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Volumn 536, Issue 2, 2014, Pages 376-384

tRNA gene copy number variation in humans

Author keywords

Anti codon; Codon; Genome wide; Next generation; Sequencing; Translation

Indexed keywords

GENOMIC DNA; MESSENGER RNA; TRANSFER RNA;

EID: 84892436616     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2013.11.049     Document Type: Article
Times cited : (51)

References (49)
  • 1
    • 84868256656 scopus 로고    scopus 로고
    • The absence of A-to-I editing in the anticodon of plant cytoplasmic tRNA (Arg) ACG demands a relaxation of the wobble decoding rules
    • Aldinger C.A., Leisinger A.K., Gaston K.W., Limbach P.A., Igloi G.L. The absence of A-to-I editing in the anticodon of plant cytoplasmic tRNA (Arg) ACG demands a relaxation of the wobble decoding rules. RNA Biol. 2012, 9:1239-1246.
    • (2012) RNA Biol. , vol.9 , pp. 1239-1246
    • Aldinger, C.A.1    Leisinger, A.K.2    Gaston, K.W.3    Limbach, P.A.4    Igloi, G.L.5
  • 2
    • 84861671920 scopus 로고    scopus 로고
    • Translational control of cell division by elongator
    • Bauer F., et al. Translational control of cell division by elongator. Cell Rep. 2012, 1:424-433.
    • (2012) Cell Rep. , vol.1 , pp. 424-433
    • Bauer, F.1
  • 3
    • 36749085941 scopus 로고    scopus 로고
    • Trm9-catalyzed tRNA modifications link translation to the DNA damage response
    • Begley U., et al. Trm9-catalyzed tRNA modifications link translation to the DNA damage response. Mol. Cell 2007, 28:860-870.
    • (2007) Mol. Cell , vol.28 , pp. 860-870
    • Begley, U.1
  • 4
    • 0031586223 scopus 로고    scopus 로고
    • Growth rate-optimised tRNA abundance and codon usage
    • Berg O.G., Kurland C.G. Growth rate-optimised tRNA abundance and codon usage. J. Mol. Biol. 1997, 270:544-550.
    • (1997) J. Mol. Biol. , vol.270 , pp. 544-550
    • Berg, O.G.1    Kurland, C.G.2
  • 6
    • 58149189877 scopus 로고    scopus 로고
    • GtRNAdb: a database of transfer RNA genes detected in genomic sequence
    • Chan P.P., Lowe T.M. GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res. 2009, 37:D93-D97.
    • (2009) Nucleic Acids Res. , vol.37
    • Chan, P.P.1    Lowe, T.M.2
  • 7
    • 78650683942 scopus 로고    scopus 로고
    • A quantitative systems approach reveals dynamic control of tRNA modifications during cellular stress
    • Chan C.T., Dyavaiah M., DeMott M.S., Taghizadeh K., Dedon P.C., Begley T.J. A quantitative systems approach reveals dynamic control of tRNA modifications during cellular stress. PLoS Genet. 2010, 6:e1001247.
    • (2010) PLoS Genet. , vol.6
    • Chan, C.T.1    Dyavaiah, M.2    DeMott, M.S.3    Taghizadeh, K.4    Dedon, P.C.5    Begley, T.J.6
  • 8
    • 0042835761 scopus 로고    scopus 로고
    • Disruption of a receptor-mediated mechanism for intracellular sorting of proinsulin in familial hyperproinsulinemia
    • Dhanvantari S., et al. Disruption of a receptor-mediated mechanism for intracellular sorting of proinsulin in familial hyperproinsulinemia. Mol. Endocrinol. 2003, 17:1856-1867.
    • (2003) Mol. Endocrinol. , vol.17 , pp. 1856-1867
    • Dhanvantari, S.1
  • 9
    • 0034237669 scopus 로고    scopus 로고
    • TRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes
    • Duret L. tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes. Trends Genet. 2000, 16:287-289.
    • (2000) Trends Genet. , vol.16 , pp. 287-289
    • Duret, L.1
  • 10
    • 77952154803 scopus 로고    scopus 로고
    • E pluribus unum
    • Editorial
    • Editorial E pluribus unum. Nat. Methods 2010, 7:331.
    • (2010) Nat. Methods , vol.7 , pp. 331
  • 11
    • 33749078546 scopus 로고    scopus 로고
    • Elevated levels of two tRNA species bypass the requirement for elongator complex in transcription and exocytosis
    • Esberg A., Huang B., Johansson M.J., Bystrom A.S. Elevated levels of two tRNA species bypass the requirement for elongator complex in transcription and exocytosis. Mol. Cell 2006, 24:139-148.
    • (2006) Mol. Cell , vol.24 , pp. 139-148
    • Esberg, A.1    Huang, B.2    Johansson, M.J.3    Bystrom, A.S.4
  • 12
    • 77950121267 scopus 로고    scopus 로고
    • Gene copy number variation and common human disease
    • Fanciulli M., Petretto E., Aitman T.J. Gene copy number variation and common human disease. Clin. Genet. 2010, 77:201-213.
    • (2010) Clin. Genet. , vol.77 , pp. 201-213
    • Fanciulli, M.1    Petretto, E.2    Aitman, T.J.3
  • 14
    • 84975742565 scopus 로고    scopus 로고
    • A map of human genome variation from population-scale sequencing
    • Genomes Project C., et al. A map of human genome variation from population-scale sequencing. Nature 2010, 467:1061-1073.
    • (2010) Nature , vol.467 , pp. 1061-1073
    • Genomes Project, C.1
  • 15
    • 33845635732 scopus 로고    scopus 로고
    • Diversity of tRNA genes in eukaryotes
    • Goodenbour J.M., Pan T. Diversity of tRNA genes in eukaryotes. Nucleic Acids Res. 2006, 34:6137-6146.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 6137-6146
    • Goodenbour, J.M.1    Pan, T.2
  • 16
    • 0020491327 scopus 로고
    • Codon usage in bacteria: correlation with gene expressivity
    • Gouy M., Gautier C. Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res. 1982, 10:7055-7074.
    • (1982) Nucleic Acids Res. , vol.10 , pp. 7055-7074
    • Gouy, M.1    Gautier, C.2
  • 17
    • 0020363515 scopus 로고
    • Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes
    • Grosjean H., Fiers W. Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes. Gene 1982, 18:199-209.
    • (1982) Gene , vol.18 , pp. 199-209
    • Grosjean, H.1    Fiers, W.2
  • 18
    • 84874028131 scopus 로고    scopus 로고
    • Essential nontranslational functions of tRNA synthetases
    • Guo M., Schimmel P. Essential nontranslational functions of tRNA synthetases. Nat. Chem. Biol. 2013, 9:145-153.
    • (2013) Nat. Chem. Biol. , vol.9 , pp. 145-153
    • Guo, M.1    Schimmel, P.2
  • 19
    • 54149105223 scopus 로고    scopus 로고
    • Coevolution of codon usage and tRNA genes leads to alternative stable states of biased codon usage
    • Higgs P.G., Ran W. Coevolution of codon usage and tRNA genes leads to alternative stable states of biased codon usage. Mol. Biol. Evol. 2008, 25:2279-2291.
    • (2008) Mol. Biol. Evol. , vol.25 , pp. 2279-2291
    • Higgs, P.G.1    Ran, W.2
  • 21
    • 84862529706 scopus 로고    scopus 로고
    • Yeast tRNAomics: tRNA gene copy number variation and codon use provide bioinformatics evidence of a new wobble pair in a eukaryote
    • Iben J.R., Maraia R.J. Yeast tRNAomics: tRNA gene copy number variation and codon use provide bioinformatics evidence of a new wobble pair in a eukaryote. RNA 2012, 18:1358-1372.
    • (2012) RNA , vol.18 , pp. 1358-1372
    • Iben, J.R.1    Maraia, R.J.2
  • 22
    • 79959455084 scopus 로고    scopus 로고
    • Comparative whole genome sequencing reveals phenotypic tRNA gene duplication in spontaneous Schizosaccharomyces pombe La mutants
    • Iben J.R., et al. Comparative whole genome sequencing reveals phenotypic tRNA gene duplication in spontaneous Schizosaccharomyces pombe La mutants. Nucleic Acids Res. 2011, 39:4728-4742.
    • (2011) Nucleic Acids Res. , vol.39 , pp. 4728-4742
    • Iben, J.R.1
  • 23
    • 0019824131 scopus 로고
    • Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system
    • Ikemura T. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J. Mol. Biol. 1981, 151:389-409.
    • (1981) J. Mol. Biol. , vol.151 , pp. 389-409
    • Ikemura, T.1
  • 24
    • 0038476173 scopus 로고    scopus 로고
    • Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models
    • Jansen R., Bussemaker H.J., Gerstein M. Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models. Nucleic Acids Res. 2003, 31:2242-2251.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 2242-2251
    • Jansen, R.1    Bussemaker, H.J.2    Gerstein, M.3
  • 25
    • 77958188414 scopus 로고    scopus 로고
    • Reference-unbiased copy number variant analysis using CGH microarrays
    • Ju Y.S., et al. Reference-unbiased copy number variant analysis using CGH microarrays. Nucleic Acids Res. 2010, 38:e190.
    • (2010) Nucleic Acids Res. , vol.38
    • Ju, Y.S.1
  • 26
    • 33846504706 scopus 로고    scopus 로고
    • A "silent" polymorphism in the MDR1 gene changes substrate specificity
    • Kimchi-Sarfaty C., et al. A "silent" polymorphism in the MDR1 gene changes substrate specificity. Science 2007, 315:525-528.
    • (2007) Science , vol.315 , pp. 525-528
    • Kimchi-Sarfaty, C.1
  • 27
    • 0017905778 scopus 로고
    • Tumour-specific phenylalanine tRNA contains two supernumerary methylated bases
    • Kuchino Y., Borek E. Tumour-specific phenylalanine tRNA contains two supernumerary methylated bases. Nature 1978, 271:126-129.
    • (1978) Nature , vol.271 , pp. 126-129
    • Kuchino, Y.1    Borek, E.2
  • 28
  • 29
    • 84880693760 scopus 로고    scopus 로고
    • Lack of tRNA modification isopentenyl-A37 alters mRNA decoding and causes metabolic deficiencies in fission yeast
    • Lamichhane T.N., et al. Lack of tRNA modification isopentenyl-A37 alters mRNA decoding and causes metabolic deficiencies in fission yeast. Mol. Cell. Biol. 2013, 33:2918-2929.
    • (2013) Mol. Cell. Biol. , vol.33 , pp. 2918-2929
    • Lamichhane, T.N.1
  • 30
    • 78649656286 scopus 로고    scopus 로고
    • Control of translation efficiency in yeast by codon-anticodon interactions
    • Letzring D.P., Dean K.M., Grayhack E.J. Control of translation efficiency in yeast by codon-anticodon interactions. RNA 2010, 16:2516-2528.
    • (2010) RNA , vol.16 , pp. 2516-2528
    • Letzring, D.P.1    Dean, K.M.2    Grayhack, E.J.3
  • 31
    • 68549104404 scopus 로고    scopus 로고
    • The Sequence Alignment/Map format and SAMtools
    • Li H., et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics (Oxford, England) 2009, 25:2078-2079.
    • (2009) Bioinformatics (Oxford, England) , vol.25 , pp. 2078-2079
    • Li, H.1
  • 32
    • 0030854739 scopus 로고    scopus 로고
    • TRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
    • Lowe T.M., Eddy S.R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997, 25:955-964.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 33
    • 76349105934 scopus 로고    scopus 로고
    • High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians
    • Matsuzaki H., Wang P.H., Hu J., Rava R., Fu G.K. High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians. Genome Biol. 2009, 10:R125.
    • (2009) Genome Biol. , vol.10
    • Matsuzaki, H.1    Wang, P.H.2    Hu, J.3    Rava, R.4    Fu, G.K.5
  • 34
    • 57149090077 scopus 로고    scopus 로고
    • Dissection of a QTL hotspot on mouse distal chromosome 1 that modulates neurobehavioral phenotypes and gene expression
    • Mozhui K., Ciobanu D.C., Schikorski T., Wang X., Lu L., Williams R.W. Dissection of a QTL hotspot on mouse distal chromosome 1 that modulates neurobehavioral phenotypes and gene expression. PLoS Genet. 2008, 4:e1000260.
    • (2008) PLoS Genet. , vol.4
    • Mozhui, K.1    Ciobanu, D.C.2    Schikorski, T.3    Wang, X.4    Lu, L.5    Williams, R.W.6
  • 35
    • 84859174156 scopus 로고    scopus 로고
    • A role for tRNA modifications in genome structure and codon usage
    • Novoa E.M., Pavon-Eternod M., Pan T., Ribas de Pouplana L. A role for tRNA modifications in genome structure and codon usage. Cell 2012, 149:202-213.
    • (2012) Cell , vol.149 , pp. 202-213
    • Novoa, E.M.1    Pavon-Eternod, M.2    Pan, T.3    Ribas de Pouplana, L.4
  • 36
    • 84862338006 scopus 로고    scopus 로고
    • Low level genome mistranslations deregulate the transcriptome and translatome and generate proteotoxic stress in yeast
    • Paredes J.A., et al. Low level genome mistranslations deregulate the transcriptome and translatome and generate proteotoxic stress in yeast. BMC Biol. 2012, 10:55.
    • (2012) BMC Biol. , vol.10 , pp. 55
    • Paredes, J.A.1
  • 37
    • 84867259656 scopus 로고    scopus 로고
    • Increased tRNA modification and gene-specific codon usage regulate cell cycle progression during the DNA damage response
    • Patil A., et al. Increased tRNA modification and gene-specific codon usage regulate cell cycle progression during the DNA damage response. Cell Cycle 2012, 11:3656-3665.
    • (2012) Cell Cycle , vol.11 , pp. 3656-3665
    • Patil, A.1
  • 39
    • 84873570699 scopus 로고    scopus 로고
    • Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding
    • Pechmann S., Frydman J. Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding. Nat. Struct. Mol. Biol. 2013, 20:237-243.
    • (2013) Nat. Struct. Mol. Biol. , vol.20 , pp. 237-243
    • Pechmann, S.1    Frydman, J.2
  • 40
    • 78650304100 scopus 로고    scopus 로고
    • Synonymous but not the same: the causes and consequences of codon bias
    • Plotkin J.B., Kudla G. Synonymous but not the same: the causes and consequences of codon bias. Nat. Rev. Genet. 2011, 12:32-42.
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 32-42
    • Plotkin, J.B.1    Kudla, G.2
  • 42
    • 24744432691 scopus 로고    scopus 로고
    • TRNAs and tRNA mimics as cornerstones of aminoacyl-tRNA synthetase regulations
    • Ryckelynck M., Giege R., Frugier M. tRNAs and tRNA mimics as cornerstones of aminoacyl-tRNA synthetase regulations. Biochimie 2005, 87:835-845.
    • (2005) Biochimie , vol.87 , pp. 835-845
    • Ryckelynck, M.1    Giege, R.2    Frugier, M.3
  • 43
    • 69749121852 scopus 로고    scopus 로고
    • High-resolution mapping and analysis of copy number variations in the human genome: a data resource for clinical and research applications
    • Shaikh T.H., et al. High-resolution mapping and analysis of copy number variations in the human genome: a data resource for clinical and research applications. Genome Res. 2009, 19:1682-1690.
    • (2009) Genome Res. , vol.19 , pp. 1682-1690
    • Shaikh, T.H.1
  • 44
    • 0023046874 scopus 로고
    • Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes
    • Sharp P.M., Tuohy T.M., Mosurski K.R. Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res. 1986, 14:5125-5143.
    • (1986) Nucleic Acids Res. , vol.14 , pp. 5125-5143
    • Sharp, P.M.1    Tuohy, T.M.2    Mosurski, K.R.3
  • 46
    • 80052375980 scopus 로고    scopus 로고
    • Deficit of tRNALys modification by Cdkal1 causes the development of type 2 diabetes in mice
    • Wei F., et al. Deficit of tRNALys modification by Cdkal1 causes the development of type 2 diabetes in mice. J. Clin. Invest. 2011, 121:3598-3608.
    • (2011) J. Clin. Invest. , vol.121 , pp. 3598-3608
    • Wei, F.1
  • 47
    • 84874722535 scopus 로고    scopus 로고
    • Non-optimal codon usage is a mechanism to achieve circadian clock conditionality
    • Xu Y., Ma P., Shah P., Rokas A., Liu Y., Johnson C.H. Non-optimal codon usage is a mechanism to achieve circadian clock conditionality. Nature 2013, 495:116-120.
    • (2013) Nature , vol.495 , pp. 116-120
    • Xu, Y.1    Ma, P.2    Shah, P.3    Rokas, A.4    Liu, Y.5    Johnson, C.H.6
  • 49
    • 84874683740 scopus 로고    scopus 로고
    • Non-optimal codon usage affects expression, structure and function of clock protein FRQ
    • Zhou M., et al. Non-optimal codon usage affects expression, structure and function of clock protein FRQ. Nature 2013, 495:111-115.
    • (2013) Nature , vol.495 , pp. 111-115
    • Zhou, M.1


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