misu (NSun2) is required for mitotic spindle stability. J Cell Biol 186: 2740
  • Hussain S, Aleksic J, Blanco S, Dietmann S, Frye M (2013a) Characterizing 5-methylcytosine in the mammalian epitranscriptome. Genome Biol 14: 215
  • Hussain S, Sajini AA, Blanco S, Dietmann S, Lombard P, Sugimoto Y, Paramor M, Gleeson JG, Odom DT, Ule J, Frye M (2013b) NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs. Cell Rep 4: 255261
  • Hussain S, Tuorto F, Menon S, Blanco S, Cox C, Flores JV, Watt S, Kudo NR, Lyko F, Frye M (2013c) The mouse cytosine-5 RNA methyltransferase NSun2 is a component of the chromatoid body and required for testis differentiation. Mol Cell Biol 33: 15611570
  • Ippolito DM, Eroglu C (2010) Quantifying synapses: an immunocytochemistry-based assay to quantify synapse number. J Vis Exp 45: 2270
  • Ivanov P, Emara MM, Villen J, Gygi SP, Anderson P (2011) Angiogenin-induced tRNA fragments inhibit translation initiation. Mol Cell 43: 613623
  • Jablonowski D, Zink S, Mehlgarten C, Daum G, Schaffrath R (2006) tRNAGlu wobble uridine methylation by Trm9 identifies Elongator's key role for zymocin-induced cell death in yeast. Mol Microbiol 59: 677688
  • Karaca E, Weitzer S, Pehlivan D, Shiraishi H, Gogakos T, Hanada T, Jhangiani SN, Wiszniewski W, Withers M, Campbell IM, Erdin S, Isikay S, Franco LM, Gonzaga-Jauregui C, Gambin T, Gelowani V, Hunter JV, Yesil G, Koparir E, Yilmaz S et al (2014) Human CLP1 mutations alter tRNA biogenesis, affecting both peripheral and central nervous system function. Cell 157: 636650
  • Kao RY, Jenkins JL, Olson KA, Key ME, Fett JW, Shapiro R (2002) A small-molecule inhibitor of the ribonucleolytic activity of human angiogenin that possesses antitumor activity. Proc Natl Acad Sci USA 99: 1006610071
  • Kedersha NL, Gupta M, Li W, Miller I, Anderson P (1999) RNA-binding proteins TIA-1 and TIAR link the phosphorylation of eIF-2 alpha to the assembly of mammalian stress granules. J Cell Biol 147: 14311442
  • Kedersha N, Anderson P (2007) Mammalian stress granules and processing bodies. Methods Enzymol 431: 6181
  • Khan MA, Rafiq MA, Noor A, Hussain S, Flores JV, Rupp V, Vincent AK, Malli R, Ali G, Khan FS, Ishak GE, Doherty D, Weksberg R, Ayub M, Windpassinger C, Ibrahim S, Frye M, Ansar M, Vincent JB (2012) Mutation in NSUN2, which encodes an RNA methyltransferase, causes autosomal-recessive intellectual disability. Am J Hum Genet 90: 856863
  • Khoddami V, Cairns BR (2013) Identification of direct targets and modified bases of RNA cytosine methyltransferases. Nat Biotechnol 31: 458464
  • Kim SH, Suddath FL, Quigley GJ, McPherson A, Sussman JL, Wang AH, Seeman NC, Rich A (1974) Three-dimensional tertiary structure of yeast phenylalanine transfer RNA. Science 185: 435440
  • Kim SW, Li Z, Moore PS, Monaghan AP, Chang Y, Nichols M, John B (2010) A sensitive non-radioactive northern blot method to detect small RNAs. Nucleic Acids Res 38: e98
  • Krueger F, Andrews SR (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27: 15711572
  • Kutter C, Brown GD, Goncalves A, Wilson MD, Watt S, Brazma A, White RJ, Odom DT (2011) Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes. Nat Genet 43: 948955
  • Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25
  • Lee SR, Collins K (2005) Starvation-induced cleavage of the tRNA anticodon loop in Tetrahymena thermophila. J Biol Chem 280: 4274442749
  • Lee YS, Shibata Y, Malhotra A, Dutta A (2009) A novel class of small RNAs: tRNA-derived RNA fragments (tRFs). Genes Dev 23: 26392649
  • de Ligt J, Willemsen MH, van Bon BW, Kleefstra T, Yntema HG, Kroes T, Vulto-van Silfhout AT, Koolen DA, de Vries P, Gilissen C, del Rosario M, Hoischen A, Scheffer H, de Vries BB, Brunner HG, Veltman JA, Vissers LE (2012) Diagnostic exome sequencing in persons with severe intellectual disability. N Engl J Med 367: 19211929
  • Lintas C, Sacco R, Persico AM (2012) Genome-wide expression studies in autism spectrum disorder, Rett syndrome, and Down syndrome. Neurobiol Dis 45: 5768
  • Liu J, Xu Y, Stoleru D, Salic A (2012) Imaging protein synthesis in cells and tissues with an alkyne analog of puromycin. Proc Natl Acad Sci USA 109: 413418
  • Lloyd AC (2013) The regulation of cell size. Cell 154: 11941205
  • Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955964
  • Martinez FJ, Lee JH, Lee JE, Blanco S, Nickerson E, Gabriel S, Frye M, Al-Gazali L, Gleeson JG (2012) Whole exome sequencing identifies a splicing mutation in NSUN2 as a cause of a Dubowitz-like syndrome. J Med Genet 49: 380385
  • Metodiev MD, Spahr H, Loguercio Polosa P, Meharg C, Becker C, Altmueller J, Habermann B, Larsson NG, Ruzzenente B (2014) NSUN4 is a dual function mitochondrial protein required for both methylation of 12S rRNA and coordination of mitoribosomal assembly. PLoS Genet 10: e1004110
  • Motorin Y, Grosjean H (1999) Multisite-specific tRNA:m5C-methyltransferase (Trm4) in yeast Saccharomyces cerevisiae: identification of the gene and substrate specificity of the enzyme. RNA 5: 11051118
  • Motorin Y, Lyko F, Helm M (2010) 5-methylcytosine in RNA: detection, enzymatic formation and biological functions. Nucleic Acids Res 38: 14151430
  • Rai K, Chidester S, Zavala CV, Manos EJ, James SR, Karpf AR, Jones DA, Cairns BR (2007) Dnmt2 functions in the cytoplasm to promote liver, brain, and retina development in zebrafish. Genes Dev 21: 261266
  • Reifur L, Garcia-Silva MR, Poubel SB, Alves LR, Arauco P, Buiar DK, Goldenberg S, Cayota A, Dallagiovanna B (2012) Distinct subcellular localization of tRNA-derived fragments in the infective metacyclic forms of Trypanosoma cruzi. Mem Inst Oswaldo Cruz 107: 816819
  • Ropers HH (2008) Genetics of intellectual disability. Curr Opin Genet Dev 18: 241250
  • Saikia M, Krokowski D, Guan BJ, Ivanov P, Parisien M, Hu GF, Anderson P, Pan T, Hatzoglou M (2012) Genome-wide identification and quantitative analysis of cleaved tRNA fragments induced by cellular stress. J Biol Chem 287: 4270842725
  • Schaefer M, Pollex T, Hanna K, Tuorto F, Meusburger M, Helm M, Lyko F (2010) RNA methylation by Dnmt2 protects transfer RNAs against stress-induced cleavage. Genes Dev 24: 15901595
  • Schaffer AE, Eggens VR, Caglayan AO, Reuter MS, Scott E, Coufal NG, Silhavy JL, Xue Y, Kayserili H, Yasuno K, Rosti RO, Abdellateef M, Caglar C, Kasher PR, Cazemier JL, Weterman MA, Cantagrel V, Cai N, Zweier C, Altunoglu U et al (2014) CLP1 founder mutation links tRNA splicing and maturation to cerebellar development and neurodegeneration. Cell 157: 651663
  • Scheper GC, van der Knaap MS, Proud CG (2007) Translation matters: protein synthesis defects in inherited disease. Nat Rev Genet 8: 711723
  • Simpson CE, Ashe MP (2012) Adaptation to stress in yeast: to translate or not? Biochem Soc Trans 40: 794799
  • Skorupa A, King MA, Aparicio IM, Dussmann H, Coughlan K, Breen B, Kieran D, Concannon CG, Marin P, Prehn JH (2012) Motoneurons secrete angiogenin to induce RNA cleavage in astroglia. J Neurosci 32: 50245038
  • Sobala A, Hutvagner G (2013) Small RNAs derived from the 5′ end of tRNA can inhibit protein translation in human cells. RNA Biol 10: 553563
  • Spriggs KA, Bushell M, Willis AE (2010) Translational regulation of gene expression during conditions of cell stress. Mol Cell 40: 228237
  • Squires JE, Patel HR, Nousch M, Sibbritt T, Humphreys DT, Parker BJ, Suter CM, Preiss T (2012) Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA. Nucleic Acids Res 40: 50235033
  • Steidinger TU, Standaert DG, Yacoubian TA (2011) A neuroprotective role for angiogenin in models of Parkinson's disease. J Neurochem 116: 334341
  • Suzuki T, Suzuki T, Wada T, Saigo K, Watanabe K (2001) Novel taurine-containing uridine derivatives and mitochondrial human diseases. Nucleic Acids Res Suppl 1: 257258
  • Suzuki MM, Bird A (2008) DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 9: 465476
  • Thompson DM, Lu C, Green PJ, Parker R (2008) tRNA cleavage is a conserved response to oxidative stress in eukaryotes. RNA 14: 20952103
  • Thompson DM, Parker R (2009) Stressing out over tRNA cleavage. Cell 138: 215219
  • Torres AG, Batlle E, Ribas de Pouplana L (2014) Role of tRNA modifications in human diseases. Trends Mol Med 20: 306314
  • Tuorto F, Liebers R, Musch T, Schaefer M, Hofmann S, Kellner S, Frye M, Helm M, Stoecklin G, Lyko F (2012) RNA cytosine methylation by Dnmt2 and NSun2 promotes tRNA stability and protein synthesis. Nat Struct Mol Biol 19: 900905
  • Wu P, Brockenbrough JS, Paddy MR, Aris JP (1998) NCL1, a novel gene for a non-essential nuclear protein in Saccharomyces cerevisiae. Gene 220: 109117
  • Wu D, Yu W, Kishikawa H, Folkerth RD, Iafrate AJ, Shen Y, Xin W, Sims K, Hu GF (2007) Angiogenin loss-of-function mutations in amyotrophic lateral sclerosis. Ann Neurol 62: 609617
  • Yamasaki S, Ivanov P, Hu GF, Anderson P (2009) Angiogenin cleaves tRNA and promotes stress-induced translational repression. J Cell Biol 185: 3542
  • Zywicki M, Bakowska-Zywicka K, Polacek N (2012) Revealing stable processing products from ribosome-associated small RNAs by deep-sequencing data analysis. Nucleic Acids Res 40: 40134024