W. A. Cantara, P. F. Crain, J. Rozenski, J. A. Mccloskey, K. A. Harris et al., The RNA Modification Database, RNAMDB: 2011 update, Nucleic Acids Res, vol.39, pp.195-201, 2011.

, Nucleic Acids Research, vol.43, issue.22, p.11001, 2015.

A. K. Hopper and E. M. Phizicky, tRNA transfers to the limelight, Genes Dev, vol.17, pp.162-180, 2003.

M. J. Johansson and A. S. Bystrom, , 2005.

, Fine-Tuning of RNA Functions by Modification and Editing, pp.87-119

M. J. Johansson, A. Esberg, B. Huang, G. R. Bjork, and A. S. Bystrom, Eukaryotic wobble uridine modifications promote a functionally redundant decoding system, Mol. Cell. Biol, vol.28, pp.3301-3312, 2008.

B. Huang, M. J. Johansson, and A. S. Bystrom, An early step in wobble uridine tRNA modification requires the Elongator complex, RNA, vol.11, pp.424-436, 2005.

B. Huang, J. Lu, and A. S. Bystrom, A genome-wide screen identifies genes required for formation of the wobble nucleoside 5-methoxycarbonylmethyl-2-thiouridine in Saccharomyces cerevisiae, RNA, vol.14, pp.2183-2194, 2008.

F. Frohloff, L. Fichtner, D. Jablonowski, K. D. Breunig, and R. Schaffrath, Saccharomyces cerevisiae Elongator mutations confer resistance to the Kluyveromyces lactis zymocin, EMBO J, vol.20, pp.1993-2003, 2001.

S. Glatt, J. Letoquart, C. Faux, N. M. Taylor, B. Seraphin et al., The Elongator subcomplex Elp456 is a hexameric RecA-like ATPase, Nat. Struct. Mol. Biol, vol.19, pp.314-320, 2012.
URL : https://hal.archives-ouvertes.fr/hal-02179591

L. Fichtner and R. Schaffrath, KTI11 and KTI13, Saccharomyces cerevisiae genes controlling sensitivity to G1 arrest induced by Kluyveromyces lactis zymocin, Mol. Microbiol, vol.44, pp.865-875, 2002.

H. R. Kalhor and S. Clarke, Novel methyltransferase for modified uridine residues at the wobble position of tRNA, Mol. Cell. Biol, vol.23, pp.9283-9292, 2003.

P. Studte, S. Zink, D. Jablonowski, C. Bar, T. Von-der-haar et al., ) tRNA and protein methylase complexes mediate zymocin toxicity in yeast, Mol. Microbiol, vol.69, pp.1266-1277, 2008.

S. K. Purushothaman, J. M. Bujnicki, H. Grosjean, and B. Lapeyre, Trm11p and Trm112p are both required for the formation of 2-methylguanosine at position 10 in yeast tRNA, Mol. Cell. Biol, vol.25, pp.4359-4370, 2005.

V. Heurgue-hamard, M. Graille, N. Scrima, N. Ulryck, S. Champ et al., The zinc finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast, J. Biol. Chem, vol.281, pp.36140-36148, 2006.

J. White, Z. Li, R. Sardana, J. M. Bujnicki, E. M. Marcotte et al., Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of pre-40S subunits, Mol. Cell. Biol, vol.28, pp.3151-3161, 2008.

J. Letoquart, E. Huvelle, L. Wacheul, G. Bourgeois, C. Zorbas et al., Structural and functional studies of Bud23-Trm112 reveal 18S rRNA N7-G1575 methylation occurs on late 40S precursor ribosomes, Proc. Natl. Acad. Sci. U.S.A, vol.111, pp.5518-5526, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01107275

R. Sardana and A. W. Johnson, The methyltransferase adaptor protein Trm112 is involved in biogenesis of both ribosomal subunits, Mol. Biol. Cell, vol.23, pp.4313-4322, 2012.

A. Patil, M. Dyavaiah, F. Joseph, J. P. Rooney, C. T. Chan et al., Increased tRNA modification and gene-specific codon usage regulate cell cycle progression during the DNA damage response, Cell Cycle, vol.11, pp.3656-3665, 2012.

U. Begley, M. Dyavaiah, A. Patil, J. P. Rooney, D. Direnzo et al., Trm9-catalyzed tRNA modifications link translation to the DNA damage response, Mol. Cell, vol.28, pp.860-870, 2007.

A. Patil, C. T. Chan, M. Dyavaiah, J. P. Rooney, P. C. Dedon et al., Translational infidelity-induced protein stress results from a deficiency in Trm9-catalyzed tRNA modifications, RNA Biol, vol.9, pp.990-1001, 2012.

D. Fu, J. A. Brophy, C. T. Chan, K. A. Atmore, U. Begley et al., Human AlkB homolog ABH8 Is a tRNA methyltransferase required for wobble uridine modification and DNA damage survival, Mol. Cell. Biol, vol.30, pp.2449-2459, 2010.

Y. Fu, Q. Dai, W. Zhang, J. Ren, T. Pan et al., The AlkB domain of mammalian ABH8 catalyzes hydroxylation of 5-methoxycarbonylmethyluridine at the wobble position of tRNA, Angew. Chem. Int. Ed. Engl, vol.49, pp.8885-8888, 2010.

L. Songe-moller, E. Van-den-born, V. Leihne, C. B. Vagbo, T. Kristoffersen et al., Mammalian ALKBH8 possesses tRNA methyltransferase activity required for the biogenesis of multiple wobble uridine modifications implicated in translational decoding, Mol. Cell. Biol, vol.30, pp.1814-1827, 2010.

K. Shimada, M. Nakamura, S. Anai, M. De-velasco, M. Tanaka et al., A novel human AlkB homologue, ALKBH8, contributes to human bladder cancer progression, Cancer Res, vol.69, pp.3157-3164, 2009.

U. Begley, M. S. Sosa, A. Avivar-valderas, A. Patil, L. Endres et al., A human tRNA methyltransferase 9-like protein prevents tumour growth by regulating LIN9 and HIF1-alpha, EMBO Mol. Med, vol.5, pp.366-383, 2013.

K. Wolf, K. Breunig, and G. Barth, Non-conventional yeasts in genetics, biochemistry and biotechnology : practical protocols, 2003.

D. Liger, L. Mora, N. Lazar, S. Figaro, J. Henri et al., Mechanism of activation of methyltransferases involved in translation by the Trm112 'hub' protein, Nucleic Acids Res, vol.39, pp.6249-6259, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00624935

M. S. Longtine, . Mckenzie, D. J. Demarini, N. G. Shah, A. Wach et al., Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae, Yeast, vol.14, pp.953-961, 1998.

A. Toulmay and R. Schneiter, A two-step method for the introduction of single or multiple defined point mutations into the genome of Saccharomyces cerevisiae, Yeast, vol.23, pp.825-831, 2006.

F. W. Studier, Protein production by auto-induction in high density shaking cultures, Protein Expr. Purif, vol.41, pp.207-234, 2005.

W. Kabsch, Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants, J. Appl. Cryst, vol.26, pp.795-800, 1993.

P. D. Adams, R. W. Grosse-kunstleve, L. W. Hung, T. R. Ioerger, A. J. Mccoy et al., PHENIX: building new software for automated crystallographic structure determination, Acta Crystallogr. D. Biol. Crystallogr, vol.58, pp.1948-1954, 2002.

G. Bricogne, C. Vonrhein, C. Flensburg, M. Schiltz, and W. Paciorek, Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP 2.0, Acta Crystallogr. D Biol. Crystallogr, vol.59, pp.2023-2030, 2003.

A. Vagin and A. Teplyakov, MOLREP: an automated program for molecular replacement, J. Appl. Cryst, vol.30, pp.1022-1025, 1997.

P. Emsley and K. Cowtan, Coot: model-building tools for molecular graphics, Acta Crystallogr. D Biol. Crystallogr, vol.60, pp.2126-2132, 2004.

R. A. Laskowski, M. W. Macarthur, D. S. Moss, and J. M. Thornton, PROCHECK: a program to check the stereochemical quality of protein structures, J. Appl. Crystallogr, vol.26, pp.283-291, 1993.

C. Chen, B. Huang, J. T. Anderson, and A. S. Bystrom, Unexpected accumulation of ncm(5)U and ncm(5)S(2) (U) in a trm9 mutant suggests an additional step in the synthesis of mcm(5)U and mcm(5)S(2)U, PLoS One, vol.6, p.20783, 2011.

S. Avital and D. Elson, A convenient procedure for preparing transfer ribonucleic acid from Escherichia coli, Biochim. Biophys. Acta, vol.179, pp.297-307, 1969.

W. Cao and E. M. De-la-cruz, Quantitative full time course analysis of nonlinear enzyme cycling kinetics, Sci. Rep, vol.3, p.2658, 2013.

G. G. Krivov, M. V. Shapovalov, and R. L. Dunbrack, Improved prediction of protein side-chain conformations with SCWRL4, Proteins, vol.77, pp.778-795, 2009.

A. D. Mackerell, D. Bashford, . Bellott, R. L. Dunbrack, J. D. Evanseck et al., All-atom empirical potential for molecular modeling and dynamics studies of proteins, J. Phys. Chem. B, vol.102, pp.3586-3616, 1998.

B. R. Brooks, C. L. Brooks, A. D. Mackerell, . Jr, L. Nilsson et al., , vol.187

L. Abbasi-moheb, S. Mertel, M. Gonsior, L. Nouri-vahid, K. Kahrizi et al., Mutations in NSUN2 cause autosomal-recessive intellectual disability, Am J Hum Genet, vol.90, issue.5, pp.847-855, 2012.

P. D. Adams, P. V. Afonine, G. Bunkoczi, V. B. Chen, I. W. Davis et al., PHENIX: a comprehensive Python-based system for macromolecular structure solution, Acta Crystallogr D Biol Crystallogr, vol.66, pp.213-221, 2010.

C. E. Aitken, P. Beznoskova, V. Vlckova, W. L. Chiu, F. Zhou et al., Eukaryotic translation initiation factor 3 plays distinct roles at the mRNA entry and exit channels of the ribosomal preinitiation complex, J. R, p.5, 2016.

Q. Al-hadid, K. Roy, G. Chanfreau, and S. G. Clarke, Methylation of yeast ribosomal protein Rpl3 promotes translational elongation fidelity, RNA, vol.22, issue.4, pp.489-498, 2016.

Q. Al-hadid, K. Roy, W. Munroe, M. C. Dzialo, G. F. Chanfreau et al., Histidine methylation of yeast ribosomal protein Rpl3p is required for proper 60S subunit assembly, Mol Cell Biol, vol.34, issue.15, pp.2903-2916, 2014.

Q. Al-hadid, J. White, and S. Clarke, Ribosomal protein methyltransferases in the yeast Saccharomyces cerevisiae: Roles in ribosome biogenesis and translation, Biochem Biophys Res Commun, vol.470, issue.3, pp.552-557, 2016.

A. Alexandrov, I. Chernyakov, W. Gu, S. L. Hiley, T. R. Hughes et al., Rapid tRNA decay can result from lack of nonessential modifications, Mol Cell, vol.21, issue.1, pp.87-96, 2006.

T. Allers, Overexpression and purification of halophilic proteins in Haloferax volcanii, Bioeng Bugs, vol.1, issue.4, pp.288-290, 2010.

T. Allers, S. Barak, S. Liddell, K. Wardell, and M. Mevarech, Improved strains and plasmid vectors for conditional overexpression of His-tagged proteins in Haloferax volcanii, Appl Environ Microbiol, vol.76, issue.6, pp.1759-1769, 2010.

N. Altman-price and M. Mevarech, Genetic evidence for the importance of protein acetylation and protein deacetylation in the halophilic archaeon Haloferax volcanii, J Bacteriol, vol.191, issue.5, pp.1610-1617, 2009.

V. Anantharaman, E. V. Koonin, and L. Aravind, SPOUT: a class of methyltransferases that includes spoU and trmD RNA methylase superfamilies, and novel superfamilies of predicted prokaryotic RNA methylases, J Mol Microbiol Biotechnol, vol.4, issue.1, pp.71-75, 2002.

A. M. Anger, J. P. Armache, O. Berninghausen, M. Habeck, M. Subklewe et al., Structures of the human and Drosophila 80S ribosome, Nature, vol.497, issue.7447, pp.80-85, 2013.

C. D. Appel and E. S. Maxwell, Structural features of the guide:target RNA duplex required for archaeal box C/D sRNA-guided nucleotide 2'-O-methylation, RNA, vol.13, issue.6, pp.899-911, 2007.

L. Aravind and E. V. Koonin, THUMP--a predicted RNA-binding domain shared by 4-thiouridine, pseudouridine synthases and RNA methylases, Trends Biochem Sci, vol.26, issue.4, pp.215-217, 2001.

J. P. Armache, A. Jarasch, A. M. Anger, E. Villa, T. Becker et al.,

R. Beckmann, Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution, Proc Natl Acad Sci U S A, vol.107, issue.46, pp.19748-19753, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00530586

J. Armengaud, J. Urbonavicius, B. Fernandez, G. Chaussinand, J. M. Bujnicki et al., N2-methylation of guanosine at position 10 in tRNA is catalyzed by a THUMP domaincontaining, S-adenosylmethionine-dependent methyltransferase, conserved in Archaea and Eukaryota, J Biol Chem, vol.279, issue.35, pp.37142-37152, 2004.

M. E. Armengod, I. Moukadiri, S. Prado, R. Ruiz-partida, A. Benitez-paez et al.,

C. Navarro-gonzalez, Enzymology of tRNA modification in the bacterial MnmEG pathway, Biochimie, vol.94, issue.7, 2012.

H. Ashkenazy, E. Erez, E. Martz, T. Pupko, and N. Ben-tal, ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids, Nucleic Acids Res, vol.38, pp.529-533, 2010.

P. Auffinger and E. Westhof, An extended structural signature for the tRNA anticodon loop, RNA, vol.7, issue.3, pp.334-341, 2001.

T. Awai, S. Kimura, C. Tomikawa, A. Ochi, . Ihsanawati et al., Aquifex aeolicus tRNA (N2,N2-guanine)-dimethyltransferase (Trm1) catalyzes transfer of methyl groups not only to guanine 26 but also to guanine 27 in tRNA, J Biol Chem, vol.284, issue.31, pp.20467-20478, 2009.

A. K. Banerjee, 5'-terminal cap structure in eucaryotic messenger ribonucleic acids, Microbiol Rev, vol.44, issue.2, pp.175-205, 1980.

T. Becker, S. Franckenberg, S. Wickles, C. J. Shoemaker, A. M. Anger et al.,

R. Beckmann, Structural basis of highly conserved ribosome recycling in eukaryotes and archaea, Nature, vol.482, issue.7386, pp.501-506, 2012.

U. Begley, M. Dyavaiah, A. Patil, J. P. Rooney, D. Direnzo et al.,

T. J. Begley, Trm9-catalyzed tRNA modifications link translation to the DNA damage response, Mol Cell, vol.28, issue.5, pp.860-870, 2007.

U. Begley, M. S. Sosa, A. Avivar-valderas, A. Patil, L. Endres et al.,

T. Begley, A human tRNA methyltransferase 9-like protein prevents tumour growth by regulating LIN9 and HIF1-alpha, EMBO Mol Med, vol.5, issue.3, pp.366-383, 2013.

A. Ben-shem, N. Garreau-de-loubresse, S. Melnikov, L. Jenner, G. Yusupova et al., The structure of the eukaryotic ribosome at 3.0 A resolution, Science, vol.334, issue.6062, pp.1524-1529, 2011.

S. Blanchet, M. Rowe, T. Von-der-haar, C. Fabret, S. Demais et al., New insights into stop codon recognition by eRF1, Nucleic Acids Res, vol.43, issue.6, pp.3298-3308, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01464855

S. Boschi-muller and Y. Motorin, Chemistry enters nucleic acids biology: enzymatic mechanisms of RNA modification, Biochemistry (Mosc), vol.78, issue.13, pp.1392-1404, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01467256

G. Bourgeois, J. Letoquart, N. Van-tran, and M. Graille, Trm112, a Protein Activator of Methyltransferases Modifying Actors of the Eukaryotic Translational Apparatus, Biomolecules, vol.7, issue.1, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01948152

G. Bourgeois, J. Marcoux, J. M. Saliou, S. Cianferani, and M. Graille, Activation mode of the eukaryotic m2G10 tRNA methyltransferase Trm11 by its partner protein Trm112, Nucleic Acids Res, vol.45, issue.4, pp.1971-1982, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01953006

G. Bourgeois, M. Ney, I. Gaspar, C. Aigueperse, M. Schaefer et al.,

Y. Motorin, Eukaryotic rRNA Modification by Yeast 5-Methylcytosine-Methyltransferases and Human Proliferation-Associated Antigen p120, PLoS One, vol.10, issue.7, p.133321, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01451668

G. Bricogne, E. Blanc, M. Brandl, C. Flensburg, P. Keller et al.,

T. O. Womack, BUSTER version 2.10.2. Cambridge, United Kingdom: Global Phasing Ltd, 2016.

C. Brochier-armanet, P. Forterre, and S. Gribaldo, Phylogeny and evolution of the Archaea: one hundred genomes later, Curr Opin Microbiol, vol.14, issue.3, pp.274-281, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00598326

A. Brown, S. Shao, J. Murray, R. S. Hegde, and V. Ramakrishnan, Structural basis for stop codon recognition in eukaryotes, Nature, vol.524, issue.7566, pp.493-496, 2015.

K. M. Brown and G. M. Gilmartin, A mechanism for the regulation of pre-mRNA 3' processing by human cleavage factor Im, Mol Cell, vol.12, issue.6, pp.1467-1476, 2003.

J. M. Bujnicki, L. Droogmans, H. Grosjean, S. K. Purushothaman, and B. Lapeyre, , 2004.

, Bioinformatics-guided identification and experimental char-acterization of novel RNA methyltransferases, Practical Bioinformatics, vol.15, pp.139-168

O. Cakici, M. Sikorski, T. Stepkowski, G. Bujacz, and M. Jaskolski, Crystal structures of NodS N-methyltransferase from Bradyrhizobium japonicum in ligand-free form and as SAH complex, J Mol Biol, vol.404, issue.5, pp.874-889, 2010.

W. A. Cantara, P. F. Crain, J. Rozenski, J. A. Mccloskey, K. A. Harris et al.,

P. F. Agris, The RNA Modification Database, RNAMDB: 2011 update, Nucleic Acids Res, vol.39, pp.195-201, 2011.

G. L. Cantoni, Biological methylation: selected aspects, Annu Rev Biochem, vol.44, pp.435-451, 1975.

W. Cao, . De-la, and E. M. Cruz, Quantitative full time course analysis of nonlinear enzyme cycling kinetics, Sci Rep, vol.3, p.2658, 2013.

C. Carapito, A. Burel, P. Guterl, A. Walter, F. Varrier et al., , 2014.

, MSDA, a proteomics software suite for in-depth Mass Spectrometry Data Analysis using grid computing, Proteomics, vol.14, issue.9, pp.1014-1019

C. Carapito, L. Lane, M. Benama, A. Opsomer, E. Mouton-barbosa et al., Computational and Mass-Spectrometry-Based Workflow for the Discovery and Validation of Missing Human Proteins: Application to Chromosomes 2 and 14, J Proteome Res, vol.14, issue.9, pp.3621-3634, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02191518

J. P. Cecchini and R. Miassod, Studies on the methylation of cytoplasmic ribosomal RNA from cultured higher plant cells, Eur J Biochem, vol.98, issue.1, pp.203-214, 1979.

C. Chen, B. Huang, J. T. Anderson, and A. S. Bystrom, Unexpected accumulation of ncm(5)U and ncm(5)S(2) (U) in a trm9 mutant suggests an additional step in the synthesis of mcm(5)U and mcm(5)S(2)U, PLoS One, vol.6, issue.6, p.20783, 2011.

X. Cheng, S. Kumar, J. Posfai, J. W. Pflugrath, and R. J. Roberts, Crystal structure of the HhaI DNA methyltransferase complexed with S-adenosyl-L-methionine, Cell, vol.74, issue.2, pp.299-307, 1993.

X. Cheng and R. J. Roberts, AdoMet-dependent methylation, DNA methyltransferases and base flipping, Nucleic Acids Res, vol.29, issue.18, pp.3784-3795, 2001.

Z. Cheng, K. Saito, A. V. Pisarev, M. Wada, V. P. Pisareva et al., Structural insights into eRF3 and stop codon recognition by eRF1, Genes Dev, vol.23, issue.9, pp.1106-1118, 2009.

J. Choi, K. W. Ieong, H. Demirci, J. Chen, A. Petrov et al., N(6)-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics, Nat Struct Mol Biol, vol.23, issue.2, pp.110-115, 2016.

T. A. Couttas, M. J. Raftery, M. P. Padula, B. R. Herbert, and M. R. Wilkins, Methylation of translation-associated proteins in Saccharomyces cerevisiae: Identification of methylated lysines and their methyltransferases, Proteomics, vol.12, issue.7, pp.960-972, 2012.

C. J. Cox, P. G. Foster, R. P. Hirt, S. R. Harris, and T. M. Embley, The archaebacterial origin of eukaryotes, Proc Natl Acad Sci U S A, vol.105, issue.51, pp.20356-20361, 2008.

M. Davila-lopez and T. Samuelsson, Early evolution of histone mRNA 3' end processing, RNA, vol.14, issue.1, pp.1-10, 2008.

E. Davydova, A. Y. Ho, J. Malecki, A. Moen, J. M. Enserink et al., Identification and characterization of a novel evolutionarily conserved lysine-specific methyltransferase targeting eukaryotic translation elongation factor 2 (eEF2), J Biol Chem, vol.289, issue.44, pp.30499-30510, 2014.

W. A. Decatur and M. J. Fournier, rRNA modifications and ribosome function, Trends Biochem Sci, vol.27, issue.7, pp.344-351, 2002.

B. Delatte, F. Wang, L. V. Ngoc, E. Collignon, E. Bonvin et al., RNA biochemistry. Transcriptome-wide distribution and function of RNA hydroxymethylcytosine, Science, vol.351, issue.6270, pp.282-285, 2016.

W. Deng, I. R. Babu, D. Su, S. Yin, T. J. Begley et al., Trm9-Catalyzed tRNA Modifications Regulate Global Protein Expression by Codon-Biased Translation, PLoS Genet, vol.11, issue.12, p.1005706, 2015.

X. Deng, K. Chen, G. Z. Luo, X. Weng, Q. Ji et al., Widespread occurrence of N6-methyladenosine in bacterial mRNA, Nucleic Acids Res, vol.43, issue.13, pp.6557-6567, 2015.

P. P. Dennis, V. Tripp, L. Lui, T. Lowe, and L. Randau, , 2015.

C. , box sRNA-guided 2'-O-methylation patterns of archaeal rRNA molecules, BMC Genomics, vol.16, p.632

T. E. Dever and R. Green, The elongation, termination, and recycling phases of translation in eukaryotes, Cold Spring Harb Perspect Biol, vol.4, issue.7, p.13706, 2012.

S. C. Dillon, X. Zhang, R. C. Trievel, and X. Cheng, The SET-domain protein superfamily: protein lysine methyltransferases, Genome Biol, vol.6, issue.8, p.227, 2005.

C. Dina, D. Meyre, S. Gallina, E. Durand, A. Korner et al.,

P. Froguel, Variation in FTO contributes to childhood obesity and severe adult obesity, Nat Genet, vol.39, issue.6, pp.724-726, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00173651

V. Dincbas-renqvist, A. Engstrom, L. Mora, V. Heurgue-hamard, R. Buckingham et al., A post-translational modification in the GGQ motif of RF2 from Escherichia coli stimulates termination of translation, EMBO J, vol.19, issue.24, pp.6900-6907, 2000.

A. Doll and K. H. Grzeschik, Characterization of two novel genes, WBSCR20 and WBSCR22, deleted in Williams-Beuren syndrome, Cytogenet Cell Genet, vol.95, issue.1-2, pp.20-27, 2001.

D. Dominissini, S. Moshitch-moshkovitz, S. Schwartz, M. Salmon-divon, L. Ungar et al.,

G. Rechavi, Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq, Nature, vol.485, issue.7397, pp.201-206, 2012.

D. Dominissini, S. Nachtergaele, S. Moshitch-moshkovitz, E. Peer, N. Kol et al., The dynamic N(1)-methyladenosine methylome in eukaryotic messenger RNA, Nature, vol.530, issue.7591, pp.441-446, 2016.

M. Dontsova, L. Frolova, J. Vassilieva, W. Piendl, L. Kisselev et al., Translation termination factor aRF1 from the archaeon Methanococcus jannaschii is active with eukaryotic ribosomes, FEBS Lett, vol.472, issue.2-3, pp.213-216, 2000.

M. C. Dzialo, K. J. Travaglini, S. Shen, K. Roy, G. F. Chanfreau et al., Translational roles of elongation factor 2 protein lysine methylation, J Biol Chem, vol.289, issue.44, pp.30511-30524, 2014.

P. Emsley, B. Lohkamp, W. G. Scott, and K. Cowtan, Features and development of Coot, Acta Crystallogr D Biol Crystallogr, vol.66, pp.486-501, 2010.

D. E. Eyler, K. A. Wehner, and R. Green, Eukaryotic release factor 3 is required for multiple turnovers of peptide release catalysis by eukaryotic release factor 1, J Biol Chem, vol.288, issue.41, pp.29530-29538, 2013.

H. Fan-minogue, M. Du, A. V. Pisarev, A. K. Kallmeyer, J. Salas-marco et al.,

D. M. Bedwell, Distinct eRF3 requirements suggest alternate eRF1 conformations mediate peptide release during eukaryotic translation termination, Mol Cell, vol.30, issue.5, pp.599-609, 2008.

S. M. Fica, N. Tuttle, T. Novak, N. S. Li, J. Lu et al., RNA catalyses nuclear pre-mRNA splicing, Nature, vol.503, issue.7475, pp.229-234, 2013.

S. Figaro, N. Scrima, R. H. Buckingham, and V. Heurgue-hamard, HemK2 protein, encoded on human chromosome 21, methylates translation termination factor eRF1, FEBS Lett, vol.582, issue.16, pp.2352-2356, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00348794

S. Figaro, L. Wacheul, S. Schillewaert, M. Graille, E. Huvelle et al.,

V. Heurgue-hamard, Trm112 is required for Bud23-mediated methylation of the 18S rRNA at position G1575, Mol Cell Biol, vol.32, issue.12, pp.2254-2267, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00709211

S. Fischer, J. Benz, B. Spath, L. K. Maier, J. Straub et al., The archaeal Lsm protein binds to small RNAs, J Biol Chem, vol.285, issue.45, pp.34429-34438, 2010.

M. Fislage, M. Roovers, I. Tuszynska, J. M. Bujnicki, L. Droogmans et al., Crystal structures of the tRNA:m2G6 methyltransferase Trm14/TrmN from two domains of life, Nucleic Acids Res, vol.40, issue.11, pp.5149-5161, 2012.

M. Fontecave, M. Atta, and E. Mulliez, S-adenosylmethionine: nothing goes to waste, Trends Biochem Sci, vol.29, issue.5, pp.243-249, 2004.

S. Franckenberg, T. Becker, and R. Beckmann, Structural view on recycling of archaeal and eukaryotic ribosomes after canonical termination and ribosome rescue, Curr Opin Struct Biol, vol.22, issue.6, pp.786-796, 2012.

C. S. Francklyn and A. Minajigi, tRNA as an active chemical scaffold for diverse chemical transformations, FEBS Lett, vol.584, issue.2, pp.366-375, 2010.

D. Fu, J. A. Brophy, C. T. Chan, K. A. Atmore, U. Begley et al.,

L. D. Samson, Human AlkB homolog ABH8 Is a tRNA methyltransferase required for wobble uridine modification and DNA damage survival, Mol Cell Biol, vol.30, issue.10, pp.2449-2459, 2010.

L. Fu, C. R. Guerrero, N. Zhong, N. J. Amato, Y. Liu et al., Tet-mediated formation of 5-hydroxymethylcytosine in RNA, J Am Chem Soc, vol.136, issue.33, pp.11582-11585, 2014.

Y. Fu, Q. Dai, W. Zhang, J. Ren, T. Pan et al., The AlkB domain of mammalian ABH8 catalyzes hydroxylation of 5-methoxycarbonylmethyluridine at the wobble position of tRNA, 2010.

, Angew Chem Int Ed Engl, vol.49, issue.47, pp.8885-8888

Y. Furuichi, Discovery of m(7)G-cap in eukaryotic mRNAs, Proc Jpn Acad Ser B Phys Biol Sci, vol.91, issue.8, pp.394-409, 2015.

J. M. Fustin, M. Doi, Y. Yamaguchi, H. Hida, S. Nishimura et al.,

H. Okamura, RNA-methylation-dependent RNA processing controls the speed of the circadian clock, Cell, vol.155, issue.4, pp.793-806, 2013.

S. Galardi, A. Fatica, A. Bachi, A. Scaloni, C. Presutti et al., Purified box C/D snoRNPs are able to reproduce site-specific 2'-O-methylation of target RNA in vitro, Mol Cell Biol, vol.22, issue.19, pp.6663-6668, 2002.

A. C. Gavin, M. Bosche, R. Krause, P. Grandi, M. Marzioch et al., Functional organization of the yeast proteome by systematic analysis of protein complexes, Nature, issue.6868, pp.141-147, 2002.

G. Giaever, A. M. Chu, L. Ni, C. Connelly, L. Riles et al.,

M. Johnston, Functional profiling of the Saccharomyces cerevisiae genome, Nature, vol.418, issue.6896, pp.387-391, 2002.

W. V. Gilbert, T. A. Bell, and C. Schaening, Messenger RNA modifications: Form, distribution, and function, Science, vol.352, issue.6292, pp.1408-1412, 2016.

S. Glatt, J. Letoquart, C. Faux, N. M. Taylor, B. Seraphin et al., The Elongator subcomplex Elp456 is a hexameric RecA-like ATPase, Nat Struct Mol Biol, vol.19, issue.3, pp.314-320, 2012.
URL : https://hal.archives-ouvertes.fr/hal-02179591

S. Glatt, R. Zabel, O. Kolaj-robin, O. F. Onuma, F. Baudin et al.,

C. W. Muller, Structural basis for tRNA modification by Elp3 from Dehalococcoides mccartyi, Nat Struct Mol Biol, vol.23, issue.9, pp.794-802, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01413474

M. Graille, S. Figaro, S. Kervestin, R. H. Buckingham, D. Liger et al., Methylation of class I translation termination factors: structural and functional aspects, Biochimie, vol.94, issue.7, pp.1533-1543, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00709208

M. Graille, V. Heurgue-hamard, S. Champ, L. Mora, N. Scrima et al.,

R. H. Buckingham, Molecular basis for bacterial class I release factor methylation by PrmC, Mol Cell, vol.20, issue.6, pp.917-927, 2005.

P. Grandi, V. Rybin, J. Bassler, E. Petfalski, D. Strauss et al., 90S preribosomes include the 35S pre-rRNA, the U3 snoRNP, and 40S subunit processing factors but predominantly lack 60S synthesis factors, Mol Cell, vol.10, issue.1, pp.105-115, 2002.

S. Granneman and S. J. Baserga, Ribosome biogenesis: of knobs and RNA processing, Exp Cell Res, vol.296, issue.1, pp.43-50, 2004.

H. Grosjean, RNA modification: the Golden Period, RNA, vol.21, issue.4, pp.625-626, 1995.
URL : https://hal.archives-ouvertes.fr/hal-01464801

H. Grosjean, V. De-crecy-lagard, and C. Marck, Deciphering synonymous codons in the three domains of life: co-evolution with specific tRNA modification enzymes, FEBS Lett, vol.584, issue.2, pp.252-264, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00506393

H. Grosjean, C. Gaspin, C. Marck, W. A. Decatur, and V. De-crecy-lagard, RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes, BMC Genomics, vol.9, p.470, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00354522

C. Gu, T. J. Begley, and P. C. Dedon, tRNA modifications regulate translation during cellular stress, FEBS Lett, vol.588, issue.23, pp.4287-4296, 2014.

T. Gu, H. He, Y. Zhang, Z. Han, G. Hou et al.,

Q. Wu, Trmt112 gene expression in mouse embryonic development, Acta Histochem Cytochem, vol.45, issue.2, pp.113-119, 2012.

R. Gumienny, D. J. Jedlinski, A. Schmidt, F. Gypas, G. Martin et al., High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq, Nucleic Acids Res, 2016.

R. Gupta, Halobacterium volcanii tRNAs. Identification of 41 tRNAs covering all amino acids, and the sequences of 33 class I tRNAs, Journal of Biological Chemistry, vol.259, issue.15, pp.9461-9471, 1984.

F. Halbach, M. Rode, and E. Conti, The crystal structure of S. cerevisiae Ski2, a DExH helicase associated with the cytoplasmic functions of the exosome, RNA, vol.18, issue.1, pp.124-134, 2012.

J. J. Hamey, D. L. Winter, D. Yagoub, C. M. Overall, G. Hart-smith et al., Novel N-terminal and Lysine Methyltransferases That Target Translation Elongation Factor 1A in Yeast and Human, Mol Cell Proteomics, vol.15, issue.1, pp.164-176, 2016.

A. L. Hartman, C. Norais, J. H. Badger, S. Delmas, S. Haldenby et al.,

J. A. Eisen, The complete genome sequence of Haloferax volcanii DS2, a model archaeon, PLoS One, vol.5, issue.3, p.9605, 2010.

Y. Hashem, A. Des-georges, J. Fu, S. N. Buss, F. Jossinet et al., Highresolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome, Nature, vol.494, issue.7437, pp.385-389, 2013.

A. K. Henras, J. Soudet, M. Gerus, S. Lebaron, M. Caizergues-ferrer et al., The post-transcriptional steps of eukaryotic ribosome biogenesis, Cell Mol Life Sci, vol.65, issue.15, pp.2334-2359, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00309051

V. Heurgue-hamard, S. Champ, A. Engstrom, M. Ehrenberg, and R. H. Buckingham, The hemK gene in Escherichia coli encodes the N(5)-glutamine methyltransferase that modifies peptide release factors, EMBO J, vol.21, issue.4, pp.769-778, 2002.

V. Heurgue-hamard, S. Champ, L. Mora, T. Merkulova-rainon, L. L. Kisselev et al., The glutamine residue of the conserved GGQ motif in Saccharomyces cerevisiae release factor eRF1 is methylated by the product of the YDR140w gene, J Biol Chem, vol.280, issue.4, pp.2439-2445, 2005.

V. Heurgue-hamard, M. Graille, N. Scrima, N. Ulryck, S. Champ et al., The zinc finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast, J Biol Chem, vol.281, issue.47, pp.36140-36148, 2006.

A. G. Hinnebusch and J. R. Lorsch, The mechanism of eukaryotic translation initiation: new insights and challenges, Cold Spring Harb Perspect Biol, issue.10, p.4, 2012.

A. Hirata, S. Nishiyama, T. Tamura, A. Yamauchi, and H. Hori, Structural and functional analyses of the archaeal tRNA m2G/m22G10 methyltransferase aTrm11 provide mechanistic insights into site specificity of a tRNA methyltransferase that contains common RNA-binding modules, Nucleic Acids Res, vol.44, issue.13, pp.6377-6390, 2016.

P. H. Hirel, M. J. Schmitter, P. Dessen, G. Fayat, and S. Blanquet, Extent of N-terminal methionine excision from Escherichia coli proteins is governed by the side-chain length of the penultimate amino acid, Proc Natl Acad Sci U S A, vol.86, issue.21, pp.8247-8251, 1989.

S. Hocine, R. H. Singer, and D. Grunwald, RNA processing and export, Cold Spring Harb Perspect Biol, vol.2, issue.12, p.752, 2010.

T. P. Hoernes and M. D. Erlacher, Translating the epitranscriptome, Wiley Interdiscip Rev RNA, vol.8, issue.1, 2017.

L. Holm and P. Rosenstrom, Dali server: conservation mapping in 3D, Nucleic Acids Res, vol.38, pp.545-549, 2010.

A. K. Hopper, Transfer RNA post-transcriptional processing, turnover, and subcellular dynamics in the yeast Saccharomyces cerevisiae, Genetics, vol.194, issue.1, pp.43-67, 2013.

H. Hori, Transfer RNA methyltransferases with a SpoU-TrmD (SPOUT) fold and their modified nucleosides in tRNA, Biomolecules, vol.7, issue.1, 2017.

Y. M. Hou and J. J. Perona, Stereochemical mechanisms of tRNA methyltransferases, FEBS Lett, vol.584, issue.2, pp.278-286, 2010.

Z. Hu, Z. Qin, M. Wang, C. Xu, G. Feng et al.,

Y. Hu, The Arabidopsis SMO2, a homologue of yeast TRM112, modulates progression of cell division during organ growth, Plant J, vol.61, issue.4, pp.600-610, 2010.

B. Huang, J. Lu, and A. S. Bystrom, A genome-wide screen identifies genes required for formation of the wobble nucleoside 5-methoxycarbonylmethyl-2-thiouridine in Saccharomyces cerevisiae, RNA, vol.14, issue.10, pp.2183-2194, 2008.

T. Hussain, J. L. Llacer, I. S. Fernandez, A. Munoz, P. Martin-marcos et al.,

V. Ramakrishnan, Structural changes enable start codon recognition by the eukaryotic translation initiation complex, Cell, vol.159, issue.3, pp.597-607, 2014.

L. A. Isaksson and J. H. Phillips, Studies on microbial RNA. V. A comparison of the in vivo methylated components of ribosomal RNA from Escherichia coli and Saccharomyces cerevisiae, Biochim Biophys Acta, vol.155, issue.1, pp.63-71, 1968.

E. Izaurralde, C. Mcguigan, and I. W. Mattaj, Nuclear localization of a cap-binding protein complex, Cold Spring Harb Symp Quant Biol, vol.60, pp.669-675, 1995.

J. E. Jackman and J. D. Alfonzo, Transfer RNA modifications: nature's combinatorial chemistry playground, Wiley Interdiscip Rev RNA, vol.4, issue.1, pp.35-48, 2013.

R. J. Jackson, C. U. Hellen, and T. V. Pestova, The mechanism of eukaryotic translation initiation and principles of its regulation, Nat Rev Mol Cell Biol, vol.11, issue.2, pp.113-127, 2010.

R. J. Jackson, C. U. Hellen, and T. V. Pestova, Termination and post-termination events in eukaryotic translation, Adv Protein Chem Struct Biol, vol.86, pp.45-93, 2012.

M. Jangani, T. M. Poolman, L. Matthews, N. Yang, S. N. Farrow et al., The methyltransferase WBSCR22/Merm1 enhances glucocorticoid receptor function and is regulated in lung inflammation and cancer, J Biol Chem, vol.289, issue.13, pp.8931-8946, 2014.

L. Jenner, S. Melnikov, N. Garreau-de-loubresse, A. Ben-shem, M. Iskakova et al.,

M. Yusupov, Crystal structure of the 80S yeast ribosome, Curr Opin Struct Biol, vol.22, issue.6, pp.759-767, 2012.

W. Kabsch, Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants, J. Appl. Cryst, vol.26, pp.795-800, 1993.

H. R. Kalhor and S. Clarke, Novel methyltransferase for modified uridine residues at the wobble position of tRNA, Mol Cell Biol, vol.23, issue.24, pp.9283-9292, 2003.

L. D. Kapp and J. R. Lorsch, The molecular mechanics of eukaryotic translation, Annu Rev Biochem, vol.73, pp.657-704, 2004.

L. Keller, W. Xu, H. X. Wang, B. Winblad, L. Fratiglioni et al., The obesity related gene, FTO, interacts with APOE, and is associated with Alzheimer's disease risk: a prospective cohort study, J Alzheimers Dis, vol.23, issue.3, pp.461-469, 2011.

K. Kiosze-becker, A. Ori, M. Gerovac, A. Heuer, E. Nurenberg-goloub et al.,

R. Tampe, Structure of the ribosome post-recycling complex probed by chemical cross-linking and mass spectrometry, Nat Commun, vol.7, p.13248, 2016.

B. P. Klaholz, Molecular recognition and catalysis in translation termination complexes, Trends Biochem Sci, vol.36, issue.5, pp.282-292, 2011.

S. Klinge, F. Voigts-hoffmann, M. Leibundgut, and N. Ban, Atomic structures of the eukaryotic ribosome, Trends Biochem Sci, vol.37, issue.5, pp.189-198, 2012.

K. Kobayashi, K. Saito, R. Ishitani, K. Ito, and O. Nureki, Structural basis for translation termination by archaeal RF1 and GTP-bound EF1alpha complex, Nucleic Acids Res, vol.40, issue.18, pp.9319-9328, 2012.

M. Kohli, S. M. Riska, D. W. Mahoney, H. S. Chai, D. W. Hillman et al.,

J. R. Cerhan, Germline predictors of androgen deprivation therapy response in advanced prostate cancer, Mayo Clin Proc, vol.87, issue.3, pp.240-246, 2012.

C. Kong, K. Ito, M. A. Walsh, M. Wada, Y. Liu et al., Crystal structure and functional analysis of the eukaryotic class II release factor eRF3 from S. pombe, Mol Cell, vol.14, issue.2, pp.233-245, 2004.

P. Z. Kozbial and A. R. Mushegian, Natural history of S-adenosylmethionine-binding proteins, BMC Struct Biol, vol.5, p.19, 2005.

D. Kressler, E. Hurt, and J. Bassler, Driving ribosome assembly, Biochim Biophys Acta, issue.6, pp.673-683, 2010.

N. Krogh, M. D. Jansson, S. J. Hafner, D. Tehler, U. Birkedal et al., Profiling of 2'-O-Me in human rRNA reveals a subset of fractionally modified positions and provides evidence for ribosome heterogeneity, Nucleic Acids Res, vol.44, issue.16, pp.7884-7895, 2016.

P. Kryuchkova, A. Grishin, B. Eliseev, A. Karyagina, L. Frolova et al., Two-step model of stop codon recognition by eukaryotic release factor eRF1, Nucleic Acids Res, vol.41, issue.8, pp.4573-4586, 2013.

D. Kusevic, S. Kudithipudi, and A. Jeltsch, Substrate Specificity of the HEMK2 Protein Glutamine Methyltransferase and Identification of Novel Substrates, J Biol Chem, vol.291, issue.12, pp.6124-6133, 2016.

V. V. Kushnirov, M. D. Ter-avanesyan, M. V. Telckov, A. P. Surguchov, V. N. Smirnov et al., Nucleotide sequence of the SUP2 (SUP35) gene of Saccharomyces cerevisiae, Gene, vol.66, issue.1, pp.45-54, 1988.

V. Leihne, F. Kirpekar, C. B. Vagbo, E. Van-den-born, H. E. Krokan et al., Roles of Trm9-and ALKBH8-like proteins in the formation of modified wobble uridines in Arabidopsis tRNA, Nucleic Acids Res, vol.39, issue.17, pp.7688-7701, 2011.

J. Letoquart, E. Huvelle, L. Wacheul, G. Bourgeois, C. Zorbas et al.,

D. L. Lafontaine, Structural and functional studies of Bud23-Trm112 reveal 18S rRNA N7-G1575 methylation occurs on late 40S precursor ribosomes, Proc Natl Acad Sci U S A, vol.111, issue.51, pp.5518-5526, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01107275

J. Letoquart, N. V. Tran, V. Caroline, A. Aleksandrov, N. Lazar et al.,

M. Graille, Insights into molecular plasticity in protein complexes from Trm9-Trm112 tRNA modifying enzyme crystal structure, Nucleic Acids Res, vol.43, issue.22, pp.10989-11002, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01303131

X. Li, X. Xiong, K. Wang, L. Wang, X. Shu et al., Transcriptome-wide mapping reveals reversible and dynamic N(1)-methyladenosine methylome, Nat Chem Biol, vol.12, issue.5, pp.311-316, 2016.

X. H. Liang, Q. Liu, and M. J. Fournier, rRNA modifications in an intersubunit bridge of the ribosome strongly affect both ribosome biogenesis and activity, Mol Cell, vol.28, issue.6, pp.965-977, 2007.

X. H. Liang, Q. Liu, and M. J. Fournier, Loss of rRNA modifications in the decoding center of the ribosome impairs translation and strongly delays pre-rRNA processing, RNA, vol.15, issue.9, pp.1716-1728, 2009.

D. Liger, L. Mora, N. Lazar, S. Figaro, J. Henri et al.,

M. Graille, Mechanism of activation of methyltransferases involved in translation by the Trm112 'hub' protein, Nucleic Acids Res, vol.39, issue.14, pp.6249-6259, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00624935

J. Liu, Y. Yue, D. Han, X. Wang, Y. Fu et al., A METTL3-METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation, Nat Chem Biol, vol.10, issue.2, pp.93-95, 2014.

P. Liu, S. Nie, B. Li, Z. Q. Yang, Z. M. Xu et al.,

G. L. Xu, Deficiency in a glutaminespecific methyltransferase for the release factor causes mouse embryonic lethality, Mol Cell Biol, vol.30, issue.17, pp.4245-4253, 2010.

R. J. Liu, M. Zhou, Z. P. Fang, M. Wang, X. L. Zhou et al., The tRNA recognition mechanism of the minimalist SPOUT methyltransferase, TrmL. Nucleic Acids Res, vol.41, issue.16, pp.7828-7842, 2013.

W. A. Loenen, S-adenosylmethionine: jack of all trades and master of everything?, Biochem Soc Trans, pp.330-333, 2006.

P. G. Loh and H. Song, Structural and mechanistic insights into translation termination, Curr Opin Struct Biol, vol.20, issue.1, pp.98-103, 2010.

C. Lorenz, C. E. Lunse, and M. Morl, tRNA Modifications: Impact on Structure and Thermal Adaptation, vol.7, 2017.

J. Lu, B. Huang, A. Esberg, M. J. Johansson, and A. S. Bystrom, The Kluyveromyces lactis gamma-toxin targets tRNA anticodons, RNA, vol.11, issue.11, pp.1648-1654, 2005.

A. Lunardi, G. Di-minin, P. Provero, M. Ferro, M. Carotti et al., A genome-scale protein interaction profile of Drosophila p53 uncovers additional nodes of the human p53 network, Proc Natl Acad Sci, vol.107, issue.14, pp.6322-6327, 2010.

Z. Lyu and W. B. Whitman, Evolution of the archaeal and mammalian information processing systems: towards an archaeal model for human disease, Cell Mol Life Sci, vol.74, issue.2, pp.183-212, 2017.

B. E. Maden, Identification of the locations of the methyl groups in 18 S ribosomal RNA from Xenopus laevis and man, J Mol Biol, vol.189, issue.4, pp.681-699, 1986.

D. A. Mangus, M. C. Evans, and A. Jacobson, Poly(A)-binding proteins: multifunctional scaffolds for the post-transcriptional control of gene expression, Genome Biol, vol.4, issue.7, p.223, 2003.

V. Marchand, F. Pichot, K. Thuring, L. Ayadi, I. Freund et al., Next-Generation Sequencing-Based RiboMethSeq Protocol for Analysis of tRNA 2'-O-Methylation, Biomolecules, vol.7, issue.1, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01799272

J. L. Martin and F. M. Mcmillan, SAM (dependent) I AM: the S-adenosylmethionine-dependent methyltransferase fold, Curr Opin Struct Biol, vol.12, issue.6, pp.783-793, 2002.

M. H. Mazauric, L. Dirick, S. K. Purushothaman, G. R. Bjork, and B. Lapeyre, Trm112p is a 15-kDa zinc finger protein essential for the activity of two tRNA and one protein methyltransferases in yeast, J Biol Chem, vol.285, issue.24, pp.18505-18515, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00509840

A. A. Mccarthy and J. G. Mccarthy, The structure of two N-methyltransferases from the caffeine biosynthetic pathway, Plant Physiol, vol.144, issue.2, pp.879-889, 2007.

A. J. Mccoy, R. W. Grosse-kunstleve, P. D. Adams, M. D. Winn, L. C. Storoni et al., Phaser crystallographic software, Journal of Applied Crystallography, vol.40, issue.4, pp.658-674, 2007.

S. Melnikov, A. Ben-shem, N. Garreau-de-loubresse, L. Jenner, G. Yusupova et al., One core, two shells: bacterial and eukaryotic ribosomes, Nat Struct Mol Biol, vol.19, issue.6, pp.560-567, 2012.

S. Menezes, K. W. Gaston, K. L. Krivos, E. E. Apolinario, N. O. Reich et al., Formation of m2G6 in Methanocaldococcus jannaschii tRNA catalyzed by the novel methyltransferase Trm14, Nucleic Acids Res, vol.39, issue.17, pp.7641-7655, 2011.

G. Merla, C. Ucla, M. Guipponi, and A. Reymond, Identification of additional transcripts in the Williams-Beuren syndrome critical region, Hum Genet, vol.110, issue.5, pp.429-438, 2002.

J. Meury and M. Kohiyama, ATP is required for K+ active transport in the archaebacterium Haloferax volcanii, Archives of Microbiology, vol.151, issue.6, pp.530-536, 1989.

K. D. Meyer, Y. Saletore, P. Zumbo, O. Elemento, C. E. Mason et al., Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons, Cell, vol.149, issue.7, pp.1635-1646, 2012.

L. Mora, V. Heurgue-hamard, M. De-zamaroczy, S. Kervestin, and R. H. Buckingham, Methylation of bacterial release factors RF1 and RF2 is required for normal translation termination in vivo, J Biol Chem, vol.282, issue.49, pp.35638-35645, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00310559

Y. Motorin and M. Helm, RNA nucleotide methylation, Wiley Interdiscip Rev RNA, vol.2, issue.5, pp.611-631, 2011.

K. Nakahigashi, N. Kubo, S. Narita, T. Shimaoka, S. Goto et al.,

H. Inokuchi, , 2002.

, HemK, a class of protein methyl transferase with similarity to DNA methyl transferases, methylates polypeptide chain release factors, and hemK knockout induces defects in translational termination, Proc Natl Acad Sci U S A, vol.99, issue.3, pp.1473-1478

Y. Nakamura and K. Ito, Making sense of mimic in translation termination, Trends Biochem Sci, vol.28, issue.2, pp.99-105, 2003.

Y. Nakazawa, H. Arai, and N. Fujita, The novel metastasis promoter Merm1/Wbscr22 enhances tumor cell survival in the vasculature by suppressing Zac1/p53-dependent apoptosis, Cancer Res, vol.71, issue.3, pp.1146-1155, 2011.

M. V. Nesterchuk, P. V. Sergiev, and O. A. Dontsova, Posttranslational Modifications of Ribosomal Proteins in Escherichia coli, Acta Naturae, vol.3, issue.2, pp.22-33, 2011.

P. Neumann, K. Lakomek, P. T. Naumann, W. M. Erwin, C. T. Lauhon et al., Crystal structure of a 4-thiouridine synthetase-RNA complex reveals specificity of tRNA U8 modification, Nucleic Acids Res, vol.42, issue.10, pp.6673-6685, 2014.

D. S. Nie, Y. B. Liu, and G. X. Lu, Cloning and primarily function study of two novel putative N5-glutamine methyltransferase (Hemk) splice variants from mouse stem cells, Mol Biol Rep, vol.36, issue.8, pp.2221-2228, 2009.

K. Nishimura, T. Hosaka, S. Tokuyama, S. Okamoto, and K. Ochi, Mutations in rsmG, encoding a 16S rRNA methyltransferase, result in low-level streptomycin resistance and antibiotic overproduction in Streptomyces coelicolor A3(2), J Bacteriol, vol.189, issue.10, pp.3876-3883, 2007.

A. Noma, Y. Sakaguchi, and T. Suzuki, Mechanistic characterization of the sulfur-relay system for eukaryotic 2-thiouridine biogenesis at tRNA wobble positions, Nucleic Acids Research, vol.37, issue.4, pp.1335-1352, 2009.

K. R. Noon, E. Bruenger, and J. A. Mccloskey, Posttranscriptional modifications in 16S and 23S rRNAs of the archaeal hyperthermophile Sulfolobus solfataricus, J Bacteriol, vol.180, issue.11, pp.2883-2888, 1998.

D. O'hagan and J. W. Schmidberger, Enzymes that catalyse SN2 reaction mechanisms, Nat Prod Rep, vol.27, issue.6, pp.900-918, 2010.

M. Oeffinger, Structural biology: Moulding the ribosome, Nature, vol.537, issue.7618, 2016.

S. Oerum, C. Degut, P. Barraud, and C. Tisne, m1A Post-Transcriptional Modification in tRNAs. Biomolecules, vol.7, 2017.

K. Okada, Y. Muneyoshi, Y. Endo, and H. Hori, Production of yeast (m2G10) methyltransferase (Trm11 and Trm112 complex) in a wheat germ cell-free translation system, Nucleic Acids Symp Ser (Oxf, issue.53, pp.303-304, 2009.

R. Oliva, L. Cavallo, and A. Tramontano, Accurate energies of hydrogen bonded nucleic acid base pairs and triplets in tRNA tertiary interactions, Nucleic Acids Res, vol.34, issue.3, pp.865-879, 2006.

K. Ounap, L. Kasper, A. Kurg, and R. Kurg, The human WBSCR22 protein is involved in the biogenesis of the 40S ribosomal subunits in mammalian cells, PLoS One, vol.8, issue.9, p.75686, 2013.

K. Ounap, L. Leetsi, M. Matsoo, and R. Kurg, The Stability of Ribosome Biogenesis Factor WBSCR22 Is Regulated by Interaction with TRMT112 via Ubiquitin-Proteasome Pathway, PLoS One, vol.10, issue.7, p.133841, 2015.

C. Pastore, I. Topalidou, F. Forouhar, A. C. Yan, M. Levy et al., Crystal structure and RNA binding properties of the RNA recognition motif (RRM) and AlkB domains in human AlkB homolog 8 (ABH8), an enzyme catalyzing tRNA hypermodification, J Biol Chem, vol.287, issue.3, pp.2130-2143, 2012.

A. Patil, C. T. Chan, M. Dyavaiah, J. P. Rooney, P. C. Dedon et al., Translational infidelity-induced protein stress results from a deficiency in Trm9-catalyzed tRNA modifications, RNA Biol, vol.9, issue.7, pp.990-1001, 2012.

M. Y. Pavlov, D. V. Freistroffer, V. Dincbas, J. Macdougall, R. H. Buckingham et al., A direct estimation of the context effect on the efficiency of termination, J Mol Biol, vol.284, issue.3, pp.579-590, 1998.

C. Peifer, S. Sharma, P. Watzinger, S. Lamberth, P. Kotter et al., Yeast Rrp8p, a novel methyltransferase responsible for m1A 645 base modification of 25S rRNA, Nucleic Acids Res, vol.41, issue.2, pp.1151-1163, 2013.

T. C. Petrossian and S. G. Clarke, Multiple Motif Scanning to identify methyltransferases from the yeast proteome, Mol Cell Proteomics, vol.8, issue.7, pp.1516-1526, 2009.

T. C. Petrossian and S. G. Clarke, Uncovering the human methyltransferasome, Mol Cell Proteomics, vol.10, issue.1, 2011.

F. Pfeiffer and D. Oesterhelt, A manual curation strategy to improve genome annotation: application to a set of haloarchael genomes, Life (Basel), vol.5, issue.2, pp.1427-1444, 2015.

G. Phillips and V. De-crecy-lagard, Biosynthesis and function of tRNA modifications in Archaea, Curr Opin Microbiol, vol.14, issue.3, pp.335-341, 2011.

D. Piekna-przybylska, W. A. Decatur, and M. J. Fournier, New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA, RNA, vol.13, issue.3, pp.305-312, 2007.

D. Piekna-przybylska, P. Przybylski, A. Baudin-baillieu, J. P. Rousset, and M. J. Fournier, Ribosome performance is enhanced by a rich cluster of pseudouridines in the A-site finger region of the large subunit, J Biol Chem, vol.283, issue.38, pp.26026-26036, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00297133

W. E. Pierson, E. D. Hoffer, H. E. Keedy, C. L. Simms, C. M. Dunham et al., Uniformity of Peptide Release Is Maintained by Methylation of Release Factors, Cell Rep, vol.17, issue.1, pp.11-18, 2016.

A. V. Pisarev, C. U. Hellen, and T. V. Pestova, Recycling of eukaryotic posttermination ribosomal complexes, Cell, vol.131, issue.2, pp.286-299, 2007.

A. V. Pisarev, M. A. Skabkin, V. P. Pisareva, O. V. Skabkina, A. M. Rakotondrafara et al.,

T. V. Pestova, The role of ABCE1 in eukaryotic posttermination ribosomal recycling, Mol Cell, vol.37, issue.2, pp.196-210, 2010.

B. Polevoda and F. Sherman, Methylation of proteins involved in translation, Mol Microbiol, vol.65, issue.3, pp.590-606, 2007.

B. Polevoda, L. Span, and F. Sherman, The yeast translation release factors Mrf1p and Sup45p (eRF1) are methylated, respectively, by the methyltransferases Mtq1p and Mtq2p, J Biol Chem, vol.281, issue.5, pp.2562-2571, 2006.

A. Preis, A. Heuer, C. Barrio-garcia, A. Hauser, D. E. Eyler et al., Cryoelectron microscopic structures of eukaryotic translation termination complexes containing eRF1-eRF3 or eRF1-ABCE1, Cell Rep, vol.8, issue.1, pp.59-65, 2014.

S. K. Purushothaman, J. M. Bujnicki, H. Grosjean, and B. Lapeyre, Trm11p and Trm112p are both required for the formation of 2-methylguanosine at position 10 in yeast tRNA, Mol Cell Biol, vol.25, issue.11, pp.4359-4370, 2005.

C. Qian and M. M. Zhou, SET domain protein lysine methyltransferases: Structure, specificity and catalysis, Cell Mol Life Sci, vol.63, issue.23, pp.2755-2763, 2006.

J. Rabl, M. Leibundgut, S. F. Ataide, A. Haag, and N. Ban, Crystal structure of the eukaryotic 40S ribosomal subunit in complex with initiation factor 1, Science, vol.331, issue.6018, pp.730-736, 2011.

M. Raina and M. Ibba, tRNAs as regulators of biological processes, Front Genet, vol.5, p.171, 2014.

V. Ramakrishnan, Molecular biology. The eukaryotic ribosome, Science, vol.331, issue.6018, pp.681-682, 2011.

A. Ramanathan, G. B. Robb, and S. H. Chan, mRNA capping: biological functions and applications, Nucleic Acids Res, vol.44, issue.16, pp.7511-7526, 2016.

V. Ramirez, B. Gonzalez, A. Lopez, M. J. Castello, M. J. Gil et al.,

P. Vera, Loss of a Conserved tRNA Anticodon Modification Perturbs Plant Immunity, PLoS Genet, vol.11, issue.10, p.1005586, 2015.

A. K. Rana and S. Ankri, Reviving the RNA World: An Insight into the Appearance of RNA Methyltransferases, Front Genet, vol.7, p.99, 2016.

N. Ranjan and M. V. Rodnina, tRNA wobble modifications and protein homeostasis, Translation (Austin), vol.4, issue.1, p.1143076, 2016.

M. C. Rivera, R. Jain, J. E. Moore, and J. A. Lake, Genomic evidence for two functionally distinct gene classes, Proc Natl Acad Sci, vol.95, issue.11, pp.6239-6244, 1998.

X. Robert and P. Gouet, Deciphering key features in protein structures with the new ENDscript server, Nucleic Acids Res, vol.42, pp.320-324, 2014.

M. V. Rodnina and W. Wintermeyer, The ribosome as a molecular machine: the mechanism of tRNA-mRNA movement in translocation, Biochem Soc Trans, vol.39, issue.2, pp.658-662, 2011.

S. Roje, S-Adenosyl-L-methionine: beyond the universal methyl group donor, Phytochemistry, vol.67, issue.15, pp.1686-1698, 2006.

K. Saito, K. Kobayashi, M. Wada, I. Kikuno, A. Takusagawa et al.,

K. Ito, Omnipotent role of archaeal elongation factor 1 alpha (EF1alpha in translational elongation and termination, and quality control of protein synthesis, Proc Natl Acad Sci U S A, vol.107, issue.45, pp.19242-19247, 2010.

R. Sardana and A. W. Johnson, The methyltransferase adaptor protein Trm112 is involved in biogenesis of both ribosomal subunits, Mol Biol Cell, vol.23, issue.21, pp.4313-4322, 2012.

R. Sardana, X. Liu, S. Granneman, J. Zhu, M. Gill et al., The DEAH-box helicase Dhr1 dissociates U3 from the pre-rRNA to promote formation of the central pseudoknot, PLoS Biol, vol.13, issue.2, p.1002083, 2015.

R. Sardana, J. P. White, and A. W. Johnson, The rRNA methyltransferase Bud23 shows functional interaction with components of the SSU processome and RNase MRP, RNA, vol.19, issue.6, pp.828-840, 2013.

R. Sardana, J. Zhu, M. Gill, and A. W. Johnson, Physical and functional interaction between the methyltransferase Bud23 and the essential DEAH-box RNA helicase Ecm16, Mol Cell Biol, vol.34, issue.12, pp.2208-2220, 2014.

T. M. Schmeing and V. Ramakrishnan, What recent ribosome structures have revealed about the mechanism of translation, Nature, issue.7268, pp.1234-1242, 2009.

T. R. Schneider and G. M. Sheldrick, Substructure solution with SHELXD, Acta Crystallogr D Biol Crystallogr, vol.58, pp.1772-1779, 2002.

H. L. Schubert, R. M. Blumenthal, and X. Cheng, Many paths to methyltransfer: a chronicle of convergence, Trends Biochem Sci, vol.28, issue.6, pp.329-335, 2003.

H. L. Schubert, K. S. Wilson, E. Raux, S. C. Woodcock, and M. J. Warren, The X-ray structure of a cobalamin biosynthetic enzyme, cobalt-precorrin-4 methyltransferase, Nat Struct Biol, vol.5, issue.7, pp.585-592, 1998.

S. Schwartz, Cracking the epitranscriptome, RNA, vol.22, issue.2, pp.169-174, 2016.

S. Schwartz, M. R. Mumbach, M. Jovanovic, T. Wang, K. Maciag et al., Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5' sites, Cell Rep, vol.8, issue.1, pp.284-296, 2014.

M. M. Scotti and M. S. Swanson, RNA mis-splicing in disease, Nat Rev Genet, vol.17, issue.1, pp.19-32, 2016.

K. Selvadurai, P. Wang, J. Seimetz, and R. H. Huang, Archaeal Elp3 catalyzes tRNA wobble uridine modification at C5 via a radical mechanism, Nat Chem Biol, vol.10, issue.10, pp.810-812, 2014.

S. Sharma and D. L. Lafontaine, View From A Bridge': A New Perspective on Eukaryotic rRNA Base Modification, Trends Biochem Sci, vol.40, issue.10, pp.560-575, 2015.

S. Sharma, J. L. Langhendries, P. Watzinger, P. Kotter, K. D. Entian et al., Yeast Kre33 and human NAT10 are conserved 18S rRNA cytosine acetyltransferases that modify tRNAs assisted by the adaptor Tan1/THUMPD1, Nucleic Acids Res, vol.43, issue.4, pp.2242-2258, 2015.

S. Sharma, J. Yang, P. Watzinger, P. Kotter, and K. D. Entian, Yeast Nop2 and Rcm1 methylate C2870 and C2278 of the 25S rRNA, respectively, Nucleic Acids Res, vol.41, issue.19, pp.9062-9076, 2013.

K. Shimada, M. Nakamura, S. Anai, M. De-velasco, M. Tanaka et al.,

N. Konishi, A novel human AlkB homologue, ALKBH8, contributes to human bladder cancer progression, Cancer Res, vol.69, issue.7, pp.3157-3164, 2009.

A. Shirai, M. Sadaie, K. Shinmyozu, and J. Nakayama, Methylation of ribosomal protein L42 regulates ribosomal function and stress-adapted cell growth, J Biol Chem, vol.285, issue.29, pp.22448-22460, 2010.

P. Sledz and M. Jinek, Structural insights into the molecular mechanism of the m(6)A writer complex. Elife, 5, 2016.

K. E. Sloan, A. S. Warda, S. Sharma, K. D. Entian, D. L. Lafontaine et al., Tuning the ribosome: The influence of rRNA modification on eukaryotic ribosome biogenesis and function, RNA Biol, pp.1-16, 2016.

H. Song, P. Mugnier, A. K. Das, H. M. Webb, D. R. Evans et al.,

D. Barford, The crystal structure of human eukaryotic release factor eRF1--mechanism of stop codon recognition and peptidyl-tRNA hydrolysis, Cell, vol.100, issue.3, pp.311-321, 2000.

J. Song and C. Yi, Chemical Modifications to RNA: A New Layer of Gene Expression Regulation, ACS Chem Biol, vol.12, issue.2, pp.316-325, 2017.

M. Sprinzl, C. Horn, M. Brown, A. Ioudovitch, and S. Steinberg, Compilation of tRNA sequences and sequences of tRNA genes, Nucleic Acids Res, vol.26, issue.1, pp.148-153, 1998.
URL : https://hal.archives-ouvertes.fr/hal-00356160

J. E. Squires, H. R. Patel, M. Nousch, T. Sibbritt, D. T. Humphreys et al., Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA, Nucleic Acids Res, vol.40, issue.11, pp.5023-5033, 2012.

B. Stefanska, D. Cheishvili, M. Suderman, A. Arakelian, J. Huang et al.,

M. Szyf, , 2014.

, Genome-wide study of hypomethylated and induced genes in patients with liver cancer unravels novel anticancer targets, Clin Cancer Res, vol.20, issue.12, pp.3118-3132

A. W. Struck, M. L. Thompson, L. S. Wong, and J. Micklefield, S-adenosyl-methioninedependent methyltransferases: highly versatile enzymes in biocatalysis, biosynthesis and other biotechnological applications, Chembiochem, vol.13, issue.18, pp.2642-2655, 2012.

P. Studte, S. Zink, D. Jablonowski, C. Bar, T. Von-der-haar et al., tRNA and protein methylase complexes mediate zymocin toxicity in yeast, Mol Microbiol, vol.69, issue.5, pp.1266-1277, 2008.

F. L. Suddath, G. J. Quigley, A. Mcpherson, D. Sneden, J. J. Kim et al., , 1974.

, Three-dimensional structure of yeast phenylalanine transfer RNA at 3.0angstroms resolution, Nature, vol.248, issue.5443, pp.20-24

W. E. Swinehart and J. E. Jackman, Diversity in mechanism and function of tRNA methyltransferases, RNA Biol, vol.12, issue.4, pp.398-411, 2015.

M. Taoka, Y. Nobe, Y. Yamaki, Y. Yamauchi, H. Ishikawa et al., The complete chemical structure of Saccharomyces cerevisiae rRNA: partial pseudouridylation of U2345 in 25S rRNA by snoRNA snR9, Nucleic Acids Res, vol.44, issue.18, pp.8951-8961, 2016.

D. Taylor, A. Unbehaun, W. Li, S. Das, J. Lei et al., Cryo-EM structure of the mammalian eukaryotic release factor eRF1-eRF3-associated termination complex, Proc Natl Acad Sci, vol.109, issue.45, pp.18413-18418, 2012.

M. D. Ter-avanesyan, V. V. Kushnirov, A. R. Dagkesamanskaya, S. A. Didichenko, Y. O. Chernoff et al., Deletion analysis of the SUP35 gene of the yeast Saccharomyces cerevisiae reveals two non-overlapping functional regions in the encoded protein, Mol Microbiol, vol.7, issue.5, pp.683-692, 1993.

T. Terwilliger, SOLVE and RESOLVE: automated structure solution, density modification and model building, J Synchrotron Radiat, issue.11, pp.49-52, 2004.

T. C. Terwilliger, R. W. Grosse-kunstleve, P. V. Afonine, N. W. Moriarty, P. H. Zwart et al.,

P. D. Adams, Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard, Acta Crystallogr D Biol Crystallogr, vol.64, pp.61-69, 2008.

E. Thomson, S. Ferreira-cerca, and E. Hurt, Eukaryotic ribosome biogenesis at a glance, J Cell Sci, vol.126, pp.4815-4821, 2013.

R. E. Tiedemann, Y. X. Zhu, J. Schmidt, C. X. Shi, C. Sereduk et al.,

A. K. Stewart, Identification of molecular vulnerabilities in human multiple myeloma cells by RNA interference lethality screening of the druggable genome, Cancer Res, vol.72, issue.3, pp.757-768, 2012.

K. L. Tkaczuk, S. Dunin-horkawicz, E. Purta, and J. M. Bujnicki, Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases, BMC Bioinformatics, vol.8, p.73, 2007.

C. Tomikawa, T. Ohira, Y. Inoue, T. Kawamura, A. Yamagishi et al., Distinct tRNA modifications in the thermo-acidophilic archaeon, Thermoplasma acidophilum, FEBS Lett, vol.587, issue.21, pp.3575-3580, 2013.

A. G. Torres, E. Batlle, and L. Ribas-de-pouplana, Role of tRNA modifications in human diseases, Trends Mol Med, vol.20, issue.6, pp.306-314, 2014.

W. L. Towns and T. J. Begley, Transfer RNA methytransferases and their corresponding modifications in budding yeast and humans: activities, predications, and potential roles in human health, DNA Cell Biol, vol.31, issue.4, pp.434-454, 2012.

L. W. Tu and C. Deutsch, A folding zone in the ribosomal exit tunnel for Kv1.3 helix formation, J Mol Biol, vol.396, issue.5, pp.1346-1360, 2010.

F. Tuorto and F. Lyko, Genome recoding by tRNA modifications, Open Biology, issue.12, p.6, 2016.

J. Urbonavicius, J. Armengaud, and H. Grosjean, Identity elements required for enzymatic formation of N2,N2-dimethylguanosine from N2-monomethylated derivative and its possible role in avoiding alternative conformations in archaeal tRNA, J Mol Biol, vol.357, issue.2, pp.387-399, 2006.

V. Y. Vare, E. R. Eruysal, A. Narendran, K. L. Sarachan, and P. F. Agris, Chemical and Conformational Diversity of Modified Nucleosides Affects tRNA Structure and Function, Biomolecules, vol.7, issue.1, 2017.

F. Voigts-hoffmann, S. Klinge, and N. Ban, Structural insights into eukaryotic ribosomes and the initiation of translation, Curr Opin Struct Biol, vol.22, issue.6, pp.768-777, 2012.

P. Wang, K. A. Doxtader, and Y. Nam, Structural Basis for Cooperative Function of Mettl3 and Mettl14 Methyltransferases, Mol Cell, vol.63, issue.2, pp.306-317, 2016.

X. Wang, J. Feng, Y. Xue, Z. Guan, D. Zhang et al.,

P. Yin, Structural basis of N(6)-adenosine methylation by the METTL3-METTL14 complex, Nature, vol.534, issue.7608, pp.575-578, 2016.

X. Wang, Z. Lu, A. Gomez, G. C. Hon, Y. Yue et al., N6-methyladenosinedependent regulation of messenger RNA stability, Nature, issue.7481, pp.117-120, 2014.

X. Wang, B. S. Zhao, I. A. Roundtree, Z. Lu, D. Han et al., N(6)-methyladenosine Modulates Messenger RNA Translation Efficiency, Cell, vol.161, issue.6, pp.1388-1399, 2015.

Y. Wang and G. Jia, New Edges of RNA Adenosine Methylation Modifications, Genomics Proteomics Bioinformatics, vol.14, issue.3, pp.172-175, 2016.

Y. Wang, Y. Li, J. I. Toth, M. D. Petroski, Z. Zhang et al., N6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells, Nat Cell Biol, vol.16, issue.2, pp.191-198, 2014.

N. J. Watkins and M. T. Bohnsack, The box C/D and H/ACA snoRNPs: key players in the modification, processing and the dynamic folding of ribosomal RNA, Wiley Interdiscip Rev RNA, vol.3, issue.3, pp.397-414, 2012.

J. White, Z. Li, R. Sardana, J. M. Bujnicki, E. M. Marcotte et al., Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of pre-40S subunits, Mol Cell Biol, vol.28, issue.10, pp.3151-3161, 2008.

D. Wichtowska, T. W. Turowski, and M. Boguta, An interplay between transcription, processing, and degradation determines tRNA levels in yeast, Wiley Interdiscip Rev RNA, vol.4, issue.6, pp.709-722, 2013.

D. N. Wilson and J. H. Cate, The structure and function of the eukaryotic ribosome, Cold Spring Harb Perspect Biol, issue.5, p.4, 2012.

C. R. Woese and G. E. Fox, Phylogenetic structure of the prokaryotic domain: the primary kingdoms, Proc Natl Acad Sci U S A, vol.74, issue.11, pp.5088-5090, 1977.

L. E. Wong, Y. Li, S. Pillay, L. Frolova, and K. Pervushin, Selectivity of stop codon recognition in translation termination is modulated by multiple conformations of GTS loop in eRF1, Nucleic Acids Res, vol.40, issue.12, pp.5751-5765, 2012.

J. L. Woolford, . Jr, and S. J. Baserga, Ribosome biogenesis in the yeast Saccharomyces cerevisiae, Genetics, vol.195, issue.3, pp.643-681, 2013.

J. Yang, S. Sharma, P. Watzinger, J. D. Hartmann, P. Kotter et al., Mapping of Complete Set of Ribose and Base Modifications of Yeast rRNA by RP-HPLC and Mung Bean Nuclease Assay, PLoS One, vol.11, issue.12, p.168873, 2016.

X. Yang, Y. Yang, B. F. Sun, Y. S. Chen, J. W. Xu et al.,

Y. G. Yang, 5-methylcytosine promotes mRNA export -NSUN2 as the methyltransferase and ALYREF as an m5C reader, Cell Res, 2017.

B. D. Young, D. I. Weiss, C. I. Zurita-lopez, K. J. Webb, S. G. Clarke et al., Identification of methylated proteins in the yeast small ribosomal subunit: a role for SPOUT methyltransferases in protein arginine methylation, Biochemistry, vol.51, issue.25, pp.5091-5104, 2012.

Y. P. Yu, Y. Ding, Z. Chen, S. Liu, A. Michalopoulos et al., Novel fusion transcripts associate with progressive prostate cancer, Am J Pathol, vol.184, issue.10, pp.2840-2849, 2014.

G. Yusupova and M. Yusupov, High-resolution structure of the eukaryotic 80S ribosome, Annu Rev Biochem, vol.83, pp.467-486, 2014.

N. Yutin, K. S. Makarova, S. L. Mekhedov, Y. I. Wolf, and E. V. Koonin, The deep archaeal roots of eukaryotes, Mol Biol Evol, vol.25, issue.8, 2008.

C. Zhang, D. Samanta, H. Lu, J. W. Bullen, H. Zhang et al., Hypoxia induces the breast cancer stem cell phenotype by HIF-dependent and ALKBH5-mediated m(6)Ademethylation of NANOG mRNA, Proc Natl Acad Sci, vol.113, issue.14, pp.2047-2056, 2016.

X. Zhao, Y. Yang, B. F. Sun, Y. Shi, X. Yang et al., FTO-dependent demethylation of N6-methyladenosine regulates mRNA splicing and is required for adipogenesis, Cell Res, vol.24, issue.12, pp.1403-1419, 2014.

G. Zheng, J. A. Dahl, Y. Niu, P. Fedorcsak, C. M. Huang et al., ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility, Mol Cell, vol.49, issue.1, pp.18-29, 2013.

C. Zorbas, E. Nicolas, L. Wacheul, E. Huvelle, V. Heurgue-hamard et al., The human 18S rRNA base methyltransferases DIMT1L and WBSCR22-TRMT112 but not rRNA modification are required for ribosome biogenesis, Mol Biol Cell, vol.26, issue.11, pp.2080-2095, 2015.