Modomics - A Database of RNA Modifications

First Author Title Journal Title PubMed ID / DOI
Hausmann S Giardia lamblia RNA cap guanine-N2 methyltransferase (Tgs2). J Biol Chem 16046409
Urbonavicius J Identification of a novel gene encoding a flavin-dependent tRNA:m5U methyltransferase in bacteria--evolutionary implications. Nucleic Acids Res 16027442
Marmier-Gourrier N A structural, phylogenetic, and functional study of 15.5-kD/Snu13 protein binding on U3 small nucleolar RNA. RNA 12810916
Hager J Substrate binding analysis of the 23S rRNA methyltransferase RrmJ. J Bacteriol 15375145
Sunita S Functional specialization of domains tandemly duplicated within 16S rRNA methyltransferase RsmC. Nucleic Acids Res 17576679
Kolodrubetz D Sequence and genetic analysis of NHP2: a moderately abundant high mobility group-like nuclear protein with an essential function in Saccharomyces cerevisiae. Yeast 2063628
Motorin Y Multisite-specific tRNA:m5C-methyltransferase (Trm4) in yeast Saccharomyces cerevisiae: identification of the gene and substrate specificity of the enzyme. RNA 10445884
Walbott H Cysteine of sequence motif VI is essential for nucleophilic catalysis by yeast tRNA m5C methyltransferase. RNA 17475914
Motorin Y The yeast tRNA:pseudouridine synthase Pus1p displays a multisite substrate specificity. RNA 9671058
Behm-Ansmant I The Saccharomyces cerevisiae U2 snRNA:pseudouridine-synthase Pus7p is a novel multisite-multisubstrate RNA:Psi-synthase also acting on tRNAs. RNA 14561887
Grosjean H Aminoacylation of the anticodon stem by a tRNA-synthetase paralog: relic of an ancient code? Trends Biochem Sci 15450604
Behm-Ansmant I The Saccharomyces cerevisiae Pus2 protein encoded by YGL063w ORF is a mitochondrial tRNA:Psi27/28-synthase. RNA 17684231
Kotelawala L Identification of yeast tRNA Um(44) 2'-O-methyltransferase (Trm44) and demonstration of a Trm44 role in sustaining levels of specific tRNA(Ser) species. RNA 18025252
Ikeuchi Y The RNA acetyltransferase driven by ATP hydrolysis synthesizes N4-acetylcytidine of tRNA anticodon. EMBO J 18668122
Kambampati R IscS is a sulfurtransferase for the in vitro biosynthesis of 4-thiouridine in Escherichia coli tRNA. Biochemistry 10600118
Bujnicki JM Bioinformatic analyses of the tRNA: (guanine 26, N2,N2)-dimethyltransferase (Trm1) family. J Mol Microbiol Biotechnol 12125821
Purushothaman SK Trm11p and Trm112p are both required for the formation of 2-methylguanosine at position 10 in yeast tRNA. Mol Cell Biol 15899842
Hamilton CS Mechanistic investigations of the pseudouridine synthase RluA using RNA containing 5-fluorouridine. Biochemistry 17002302
Bujnicki JM Structure prediction and phylogenetic analysis of a functionally diverse family of proteins homologous to the MT-A70 subunit of the human mRNA:m(6)A methyltransferase. J Mol Evol 12355263
de Beus E Yeast NOP2 encodes an essential nucleolar protein with homology to a human proliferation marker. J Cell Biol 7806561
Wolfe MD Functional diversity of the rhodanese homology domain: the Escherichia coli ybbB gene encodes a selenophosphate-dependent tRNA 2-selenouridine synthase. J Biol Chem 14594807
Jiang W An essential yeast protein, CBF5p, binds in vitro to centromeres and microtubules. Mol Cell Biol 8336724
Salazar JC A truncated aminoacyl-tRNA synthetase modifies RNA. Proc Natl Acad Sci U S A 15096612
Pierrel F MiaB protein is a bifunctional radical-S-adenosylmethionine enzyme involved in thiolation and methylation of tRNA. J Biol Chem 15339930
Roovers M A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase. Nucleic Acids Res 14739239
Hallberg BM The structure of the RNA m5C methyltransferase YebU from Escherichia coli reveals a C-terminal RNA-recruiting PUA domain. J Mol Biol 16793063
Pintard L MRM2 encodes a novel yeast mitochondrial 21S rRNA methyltransferase. EMBO J 11867542
Caldas T The FtsJ/RrmJ heat shock protein of Escherichia coli is a 23 S ribosomal RNA methyltransferase. J Biol Chem 10748051
Hausmann S Specificity and mechanism of RNA cap guanine-N2 methyltransferase (Tgs1). J Biol Chem 15590684
Frey B New function of vitamin B12: cobamide-dependent reduction of epoxyqueuosine to queuosine in tRNAs of Escherichia coli and Salmonella typhimurium. J Bacteriol 3129401
Wrzesinski J Purification, cloning, and properties of the 16S RNA pseudouridine 516 synthase from Escherichia coli. Biochemistry 7612632
Mouaikel J Hypermethylation of the cap structure of both yeast snRNAs and snoRNAs requires a conserved methyltransferase that is localized to the nucleolus. Mol Cell 11983179
Romanowski MJ Crystal structure of the Escherichia coli glucose-inhibited division protein B (GidB) reveals a methyltransferase fold. Proteins 12001236
Cabedo H The Escherichia coli trmE (mnmE) gene, involved in tRNA modification, codes for an evolutionarily conserved GTPase with unusual biochemical properties. EMBO J 10601028
Clery A Analysis of sequence and structural features that identify the B/C motif of U3 small nucleolar RNA as the recognition site for the Snu13p-Rrp9p protein pair. Mol Cell Biol 17145781
Jacq C The nucleotide sequence of Saccharomyces cerevisiae chromosome IV. Nature 9169867
Kato T A novel human tRNA-dihydrouridine synthase involved in pulmonary carcinogenesis. Cancer Res 15994936
Watanabe M Biosynthesis of archaeosine, a novel derivative of 7-deazaguanosine specific to archaeal tRNA, proceeds via a pathway involving base replacement on the tRNA polynucleotide chain. J Biol Chem 9242689
Lapeyre B Spb1p-directed formation of Gm2922 in the ribosome catalytic center occurs at a late processing stage. Mol Cell 15546625
Pintard L Trm7p catalyses the formation of two 2'-O-methylriboses in yeast tRNA anticodon loop. EMBO J 11927565
Agarwalla S Characterization of the 23 S ribosomal RNA m5U1939 methyltransferase from Escherichia coli. J Biol Chem 11779873
Massenet S Pseudouridine mapping in the Saccharomyces cerevisiae spliceosomal U small nuclear RNAs (snRNAs) reveals that pseudouridine synthase pus1p exhibits a dual substrate specificity for U2 snRNA and tRNA. Mol Cell Biol 10022901
Hagervall TG Genetic mapping and cloning of the gene (trmC) responsible for the synthesis of tRNA (mnm5s2U)methyltransferase in Escherichia coli K12. Mol Gen Genet 6387395
Lesnyak DV Methyltransferase that modifies guanine 966 of the 16 S rRNA: functional identification and tertiary structure. J Biol Chem 17189261
Kalhor HR Novel methyltransferase for modified uridine residues at the wobble position of tRNA. Mol Cell Biol 14645538
Grimm C Crystal structure of Bacillus subtilis S-adenosylmethionine:tRNA ribosyltransferase-isomerase. Biochem Biophys Res Commun 17083917
Noma A Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic phenylalanine tRNA. EMBO J 16642040
Bonnerot C Functional redundancy of Spb1p and a snR52-dependent mechanism for the 2'-O-ribose methylation of a conserved rRNA position in yeast. Mol Cell 14636587
Decoster E MSS1, a nuclear-encoded mitochondrial GTPase involved in the expression of COX1 subunit of cytochrome c oxidase. J Mol Biol 8392589
Gu XR Identification of the 16S rRNA m5C967 methyltransferase from Escherichia coli. Biochemistry 10194318
Del Campo M Identification and site of action of the remaining four putative pseudouridine synthases in Escherichia coli. RNA 11720289
Slany RK A new function of S-adenosylmethionine: the ribosyl moiety of AdoMet is the precursor of the cyclopentenediol moiety of the tRNA wobble base queuine. Biochemistry 8347586
Soma A An RNA-modifying enzyme that governs both the codon and amino acid specificities of isoleucine tRNA. Mol Cell 14527414
De Bie LG The yggH gene of Escherichia coli encodes a tRNA (m7G46) methyltransferase. J Bacteriol 12730187
Brisson-Noel A Evidence for natural gene transfer from gram-positive cocci to Escherichia coli. J Bacteriol 2832378
Michel G The structure of the RlmB 23S rRNA methyltransferase reveals a new methyltransferase fold with a unique knot. Structure 12377117
Watanabe K Functional categorization of the conserved basic amino acid residues in TrmH (tRNA (Gm18) methyltransferase) enzymes. J Biol Chem 16963456
Gutgsell N Deletion of the Escherichia coli pseudouridine synthase gene truB blocks formation of pseudouridine 55 in tRNA in vivo, does not affect exponential growth, but confers a strong selective disadvantage in competition with wild-type cells. RNA 11142385
Jager G The conserved Cys-X1-X2-Cys motif present in the TtcA protein is required for the thiolation of cytidine in position 32 of tRNA from Salmonella enterica serovar Typhimurium. J Bacteriol 14729701
Bujnicki JM Sequence-structure-function studies of tRNA:m5C methyltransferase Trm4p and its relationship to DNA:m5C and RNA:m5U methyltransferases. Nucleic Acids Res 15121902
Hagervall TG Transfer RNA(5-methylaminomethyl-2-thiouridine)-methyltransferase from Escherichia coli K-12 has two enzymatic activities. J Biol Chem 3298234
Stengl B Mechanism and substrate specificity of tRNA-guanine transglycosylases (TGTs): tRNA-modifying enzymes from the three different kingdoms of life share a common catalytic mechanism. Chembiochem 16206323
Bussey H The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI. Nature 9169875
Calvo O GCD14p, a repressor of GCN4 translation, cooperates with Gcd10p and Lhp1p in the maturation of initiator methionyl-tRNA in Saccharomyces cerevisiae. Mol Cell Biol 10330157
Tsukamoto T Isolation and characterization of the yeast mRNA capping enzyme beta subunit gene encoding RNA 5'-triphosphatase, which is essential for cell viability. Biochem Biophys Res Commun 9345280
Lauhon CT Substitutions in an active site loop of Escherichia coli IscS result in specific defects in Fe-S cluster and thionucleoside biosynthesis in vivo. J Biol Chem 14978044
Gutgsell NS A second function for pseudouridine synthases: A point mutant of RluD unable to form pseudouridines 1911, 1915, and 1917 in Escherichia coli 23S ribosomal RNA restores normal growth to an RluD-minus strain. RNA 11453071
Kressler D Spb1p is a putative methyltransferase required for 60S ribosomal subunit biogenesis in Saccharomyces cerevisiae. Nucleic Acids Res 10556316
Toh SM The methyltransferase YfgB/RlmN is responsible for modification of adenosine 2503 in 23S rRNA. RNA 18025251
Lesnyak DV Identification of Escherichia coli m2G methyltransferases: I. the ycbY gene encodes a methyltransferase specific for G2445 of the 23 S rRNA. J Mol Biol 17010378
Yim L The GTPase activity and C-terminal cysteine of the Escherichia coli MnmE protein are essential for its tRNA modifying function. J Biol Chem 12730230
Wolf J tadA, an essential tRNA-specific adenosine deaminase from Escherichia coli. EMBO J 12110595
Wu P Nop5p is a small nucleolar ribonucleoprotein component required for pre-18 S rRNA processing in yeast. J Biol Chem 9632712
Watanabe K Roles of conserved amino acid sequence motifs in the SpoU (TrmH) RNA methyltransferase family. J Biol Chem 15637073
Caillet J Molecular cloning of the Escherichia coli miaA gene involved in the formation of delta 2-isopentenyl adenosine in tRNA. J Bacteriol 3045085
Waas WF Discovery of a gene family critical to wyosine base formation in a subset of phenylalanine-specific transfer RNAs. J Biol Chem 16162496
Gutgsell NS The pseudouridine synthase RluD is required for normal ribosome assembly and function in Escherichia coli. RNA 15928344
Lauhon CT Requirement for IscS in biosynthesis of all thionucleosides in Escherichia coli. J Bacteriol 12446632
Hopper AK tRNA transfers to the limelight. Genes Dev 12533506
Baker DL RNA-guided RNA modification: functional organization of the archaeal H/ACA RNP. Genes Dev 15870259
Gustafsson C Identification of the rrmA gene encoding the 23S rRNA m1G745 methyltransferase in Escherichia coli and characterization of an m1G745-deficient mutant. J Bacteriol 9440525
Leinfelder W In vitro synthesis of selenocysteinyl-tRNA(UCA) from seryl-tRNA(UCA): involvement and characterization of the selD gene product. Proc Natl Acad Sci U S A 2405383
Basturea GN Identification and characterization of RsmE, the founding member of a new RNA base methyltransferase family. RNA 16431987
Mathews I Crystal structure of S-adenosylmethionine:tRNA ribosyltransferase-isomerase (QueA) from Thermotoga maritima at 2.0 A resolution reveals a new fold. Proteins 15822125
Ny T Cloning and restriction mapping of the trmA gene coding for transfer ribonucleic acid (5-methyluridine)-methyltransferase in Escherichia coli K-12. J Bacteriol 6247318
Nordlund ME Identification of the TRM2 gene encoding the tRNA(m5U54)methyltransferase of Saccharomyces cerevisiae. RNA 10864043
Appel CD Structural features of the guide:target RNA duplex required for archaeal box C/D sRNA-guided nucleotide 2'-O-methylation. RNA 17438123
Xing F The specificities of four yeast dihydrouridine synthases for cytoplasmic tRNAs. J Biol Chem 14970222
Rozenski J The RNA Modification Database: 1999 update. Nucleic Acids Res 9847178
Swairjo MA Crystallization and preliminary X-ray characterization of the nitrile reductase QueF: a queuosine-biosynthesis enzyme. Acta Crystallogr Sect F Struct Biol Cryst Commun 16511203
Campanacci V The Escherichia coli YadB gene product reveals a novel aminoacyl-tRNA synthetase like activity. J Mol Biol 15003446
Bishop AC Identification of the tRNA-dihydrouridine synthase family. J Biol Chem 11983710
Gerber AP An adenosine deaminase that generates inosine at the wobble position of tRNAs. Science 10550050
Nakanishi K Structural basis for lysidine formation by ATP pyrophosphatase accompanied by a lysine-specific loop and a tRNA-recognition domain. Proc Natl Acad Sci U S A 15894617
Tettelin H The nucleotide sequence of Saccharomyces cerevisiae chromosome VII. Nature 9169869
Hamma T The Cbf5-Nop10 complex is a molecular bracket that organizes box H/ACA RNPs. Nat Struct Mol Biol 16286935
Blaise M Glu-Q-tRNA(Asp) synthetase coded by the yadB gene, a new paralog of aminoacyl-tRNA synthetase that glutamylates tRNA(Asp) anticodon. Biochimie 16164993
Yim L Further insights into the tRNA modification process controlled by proteins MnmE and GidA of Escherichia coli. Nucleic Acids Res 17062623
Lee TT A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function. Cell 15766524
Cupp-Vickery JR Crystal structure of IscA, an iron-sulfur cluster assembly protein from Escherichia coli. J Mol Biol 15050828
Nasvall SJ The modified wobble nucleoside uridine-5-oxyacetic acid in tRNAPro(cmo5UGG) promotes reading of all four proline codons in vivo. RNA 15383682
Philippsen P The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications. Nature 9169873
Esberg B Identification of the miaB gene, involved in methylthiolation of isopentenylated A37 derivatives in the tRNA of Salmonella typhimurium and Escherichia coli. J Bacteriol 10572129
Ollagnier-de-Choudens S Iron-sulfur cluster assembly: characterization of IscA and evidence for a specific and functional complex with ferredoxin. J Biol Chem 11319236
Bujnicki JM Sequence analysis and structure prediction of 23S rRNA:m1G methyltransferases reveals a conserved core augmented with a putative Zn-binding domain in the N-terminus and family-specific elaborations in the C-terminus. J Mol Microbiol Biotechnol 11763974
Henras A Nhp2p and Nop10p are essential for the function of H/ACA snoRNPs. EMBO J 9843512
Girard JP GAR1 is an essential small nucleolar RNP protein required for pre-rRNA processing in yeast. EMBO J 1531632
Purta E Sequence-structure-function relationships of a tRNA (m7G46) methyltransferase studied by homology modeling and site-directed mutagenesis. Proteins 15789416
Alexandrov A Two proteins that form a complex are required for 7-methylguanosine modification of yeast tRNA. RNA 12403464
Zhang X The coiled-coil domain of the Nop56/58 core protein is dispensable for sRNP assembly but is critical for archaeal box C/D sRNP-guided nucleotide methylation. RNA 16601205
Hellmuth K Cloning and characterization of the Schizosaccharomyces pombe tRNA:pseudouridine synthase Pus1p. Nucleic Acids Res 11095668
Ozanick S The bipartite structure of the tRNA m1A58 methyltransferase from S. cerevisiae is conserved in humans. RNA 16043508
Ansmant I Identification of the Saccharomyces cerevisiae RNA:pseudouridine synthase responsible for formation of psi(2819) in 21S mitochondrial ribosomal RNA. Nucleic Acids Res 10756195
Bujnicki JM In silico analysis of the tRNA:m1A58 methyltransferase family: homology-based fold prediction and identification of new members from Eubacteria and Archaea. FEBS Lett 11684083
Anderson J The essential Gcd10p-Gcd14p nuclear complex is required for 1-methyladenosine modification and maturation of initiator methionyl-tRNA. Genes Dev 9851972
Wilkinson ML The 2'-O-methyltransferase responsible for modification of yeast tRNA at position 4. RNA 17242307
Bujnicki JM Phylogenomic analysis of 16S rRNA:(guanine-N2) methyltransferases suggests new family members and reveals highly conserved motifs and a domain structure similar to other nucleic acid amino-methyltransferases. FASEB J 11053259
Bystrom AS The structural gene (trmD) for the tRNA(m1G)methyltransferase is part of a four polypeptide operon in Escherichia coli K-12. Mol Gen Genet 6298574
Dong X Crystal structure of tRNA pseudouridine synthase TruA from Thermus thermophilus HB8. RNA Biol 17114947
Suzuki Y Crystal structure of the radical SAM enzyme catalyzing tricyclic modified base formation in tRNA. J Mol Biol 17727881
Motorin Y Transfer RNA recognition by the Escherichia coli delta2-isopentenyl-pyrophosphate:tRNA delta2-isopentenyl transferase: dependence on the anticodon arm structure. RNA 9214656
Astrom SU Rit1, a tRNA backbone-modifying enzyme that mediates initiator and elongator tRNA discrimination. Cell 7954819
Bjork GR Genetic dissection of synthesis and function of modified nucleosides in bacterial transfer RNA. Prog Nucleic Acid Res Mol Biol 7538683
Pan H The crystal structure of E. coli rRNA pseudouridine synthase RluE. J Mol Biol 17320904
Dubois DY An aminoacyl-tRNA synthetase-like protein encoded by the Escherichia coli yadB gene glutamylates specifically tRNAAsp. Proc Natl Acad Sci U S A 15096594
Soderberg T Escherichia coli dimethylallyl diphosphate:tRNA dimethylallyltransferase: essential elements for recognition of tRNA substrates within the anticodon stem-loop. Biochemistry 10828971
Lafontaine D The 18S rRNA dimethylase Dim1p is required for pre-ribosomal RNA processing in yeast. Genes Dev 7590228
Hur S How U38, 39, and 40 of many tRNAs become the targets for pseudouridylation by TruA. Mol Cell 17466622
Schubot FD Crystal structure of the transcription factor sc-mtTFB offers insights into mitochondrial transcription. Protein Sci 11567089
Anderson J The Gcd10p/Gcd14p complex is the essential two-subunit tRNA(1-methyladenosine) methyltransferase of Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 10779558
Dihanich ME Isolation and characterization of MOD5, a gene required for isopentenylation of cytoplasmic and mitochondrial tRNAs of Saccharomyces cerevisiae. Mol Cell Biol 3031456
Kaya Y A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archaea, and eukarya. RNA 12756329
Kalhor HR Protein phosphatase methyltransferase 1 (Ppm1p) is the sole activity responsible for modification of the major forms of protein phosphatase 2A in yeast. Arch Biochem Biophys 11697862
Roovers M Formation of the conserved pseudouridine at position 55 in archaeal tRNA. Nucleic Acids Res 16920741
Bujnicki JM Sequence analysis and structure prediction of aminoglycoside-resistance 16S rRNA:m7G methyltransferases. Acta Microbiol Pol 11518396
Vaidyanathan PP RluD, a highly conserved pseudouridine synthase, modifies 50S subunits more specifically and efficiently than free 23S rRNA. RNA 17872507
Kolman C SPL1-1, a Saccharomyces cerevisiae mutation affecting tRNA splicing. J Bacteriol 8444805
Johansson MJ The Saccharomyces cerevisiae TAN1 gene is required for N4-acetylcytidine formation in tRNA. RNA 15037780
Bugl H RNA methylation under heat shock control. Mol Cell 10983982
McCleverty CJ Crystal structure of human Pus10, a novel pseudouridine synthase. J Mol Biol 17900615
Basturea GN Substrate specificity and properties of the Escherichia coli 16S rRNA methyltransferase, RsmE. RNA 17872509
Taylor AB The crystal structure of Nep1 reveals an extended SPOUT-class methyltransferase fold and a pre-organized SAM-binding site. Nucleic Acids Res 18208838
Persson BC The spoU gene of Escherichia coli, the fourth gene of the spoT operon, is essential for tRNA (Gm18) 2'-O-methyltransferase activity. Nucleic Acids Res 9321663
Leipuviene R Formation of thiolated nucleosides present in tRNA from Salmonella enterica serovar Typhimurium occurs in two principally distinct pathways. J Bacteriol 14729702
Wachino J Novel plasmid-mediated 16S rRNA m1A1408 methyltransferase, NpmA, found in a clinically isolated Escherichia coli strain resistant to structurally diverse aminoglycosides. Antimicrob Agents Chemother 17875999
Pintard L Spb1p is a yeast nucleolar protein associated with Nop1p and Nop58p that is able to bind S-adenosyl-L-methionine in vitro. Mol Cell Biol 10648622
Behm-Ansmant I Pseudouridylation at position 32 of mitochondrial and cytoplasmic tRNAs requires two distinct enzymes in Saccharomyces cerevisiae. J Biol Chem 15466869
Kambampati R MnmA and IscS are required for in vitro 2-thiouridine biosynthesis in Escherichia coli. Biochemistry 12549933
Andersen NM YebU is a m5C methyltransferase specific for 16 S rRNA nucleotide 1407. J Mol Biol 16678201
Purta E YbeA is the m3Psi methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA. RNA 18755835
Matte A Structure of the pseudouridine synthase RsuA from Haemophilus influenzae. Acta Crystallogr Sect F Struct Biol Cryst Commun 16511038
Okamoto S Loss of a conserved 7-methylguanosine modification in 16S rRNA confers low-level streptomycin resistance in bacteria. Mol Microbiol 17238915
Teplova M The structure of the yrdC gene product from Escherichia coli reveals a new fold and suggests a role in RNA binding. Protein Sci 11206077
Caldas T Translational defects of Escherichia coli mutants deficient in the Um(2552) 23S ribosomal RNA methyltransferase RrmJ/FTSJ. Biochem Biophys Res Commun 10814528
Conrad J The rluC gene of Escherichia coli codes for a pseudouridine synthase that is solely responsible for synthesis of pseudouridine at positions 955, 2504, and 2580 in 23 S ribosomal RNA. J Biol Chem 9660827
Carnahan RH Dim1p is required for efficient splicing and export of mRNA encoding lid1p, a component of the fission yeast anaphase-promoting complex. Eukaryot Cell 15755920
Cupp-Vickery JR Crystal structure of IscS, a cysteine desulfurase from Escherichia coli. J Mol Biol 12860127
Xing F A conserved family of Saccharomyces cerevisiae synthases effects dihydrouridine modification of tRNA. RNA 12003496
Kalhor HR A novel methyltransferase required for the formation of the hypermodified nucleoside wybutosine in eucaryotic tRNA. Biochem Biophys Res Commun 16005430
Cavaille J The yeast Saccharomyces cerevisiae YDL112w ORF encodes the putative 2'-O-ribose methyltransferase catalyzing the formation of Gm18 in tRNAs. RNA 9917067
Elkins PA Insights into catalysis by a knotted TrmD tRNA methyltransferase. J Mol Biol 14583191
Purta E The yfhQ gene of Escherichia coli encodes a tRNA:Cm32/Um32 methyltransferase. BMC Mol Biol 16848900
Na JG Isolation and characterization of SUA5, a novel gene required for normal growth in Saccharomyces cerevisiae. Genetics 1325384
Sergiev PV The ybiN gene of Escherichia coli encodes adenine-N6 methyltransferase specific for modification of A1618 of 23 S ribosomal RNA, a methylated residue located close to the ribosomal exit tunnel. J Mol Biol 18021804
Bjork GR A primordial tRNA modification required for the evolution of life? EMBO J 11226173
Colby G MTO1 codes for a mitochondrial protein required for respiration in paromomycin-resistant mutants of Saccharomyces cerevisiae. J Biol Chem 9774408
Matsumoto K RNA recognition mechanism of eukaryote tRNA (m7G46) methyltransferase (Trm8-Trm82 complex). FEBS Lett 17382321
Tomoyasu T The Escherichia coli FtsH protein is a prokaryotic member of a protein family of putative ATPases involved in membrane functions, cell cycle control, and gene expression. J Bacteriol 8444796
Reuter K Structure and organization of Escherichia coli genes involved in biosynthesis of the deazaguanine derivative queuine, a nutrient factor for eukaryotes. J Bacteriol 1706703
Madsen CT Identifying the methyltransferases for m(5)U747 and m(5)U1939 in 23S rRNA using MALDI mass spectrometry. Nucleic Acids Res 12907714
Pan H Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA recognition through a combination of rigid docking and induced fit. Proc Natl Acad Sci U S A 14566049
Hong B Nop2p is required for pre-rRNA processing and 60S ribosome subunit synthesis in yeast. Mol Cell Biol 8972218
Reynaud A Disruption and functional analysis of six ORFs of chromosome IV: YDL103c (QRI1), YDL105w (QRI2), YDL112w (TRM3), YDL113c, YDL116w (NUP84) and YDL167c (NRP1). Yeast 11180460
Tkaczuk KL Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases. BMC Bioinformatics 17338813
Clancy MJ Induction of sporulation in Saccharomyces cerevisiae leads to the formation of N6-methyladenosine in mRNA: a potential mechanism for the activity of the IME4 gene. Nucleic Acids Res 12384598
Mueller EG Identification of a gene involved in the generation of 4-thiouridine in tRNA. Nucleic Acids Res 9592144
Jablonowski D tRNAGlu wobble uridine methylation by Trm9 identifies Elongator's key role for zymocin-induced cell death in yeast. Mol Microbiol 16390459
Lecointe F Characterization of yeast protein Deg1 as pseudouridine synthase (Pus3) catalyzing the formation of psi 38 and psi 39 in tRNA anticodon loop. J Biol Chem 9430663
Hager J Active site in RrmJ, a heat shock-induced methyltransferase. J Biol Chem 12181314
Mathevon C tRNA-modifying MiaE protein from Salmonella typhimurium is a nonheme diiron monooxygenase. Proc Natl Acad Sci U S A 17679698
Sirum-Connolly K Functional requirement of a site-specific ribose methylation in ribosomal RNA. Science 8266080
Hong B Temperature sensitive nop2 alleles defective in synthesis of 25S rRNA and large ribosomal subunits in Saccharomyces cerevisiae. Nucleic Acids Res 11452018
Sergiev PV Ribosomal RNA guanine-(N2)-methyltransferases and their targets. Nucleic Acids Res 17389639
Mao X Yeast mRNA cap methyltransferase is a 50-kilodalton protein encoded by an essential gene. Mol Cell Biol 7623811
Bujnicki JM mRNA:guanine-N7 cap methyltransferases: identification of novel members of the family, evolutionary analysis, homology modeling, and analysis of sequence-structure-function relationships. BMC Bioinformatics 11472630
Hagervall TG Reduced misreading of asparagine codons by Escherichia coli tRNALys with hypomodified derivatives of 5-methylaminomethyl-2-thiouridine in the wobble position. J Mol Biol 9811540
Monleon D Structural insights into the GTPase domain of Escherichia coli MnmE protein. Proteins 17143896
Nilsson K The cysteine desulfurase IscS is required for synthesis of all five thiolated nucleosides present in tRNA from Salmonella enterica serovar typhimurium. J Bacteriol 12446633
Hoang C Crystal structure of the highly divergent pseudouridine synthase TruD reveals a circular permutation of a conserved fold. RNA 15208439
Bujnicki JM Identification of a bifunctional enzyme MnmC involved in the biosynthesis of a hypermodified uridine in the wobble position of tRNA. RNA 15247431
White J Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of pre-40S subunits. Mol Cell Biol 18332120
Wrzesinski J A dual-specificity pseudouridine synthase: an Escherichia coli synthase purified and cloned on the basis of its specificity for psi 746 in 23S RNA is also specific for psi 32 in tRNA(phe). RNA 7493321
Lee TT Crystal structure of RumA, an iron-sulfur cluster containing E. coli ribosomal RNA 5-methyluridine methyltransferase. Structure 15016356
Henriquez R Isolation and sequencing of NOP1. A yeast gene encoding a nucleolar protein homologous to a human autoimmune antigen. J Biol Chem 2298745
O'Farrell HC Recognition of a complex substrate by the KsgA/Dim1 family of enzymes has been conserved throughout evolution. RNA 16540698
Waterman DG Crystal structure of Bacillus anthracis ThiI, a tRNA-modifying enzyme containing the predicted RNA-binding THUMP domain. J Mol Biol 16343540
Ansmant I Identification and characterization of the tRNA:Psi 31-synthase (Pus6p) of Saccharomyces cerevisiae. J Biol Chem 11406626
Liiv A Analysis of the function of E. coli 23S rRNA helix-loop 69 by mutagenesis. BMC Mol Biol 16053518
Martinez-Vicente M Effects of mutagenesis in the switch I region and conserved arginines of Escherichia coli MnmE protein, a GTPase involved in tRNA modification. J Biol Chem 15983041
Guan MX Mutation in TRMU related to transfer RNA modification modulates the phenotypic expression of the deafness-associated mitochondrial 12S ribosomal RNA mutations. Am J Hum Genet 16826519
Rashid R Crystal structure of a Cbf5-Nop10-Gar1 complex and implications in RNA-guided pseudouridylation and dyskeratosis congenita. Mol Cell 16427014
Sergiev PV Identification of Escherichia coli m2G methyltransferases: II. The ygjO gene encodes a methyltransferase specific for G1835 of the 23 S rRNA. J Mol Biol 17010380
Corollo D Crystallization and characterization of a fragment of pseudouridine synthase RluC from Escherichia coli. Acta Crystallogr D Biol Crystallogr 10089432
Roovers M The YqfN protein of Bacillus subtilis is the tRNA: m1A22 methyltransferase (TrmK). Nucleic Acids Res 18420655
Tkaczuk KL Molecular phylogenetics and comparative modeling of HEN1, a methyltransferase involved in plant microRNA biogenesis. BMC Evol Biol 16433904
Lafontaine DL The box H + ACA snoRNAs carry Cbf5p, the putative rRNA pseudouridine synthase. Genes Dev 9472021
Lovgren JM The rlmB gene is essential for formation of Gm2251 in 23S rRNA but not for ribosome maturation in Escherichia coli. J Bacteriol 11698387
Nishimura K Identification of the RsmG methyltransferase target as 16S rRNA nucleotide G527 and characterization of Bacillus subtilis rsmG mutants. J Bacteriol 17573471
Kaya Y Crystal structure of TruD, a novel pseudouridine synthase with a new protein fold. J Biol Chem 14999002
Scrima A The structure of the TrmE GTP-binding protein and its implications for tRNA modification. EMBO J 15616586
Jackman JE Identification of the yeast gene encoding the tRNA m1G methyltransferase responsible for modification at position 9. RNA 12702816
Gerber A Tad1p, a yeast tRNA-specific adenosine deaminase, is related to the mammalian pre-mRNA editing enzymes ADAR1 and ADAR2. EMBO J 9707437
Walbott H The carboxyl-terminal extension of yeast tRNA m5C methyltransferase enhances the catalytic efficiency of the amino-terminal domain. J Biol Chem 17567576
Bujnicki JM RNA:(guanine-N2) methyltransferases RsmC/RsmD and their homologs revisited--bioinformatic analysis and prediction of the active site based on the uncharacterized Mj0882 protein structure. BMC Bioinformatics 11929612
Ellis SR Isolation and characterization of the TRM1 locus, a gene essential for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNA in Saccharomyces cerevisiae. J Biol Chem 2426253
Dabbs ER The ribosomal components responsible for kasugamycin dependence, and its suppression, in a mutant of Escherichia coli. Mol Gen Genet 6988670
Das K Crystal structure of RlmAI: implications for understanding the 23S rRNA G745/G748-methylation at the macrolide antibiotic-binding site. Proc Natl Acad Sci U S A 14999102
Gautier T Nucleolar KKE/D repeat proteins Nop56p and Nop58p interact with Nop1p and are required for ribosome biogenesis. Mol Cell Biol 9372940
Mouaikel J Sequence-structure-function relationships of Tgs1, the yeast snRNA/snoRNA cap hypermethylase. Nucleic Acids Res 12907733
Gagnon KT Assembly of the archaeal box C/D sRNP can occur via alternative pathways and requires temperature-facilitated sRNA remodeling. J Mol Biol 16949610
Kaminska KH Structural bioinformatics analysis of enzymes involved in the biosynthesis pathway of the hypermodified nucleoside ms(2)io(6)A37 in tRNA. Proteins 17910062
Constantinesco F Transfer RNA modification enzymes from Pyrococcus furiosus: detection of the enzymatic activities in vitro. Nucleic Acids Res 9973619
Tscherne JS Purification, cloning, and characterization of the 16S RNA m5C967 methyltransferase from Escherichia coli. Biochemistry 10026269
Shibagaki Y mRNA capping enzyme. Isolation and characterization of the gene encoding mRNA guanylytransferase subunit from Saccharomyces cerevisiae. J Biol Chem 1315757
Watts JM Ligand-mediated anticodon conformational changes occur during tRNA methylation by a TrmD methyltransferase. Biochemistry 15850396
Hoang C Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure. Mol Cell 17188032
Seidel-Rogol BL Human mitochondrial transcription factor B1 methylates ribosomal RNA at a conserved stem-loop. Nat Genet 12496758
Persson BC Isolation of the gene (miaE) encoding the hydroxylase involved in the synthesis of 2-methylthio-cis-ribozeatin in tRNA of Salmonella typhimurium and characterization of mutants. J Bacteriol 8253666
Casamayor A Sequence analysis of a 13.4 kbp fragment from the left arm of chromosome XV reveals a malate dehydrogenase gene, a putative Ser/Thr protein kinase, the ribosomal L25 gene and four new open reading frames. Yeast 8896265
Scrima A Dimerisation-dependent GTPase reaction of MnmE: how potassium acts as GTPase-activating element. EMBO J 16763562
Yan Q Human TRMU encoding the mitochondrial 5-methylaminomethyl-2-thiouridylate-methyltransferase is a putative nuclear modifier gene for the phenotypic expression of the deafness-associated 12S rRNA mutations. Biochem Biophys Res Commun 16513084
Nolivos S The K-loop, a general feature of the Pyrococcus C/D guide RNAs, is an RNA structural motif related to the K-turn. Nucleic Acids Res 16293637
Raychaudhuri S Functional effect of deletion and mutation of the Escherichia coli ribosomal RNA and tRNA pseudouridine synthase RluA. J Biol Chem 10383384
Aravind L THUMP--a predicted RNA-binding domain shared by 4-thiouridine, pseudouridine synthases and RNA methylases. Trends Biochem Sci 11295541
Alexandrov A tRNA m7G methyltransferase Trm8p/Trm82p: evidence linking activity to a growth phenotype and implicating Trm82p in maintaining levels of active Trm8p. RNA 15811913
Kammen HO Purification, structure, and properties of Escherichia coli tRNA pseudouridine synthase I. J Biol Chem 3276686
Blaise M A minimalist glutamyl-tRNA synthetase dedicated to aminoacylation of the tRNAAsp QUC anticodon. Nucleic Acids Res 15150343
Xie W Structure of tRNA dimethylallyltransferase: RNA modification through a channel. J Mol Biol 17292915
Sunita S Domain organization and crystal structure of the catalytic domain of E.coli RluF, a pseudouridine synthase that acts on 23S rRNA. J Mol Biol 16712869
Van Lanen SG From cyclohydrolase to oxidoreductase: discovery of nitrile reductase activity in a common fold. Proc Natl Acad Sci U S A 15767583
Slany RK Transfer and isomerization of the ribose moiety of AdoMet during the biosynthesis of queuosine tRNAs, a new unique reaction catalyzed by the QueA protein from Escherichia coli. Biochimie 7849103
Torchet C The complete set of H/ACA snoRNAs that guide rRNA pseudouridylations in Saccharomyces cerevisiae. RNA 15923376
Stengl B Crystal structures of tRNA-guanine transglycosylase (TGT) in complex with novel and potent inhibitors unravel pronounced induced-fit adaptations and suggest dimer formation upon substrate binding. J Mol Biol 17524419
Lecointe F Lack of pseudouridine 38/39 in the anticodon arm of yeast cytoplasmic tRNA decreases in vivo recoding efficiency. J Biol Chem 12058040
Nishimura K Mutations in rsmG, encoding a 16S rRNA methyltransferase, result in low-level streptomycin resistance and antibiotic overproduction in Streptomyces coelicolor A3(2). J Bacteriol 17384192
Tscherne JS Purification, cloning, and characterization of the 16 S RNA m2G1207 methyltransferase from Escherichia coli. J Biol Chem 9873033
Becker HF The yeast gene YNL292w encodes a pseudouridine synthase (Pus4) catalyzing the formation of psi55 in both mitochondrial and cytoplasmic tRNAs. Nucleic Acids Res 9358157
Conrad J 16S ribosomal RNA pseudouridine synthase RsuA of Escherichia coli: deletion, mutation of the conserved Asp102 residue, and sequence comparison among all other pseudouridine synthases. RNA 10376875
Rodriguez V Chromosome 8 BAC array comparative genomic hybridization and expression analysis identify amplification and overexpression of TRMT12 in breast cancer. Genes Chromosomes Cancer 17440925
Singh SK Sequential 2'-O-methylation of archaeal pre-tRNATrp nucleotides is guided by the intron-encoded but trans-acting box C/D ribonucleoprotein of pre-tRNA. J Biol Chem 15347671
Veres Z A purified selenophosphate-dependent enzyme from Salmonella typhimurium catalyzes the replacement of sulfur in 2-thiouridine residues in tRNAs with selenium. Proc Natl Acad Sci U S A 7520175
Dobbyn HC Analysis of Snu13p mutations reveals differential interactions with the U4 snRNA and U3 snoRNA. RNA 14730029
Hansen MA Posttranscriptional modifications in the A-loop of 23S rRNAs from selected archaea and eubacteria. RNA 11911366
Kirpekar F The archaeon Haloarcula marismortui has few modifications in the central parts of its 23S ribosomal RNA. J Mol Biol 15826654
Kaminska KH Insights into the structure, function and evolution of the radical-SAM 23S rRNA methyltransferase Cfr that confers antibiotic resistance in bacteria. Nucleic Acids Res 20007606
Boal AK Structural basis for methyl transfer by a radical SAM enzyme. Science 21527678
Kehrenberg C A new mechanism for chloramphenicol, florfenicol and clindamycin resistance: methylation of 23S ribosomal RNA at A2503. Mol Microbiol 16091044
Giessing AM Identification of 8-methyladenosine as the modification catalyzed by the radical SAM methyltransferase Cfr that confers antibiotic resistance in bacteria. RNA 19144912
Yan F RlmN and Cfr are radical SAM enzymes involved in methylation of ribosomal RNA J Am Chem Soc 20184321
Yan F RNA methylation by radical SAM enzymes RlmN and Cfr proceeds via methylene transfer and hydride shift. Proc Natl Acad Sci U S A 21368151
Purta E YgdE is the 2'-O-ribose methyltransferase RlmM specific for nucleotide C2498 in bacterial 23S rRNA. Mol Microbiol 19400805
Purta E YccW is the m5C methyltransferase specific for 23S rRNA nucleotide 1962. J Mol Biol 18786544
Sunita S Crystal structure of the Escherichia coli 23S rRNA:m5C methyltransferase RlmI (YccW) reveals evolutionary links between RNA modification enzymes. J Mol Biol 18789337
Roovers M Sequence-structure-function analysis of the bifunctional enzyme MnmC that catalyses the last two steps in the biosynthesis of hypermodified nucleoside mnm5s2U in tRNA. Proteins 18186482
Pearson D Assay of both activities of the bifunctional tRNA-modifying enzyme MnmC reveals a kinetic basis for selective full modification of cmnm5s2U to mnm5s2U. Nucleic Acids Res 21306992
Kitamura A Crystal structure of the bifunctional tRNA modification enzyme MnmC from Escherichia coli. Protein Sci 21574198
Meyer S Crystal structures of the conserved tRNA-modifying enzyme GidA: implications for its interaction with MnmE and substrate. J Mol Biol 18565343
Franke J Hypermethylation of yeast telomerase RNA by the snRNA and snoRNA methyltransferase Tgs1. J Cell Sci 18840651
Numata T Snapshots of tRNA sulphuration via an adenylated intermediate. Nature 16871210
Foster PG The first structure of an RNA m5C methyltransferase, Fmu, provides insight into catalytic mechanism and specific binding of RNA substrate. Structure 14656444
Alian A Structure of a TrmA-RNA complex: A consensus RNA fold contributes to substrate selectivity and catalysis in m5U methyltransferases. Proc Natl Acad Sci U S A 18451029
Leulliot N Structure of the yeast tRNA m7G methylation complex. Structure 18184583
Nakanishi K Structural basis for translational fidelity ensured by transfer RNA lysidine synthetase. Nature 19847269
Pulicherla N Structural and functional divergence within the Dim1/KsgA family of rRNA methyltransferases. J Mol Biol 19520088
Lima CD Structure and mechanism of yeast RNA triphosphatase: an essential component of the mRNA capping apparatus. Cell 10589681
Ericsson UB X-ray structure of tRNA pseudouridine synthase TruD reveals an inserted domain with a novel fold. FEBS Lett 15135053
Kim J Structural and kinetic characterization of Escherichia coli TadA, the wobble-specific tRNA deaminase. Biochemistry 16700551
Wright JR Pre-steady-state kinetic analysis of the three Escherichia coli pseudouridine synthases TruB, TruA, and RluA reveals uniformly slow catalysis. RNA 21998096
Christian T Control of catalytic cycle by a pair of analogous tRNA modification enzymes. J Mol Biol 20452364
Gurha P Archaeal Pus10 proteins can produce both pseudouridine 54 and 55 in tRNA. RNA 18952823
Behm-Ansmant I A previously unidentified activity of yeast and mouse RNA:pseudouridine synthases 1 (Pus1p) on tRNAs. RNA 16804160
Arluison V RNA:pseudouridine synthetase Pus1 from Saccharomyces cerevisiae: oligomerization property and stoichiometry of the complex with yeast tRNA(Phe). Biochimie 10492022
Arluison V Pseudouridine synthetase Pus1 of Saccharomyces cerevisiae: kinetic characterisation, tRNA structural requirement and real-time analysis of its complex with tRNA. J Mol Biol 10356324
Arluison V Transfer RNA-pseudouridine synthetase Pus1 of Saccharomyces cerevisiae contains one atom of zinc essential for its native conformation and tRNA recognition. Biochemistry 9585540
Brégeon D Translational misreading: a tRNA modification counteracts a +2 ribosomal frameshift. Genes Dev 11544186
Moukadiri I Evolutionarily conserved proteins MnmE and GidA catalyze the formation of two methyluridine derivatives at tRNA wobble positions. Nucleic Acids Res 19767610
Umeda N Mitochondria-specific RNA-modifying enzymes responsible for the biosynthesis of the wobble base in mitochondrial tRNAs. Implications for the molecular pathogenesis of human mitochondrial diseases. J Biol Chem 15509579
Gu W tRNAHis maturation: an essential yeast protein catalyzes addition of a guanine nucleotide to the 5' end of tRNAHis. Genes Dev 14633974
Hyde SJ tRNAHis guanylyltransferase (THG1), a unique 3′-5′ nucleotidyl transferase, shares unexpected structural homology with canonical 5′-3′ DNA polymerases. Proc Natl Acad Sci U S A 21059936
Basturea GN YhiQ Is RsmJ, the Methyltransferase Responsible for Methylation of G1516 in 16S rRNA of E. coli. J Mol Biol 22079366
Kimura S Fine-tuning of the ribosomal decoding center by conserved methyl-modifications in the Escherichia coli 16S rRNA. Nucleic Acids Res 19965768
Havelund JF Identification of 5-hydroxycytidine at position 2501 concludes characterization of modified nucleotides in E. coli 23S rRNA. J Mol Biol 21723290
Beauclerk AA Sites of action of two ribosomal RNA methylases responsible for resistance to aminoglycosides. J Mol Biol 2441068
Macmaster R Structural insights into the function of aminoglycoside-resistance A1408 16S rRNA methyltransferases from antibiotic-producing and human pathogenic bacteria. Nucleic Acids Res 20639535
Husain N Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit. Nucleic Acids Res 21062819
Miles ZD Discovery of epoxyqueuosine (oQ) reductase reveals parallels between halorespiration and tRNA modification. Proc Natl Acad Sci U S A 21502530
Hausmann S Biochemical and genetic analysis of RNA cap guanine-N2 methyltransferases from Giardia lamblia and Schizosaccharomyces pombe. Nucleic Acids Res 17284461
Chen C 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 21687733
Mazauric MH Trm112p is a 15-kDa zinc finger protein essential for the activity of two tRNA and one protein methyltransferases in yeast. J Biol Chem 20400505
Golovina AY The yfiC gene of E. coli encodes an adenine-N6 methyltransferase that specifically modifies A37 of tRNA1Val(cmo5UAC). RNA 19383770
Zebarjadian Y Point mutations in yeast CBF5 can abolish in vivo pseudouridylation of rRNA. Mol Cell Biol 10523634
Krog JS 3-(3-amino-3-carboxypropyl)-5,6-Dihydrouridine is one of two novel post-transcriptional modifications in tRNA(Lys) (UUU) from Trypanosoma brucei. FEBS J 22040320
Meyer B The Bowen-Conradi syndrome protein Nep1 (Emg1) has a dual role in eukaryotic ribosome biogenesis, as an essential assembly factor and in the methylation of Psi1191 in yeast 18S rRNA. Nucleic Acids Res 20972225
Kasai H Structure of wye (Yt base) and wyosine (Yt) from Torulopsis utilis phenylalanine transfer ribonucleic acid. Biochemistry 942858
Rajbhandary UL Studies on polynucleotides, lxviii the primary structure of yeast phenylalanine transfer RNA. Proc Natl Acad Sci U S A 16591527
Thiebe R A specific modification next to the anticodon of phenylalanine transfer ribonucleic acid. Eur J Biochem 5698615
Yoshikami D A fluorescence assay for phenylalanine transfer RNA. Biochim Biophys Acta 5722700
Christian T Mechanism of N-methylation by the tRNA m1G37 methyltransferase Trm5. RNA 20980671
Lee C Yeast mitochondrial initiator tRNA is methylated at guanosine 37 by the Trm5-encoded tRNA (guanine-N1-)-methyltransferase. J Biol Chem 17652090
Brule H Isolation and characterization of the human tRNA-(N1G37) methyltransferase (TRM5) and comparison to the Escherichia coli TrmD protein. Biochemistry 15248782
Suzuki Y Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4. Nucleic Acids Res 19287006
de Crecy-Lagard V Biosynthesis of wyosine derivatives in tRNA: an ancient and highly diverse pathway in Archaea. Mol Biol Evol 20382657
Goto-Ito S Structure of an archaeal TYW1, the enzyme catalyzing the second step of wye-base biosynthesis. Acta Crystallogr D Biol Crystallogr 17881823
Umitsu M Structural basis of AdoMet-dependent aminocarboxypropyl transfer reaction catalyzed by tRNA-wybutosine synthesizing enzyme, TYW2. Proc Natl Acad Sci U S A 19717466
Phillips G Biosynthesis and function of tRNA modifications in Archaea. Curr Opin Microbiol 21470902
Menezes S Formation of m2G6 in Methanocaldococcus jannaschii tRNA catalyzed by the novel methyltransferase Trm14. Nucleic Acids Res 21693558
Mandal D Agmatidine, a modified cytidine in the anticodon of archaeal tRNA(Ile), base pairs with adenosine but not with guanosine. Proc Natl Acad Sci U S A 20133752
Ikeuchi Y Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea. Nat Chem Biol 20139989
Osawa T Structural basis of tRNA agmatinylation essential for AUA codon decoding. Nat Struct Mol Biol 22002223
Tollervey D The small nucleolar RNP protein NOP1 (fibrillarin) is required for pre-rRNA processing in yeast. EMBO J 1825809
Jansen R A U3 snoRNP protein with homology to splicing factor PRP4 and G beta domains is required for ribosomal RNA processing. EMBO J 8508778
Jansen RP Evolutionary conservation of the human nucleolar protein fibrillarin and its functional expression in yeast. J Cell Biol 2026646
Baserga SJ An intact Box C sequence in the U3 snRNA is required for binding of fibrillarin, the protein common to the major family of nucleolar snRNPs. EMBO J 1714385
Yanagida M Human fibrillarin forms a sub-complex with splicing factor 2-associated p32, protein arginine methyltransferases, and tubulins alpha 3 and beta 1 that is independent of its association with preribosomal ribonucleoprotein complexes. J Biol Chem 14583623
Aris JP cDNA cloning and sequencing of human fibrillarin, a conserved nucleolar protein recognized by autoimmune antisera. Proc Natl Acad Sci U S A 1846968
Ye K Structural organization of box C/D RNA-guided RNA methyltransferase. Proc Natl Acad Sci U S A 19666563
Lin J Structural basis for site-specific ribose methylation by box C/D RNA protein complexes. Nature 21270896
Wang H Crystal structure of a fibrillarin homologue from Methanococcus jannaschii, a hyperthermophile, at 1.6 A resolution. EMBO J 10654930
Wang H Expression, purification and preliminary X-ray analysis of a fibrillarin homolog from Methanococcus jannaschii, a hyperthermophile. Acta Crystallogr D Biol Crystallogr 10089444
Deng L Structure determination of fibrillarin from the hyperthermophilic archaeon Pyrococcus furiosus. Biochem Biophys Res Commun 14975761
Oruganti S Alternative conformations of the archaeal Nop56/58-fibrillarin complex imply flexibility in box C/D RNPs. J Mol Biol 17617422
Xue S Structural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle. Mol Cell 20864039
Aittaleb M Structural and thermodynamic evidence for a stabilizing role of Nop5p in S-adenosyl-L-methionine binding to fibrillarin. J Biol Chem 15286083
Aittaleb M Structure and function of archaeal box C/D sRNP core proteins. Nat Struct Biol 12598892
Suryadi J The crystal structure of the Methanocaldococcus jannaschii multifunctional L7Ae RNA-binding protein reveals an induced-fit interaction with the box C/D RNAs. Biochemistry 16008351
Hamma T Structure of protein L7Ae bound to a K-turn derived from an archaeal box H/ACA sRNA at 1.8 A resolution. Structure 15130481
Rozhdestvensky TS Binding of L7Ae protein to the K-turn of archaeal snoRNAs: a shared RNA binding motif for C/D and H/ACA box snoRNAs in Archaea. Nucleic Acids Res 12560482
Moore T Molecular basis of box C/D RNA-protein interactions; cocrystal structure of archaeal L7Ae and a box C/D RNA. Structure 15130473
Biswas S Comparative analysis of the 15.5kD box C/D snoRNP core protein in the primitive eukaryote Giardia lamblia reveals unique structural and functional features. Biochemistry 21366326
Vidovic I Crystal structure of the spliceosomal 15.5kD protein bound to a U4 snRNA fragment. Mol Cell 11163207
Liu S Binding of the human Prp31 Nop domain to a composite RNA-protein platform in U4 snRNP. Science 17412961
Nottrott S Functional interaction of a novel 15.5kD [U4/U6.U5] tri-snRNP protein with the 5' stem-loop of U4 snRNA. EMBO J 10545122
Ghalei H A novel Nop5-sRNA interaction that is required for efficient archaeal box C/D sRNP formation. RNA 20962039
van Nues RW Box C/D snoRNP catalysed methylation is aided by additional pre-rRNA base-pairing. EMBO J 21556049
Persson BC The ms2io6A37 modification of tRNA in Salmonella typhimurium regulates growth on citric acid cycle intermediates. J Bacteriol 9620964
Nasvall SJ The wobble hypothesis revisited: uridine-5-oxyacetic acid is critical for reading of G-ending codons. RNA 17942742
Lis AW Isolation of 5-hydroxyuridine (iso-barbituridine) from yeast ribonucleic acids. Arch Biochem Biophys 5957714
Murao K 5-methoxyuridine: a new minor constituent located in the first position of the anticodon of tRNAAla, tRNAThr, and tRNAVal from Bacillus subtilis. Nucleic Acids Res 825836
Lim K Crystal structure of YecO from Haemophilus influenzae (HI0319) reveals a methyltransferase fold and a bound S-adenosylhomocysteine. Proteins 11746687
Pope WT The identification of the tRNA substrates for the supK tRNA methylase. Nucleic Acids Res 347399
Ishikura H The presence of N-[9-(beta-D-ribofuranosyl)purin-6-ylcarbamoyl]threonine in serine, methionine and lysine transfer RNA's from Escherichia coli. Biochem Biophys Res Commun 4902784
Osawa T Conserved cysteine residues of GidA are essential for biogenesis of 5-carboxymethylaminomethyluridine at tRNA anticodon. Structure 19446527
Meyer S Kissing G domains of MnmE monitored by X-ray crystallography and pulse electron paramagnetic resonance spectroscopy. PLoS Biol 19806182
Yamanaka K Characterization of GTPase activity of TrmE, a member of a novel GTPase superfamily, from Thermotoga maritima. J Bacteriol 11092873
Wang X Deletion of the MTO2 gene related to tRNA modification causes a failure in mitochondrial RNA metabolism in the yeast Saccharomyces cerevisiae. FEBS Lett 17706197
Yan Q Mutations in MTO2 related to tRNA modification impair mitochondrial gene expression and protein synthesis in the presence of a paromomycin resistance mutation in mitochondrial 15 S rRNA. J Biol Chem 15944150
Shi R Structural basis for Fe-S cluster assembly and tRNA thiolation mediated by IscS protein-protein interactions. PLoS Biol 20404999
Ikeuchi Y Mechanistic insights into sulfur relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions. Mol Cell 16387657
Katoh E High precision NMR structure of YhhP, a novel Escherichia coli protein implicated in cell division. J Mol Biol 11080457
Numata T Structural basis for sulfur relay to RNA mediated by heterohexameric TusBCD complex. Structure 16472754
Nakai Y Yeast Nfs1p is involved in thio-modification of both mitochondrial and cytoplasmic tRNAs. J Biol Chem 14722066
Suzuki T Human mitochondrial tRNAs: biogenesis, function, structural aspects, and diseases. Annu Rev Genet 21910628
Suzuki T Human mitochondrial diseases caused by lack of taurine modification in mitochondrial tRNAs. Wiley Interdiscip Rev RNA 21957023
Kimura S Base methylations in the double-stranded RNA by a fused methyltransferase bearing unwinding activity. Nucleic Acids Res 22210896
Mikhailov SN Chemical incorporation of 1‑methyladenosine into oligonucleotides Nucl. Acids Res. 11861902
Dewez M The conserved Wobble uridine tRNA thiolase Ctu1-Ctu2 is required to maintain genome integrity. Proc Natl Acad Sci U S A 18391219
Leidel S Ubiquitin-related modifier Urm1 acts as a sulphur carrier in thiolation of eukaryotic transfer RNA. Nature 19145231
Murao K Uridin-5-oxy acetic acid: a new minor constituent from E. coli valine transfer RNA I. Biochem Biophys Res Commun 4910247
Karcher D Identification of the chloroplast adenosine-to-inosine tRNA editing enzyme. RNA 19460869
Delannoy E Arabidopsis tRNA adenosine deaminase arginine edits the wobble nucleotide of chloroplast tRNAArg(ACG) and is essential for efficient chloroplast translation. Plant Cell 19602623
Su AA A-to-I and C-to-U editing within transfer RNAs. Biochemistry (Mosc) 22022967
Paris Z Determinants of tRNA editing and modification: Avoiding conundrums, affecting function. Semin Cell Dev Biol 22024020
Randau L A cytidine deaminase edits C to U in transfer RNAs in Archaea. Science 19407206
Hamdane D Insights into folate/FAD-dependent tRNA methyltransferase mechanism: role of two highly conserved cysteines in catalysis. J Biol Chem 21846722
Hamdane D A catalytic intermediate and several flavin redox states stabilized by folate-dependent tRNA methyltransferase from Bacillus subtilis. Biochemistry 21561081
Hamdane D Expression and purification of untagged and histidine-tagged folate-dependent tRNA:m5U54 methyltransferase from Bacillus subtilis. Protein Expr Purif 20412857
Haumont E Enzymatic formation of queuosine and of glycosyl queuosine in yeast tRNAs microinjected into Xenopus laevis oocytes. The effect of the anticodon loop sequence. Eur J Biochem 3117541
Nishimura S Structure, biosynthesis, and function of queuosine in transfer RNA. Prog Nucleic Acid Res Mol Biol 6410456
Okada N Enzymatic synthesis of Q nucleoside containing mannose in the anticodon of tRNA: isolation of a novel mannosyltransferase from a cell-free extract of rat liver. Nucleic Acids Res 20603
Costa A Determination of queuosine derivatives by reverse-phase liquid chromatography for the hypomodification study of Q-bearing tRNAs from various mammal liver cells. J Chromatogr B Analyt Technol Biomed Life Sci 14751792
Kasai H Letter: The structure of Q* nucleoside isolated from rabbit liver transfer ribonucleic acid. J Am Chem Soc 950430
Nishimasu H Atomic structure of a folate/FAD-dependent tRNA T54 methyltransferase. Proc Natl Acad Sci U S A 19416846
Li S Reconstitution and structural analysis of the yeast box H/ACA RNA-guided pseudouridine synthase. Genes Dev 22085967
Piekna-Przybylska D New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA. RNA 17283215
Li S Structure of the Shq1-Cbf5-Nop10-Gar1 complex and implications for H/ACA RNP biogenesis and dyskeratosis congenita. EMBO J 22117216
Khanna M Structural study of the H/ACA snoRNP components Nop10p and the 3' hairpin of U65 snoRNA. RNA 16373493
Kiss T Box H/ACA small ribonucleoproteins. Mol Cell 20227365
Hamma T The box H/ACA ribonucleoprotein complex: interplay of RNA and protein structures in post-transcriptional RNA modification. J Biol Chem 19917616
Spears JL A single zinc ion is sufficient for an active Trypanosoma brucei tRNA editing deaminase. J Biol Chem 21507956
Ragone FL The C-terminal end of the Trypanosoma brucei editing deaminase plays a critical role in tRNA binding. RNA 21602302
Rubio MA An adenosine-to-inosine tRNA-editing enzyme that can perform C-to-U deamination of DNA. Proc Natl Acad Sci U S A 17483465
Bjork GR A novel link between the biosynthesis of aromatic amino acids and transfer RNA modification in Escherichia coli. J Mol Biol 6160251
Chatterjee K The archaeal COG1901/DUF358 SPOUT-methyltransferase members, together with pseudouridine synthase Pus10, catalyze the formation of 1-methylpseudouridine at position 54 of tRNA. RNA 22274953
Wurm JP Identification of the enzyme responsible for N1-methylation of pseudouridine 54 in archaeal tRNAs. RNA 22274954
Chen HY Crystal structure of Mj1640/DUF358 protein reveals a putative SPOUT-class RNA methyltransferase. J Mol Cell Biol 21098051
Suzuki T Discovery and characterization of tRNAIle lysidine synthetase (TilS). FEBS Lett 19944692
Fabret C Life without the essential bacterial tRNA Ile2-lysidine synthetase TilS: a case of tRNA gene recruitment in Bacillus subtilis. Mol Microbiol 21435031
Terasaka N Biogenesis of 2-agmatinylcytidine catalyzed by the dual protein and RNA kinase TiaS. Nat Struct Mol Biol 22002222
Shigi N Common thiolation mechanism in the biosynthesis of tRNA thiouridine and sulphur-containing cofactors. EMBO J 19037260
Shigi N Identification of two tRNA thiolation genes required for cell growth at extremely high temperatures. J Biol Chem 16547008
Palenchar PM Evidence that ThiI, an enzyme shared between thiamin and 4-thiouridine biosynthesis, may be a sulfurtransferase that proceeds through a persulfide intermediate. J Biol Chem 10722656
Kambampati R Evidence for the transfer of sulfane sulfur from IscS to ThiI during the in vitro biosynthesis of 4-thiouridine in Escherichia coli tRNA. J Biol Chem 10753862
Mueller EG The role of the cysteine residues of ThiI in the generation of 4-thiouridine in tRNA. J Biol Chem 11443125
Wright CM A paradigm for biological sulfur transfers via persulfide groups: a persulfide-disulfide-thiol cycle in 4-thiouridine biosynthesis. Chem Commun (Camb) 12510310
Tanaka Y Deduced RNA binding mechanism of ThiI based on structural and binding analyses of a minimal RNA ligand. RNA 19509301
You D Direct evidence that ThiI is an ATP pyrophosphatase for the adenylation of uridine in 4-thiouridine biosynthesis. Chembiochem 18604845
Wright CM Direct evidence for enzyme persulfide and disulfide intermediates during 4-thiouridine biosynthesis. Chem Commun (Camb) 16855700
Cantara WA Modifications Modulate Anticodon Loop Dynamics and Codon Recognition of E. coli tRNA(Arg1,2). J Mol Biol 22240457
Carbon J Thiobases in Escherchia coli Transfer RNA: 2-Thiocytosine and 5-Methylaminomethyl-2-thiouracil. Science 17812290
Fontecave M Iron-sulfur cluster biosynthesis in bacteria: Mechanisms of cluster assembly and transfer. Arch Biochem Biophys 18191630
Bjork GR A conserved modified wobble nucleoside (mcm5s2U) in lysyl-tRNA is required for viability in yeast. RNA 17592039
Leulliot N The yeast ribosome synthesis factor Emg1 is a novel member of the superfamily of alpha/beta knot fold methyltransferases. Nucleic Acids Res 18063569
Lee HH Overexpression, crystallization and preliminary X-ray crystallographic analysis of Pseudomonas aeruginosa MnmE, a GTPase involved in tRNA modification. Acta Crystallogr Sect F Struct Biol Cryst Commun 20693664
Chimnaronk S RNA helicase module in an acetyltransferase that modifies a specific tRNA anticodon. EMBO J 19322199
Porcher S. Synthesis of 2′-O-[(Triisopropylsilyl)oxy]methyl (= tom)-Protected Ribonucleoside Phosphoramidites Containing Various Nucleobase Analogues HELVETICA CHIMICA ACTA 10.1002/hlca.200590209
Agris PF. Site-selected introduction of modified purine and pyrimidine ribonucleosides into RNA by automated phosphoramidite chemistry. Biochimie 7599270
Höbartner, C The synthesis of 2'-O-[(Triisopropylsilyl)oxy] methyl (TOM) phosphoramidites of methylated ribonucleosides (m1G, m2G, m22G, m1I, m3U, m4C, m6A, m62A) for use in automated RNA solid-phase synthesis Monatshefte fuer Chemie
Boudou V. Synthesis of the Anticodon Hairpin tRNAfMet Containing N-{[9-(β-D-Ribofuranosyl)-9H-purin-6-yl]carbamoyl}-L-threonine (=N6-{{[(1S,2R)-1-Carboxy-2-hydroxypropyl]amino}carbonyl}adenosine, t6A) Helvetica Chimica Acta 10.1002/(SICI)1522-2675(20000119)83:1<152::AID-HLC
Clarke L The nucleotide sequence of a threonine transfer ribonucleic acid from Escherichia coli. J Biol Chem 4608712
Komine Y Nucleotide sequence of tRNA(Thr1) of Escherichia coli and of the gene (thrV) that encodes it. Nucleic Acids Res 1380693
Mallikarjun Sundaram Synthesis and Characterization of the Native Anticodon Domain of E. coli tRNALys:  Simultaneous Incorporation of Modified Nucleosides mnm5s2U, t6A, and Pseudouridine Using Phosphoramidite Chemistry J. Org. Chem. 10970299
Bajji AC Synthesis of the tRNALys,3 Anticodon Stem-Loop Domain Containing the Hypermodified ms2t6A Nucleoside J. Org. Chem 12126427
Jasenka Matulic-Adamic An Improved Synthesis of Inosine 3′-Phosphoramidite SYNTHETIC COMMUNICATIONS 10.1080/00397910008086956
Chui HM Synthesis of a 3-methyluridine phosphoramidite to investigate the role of methylation in a ribosomal RNA hairpin. Bioorg Med Chem 11741781
Chui HM Synthesis of helix 69 of Escherichia coli 23S rRNA containing its natural modified nucleosides, m(3)Psi and Psi. J Org Chem 12467398
O'Connor M Mutagenesis of the peptidyltransferase center of 23S rRNA: the invariant U2449 is dispensable. Nucleic Acids Res 11160893
Kumar RK Synthesis and studies on the effect of 2-thiouridine and 4-thiouridine on sugar conformation and RNA duplex stability. Nucleic Acids Res 9092639
Chaix C Solid phase synthesis of the 5'-half of the initiator t-RNA from B. subtilis. Nucleic Acids Res 2508060
Shibahara S Site-directed cleavage of RNA. Nucleic Acids Res 2438655
Inoue H Synthesis and hybridization studies on two complementary nona(2'-O-methyl)ribonucleotides. Nucleic Acids Res 3627981
Beier M Synthesis of N-Methylated Ribonucleosides for RNA Synthesis Helvetica Chimica Acta 10.1002/hlca.200390205
Kierzek E The synthesis of oligoribonucleotides containing N6-alkyladenosines and 2-methylthio-N6-alkyladenosines via post-synthetic modification of precursor oligomers. Nucleic Acids Res 12888506
Davis DR Introduction of hypermodified nucleotides in RNA. Methods Mol Biol 15333904
Rossa B. S. Synthesis and Incorporation of 2′-O-Methyl-Pseudouridine into Oligonucleotides Nucleosides and Nucleotides 10.1080/07328319708006226
Pieles U. New and convenient protection system for pseudouridine, highly suitable for solid-phase oligoribonucleotide synthesis J. Chem. Soc. 10.1039/P19940003423
Gasparutto D Chemical synthesis of a biologically active natural tRNA with its minor bases. Nucleic Acids Res 1383941
Ogata Chemical synthesis of RNA including 5-taurinomethyluridine Nucleic Acids Symposium 10.1093/nass/nrl005
Meroueh M Unique structural and stabilizing roles for the individual pseudouridine residues in the 1920 region of Escherichia coli 23S rRNA. Nucleic Acids Res 10773075
Kowtoniuk WE A chemical screen for biological small molecule-RNA conjugates reveals CoA-linked RNA. Proc Natl Acad Sci U S A 19416889
Chen YG LC/MS analysis of cellular RNA reveals NAD-linked RNA. Nat Chem Biol 19820715
Kato N Nucleotide sequence of nuclear 5.4 S RNA of mouse cells. Biochim Biophys Acta 6202321
Mao X Mutational analysis of the Saccharomyces cerevisiae ABD1 gene: cap methyltransferase activity is essential for cell growth. Mol Cell Biol 8552073
Wang SP Structure-function analysis of the mRNA cap methyltransferase of Saccharomyces cerevisiae. J Biol Chem 9169431
Schroeder SC Dynamic association of capping enzymes with transcribing RNA polymerase II. Genes Dev 11018011
Bellemer C Genetic interactions show the importance of rRNA modification machinery for the role of Rps15p during ribosome biogenesis in S. cerevisiae. PLoS One 20454621
Figaro S Trm112 Is Required for Bud23-Mediated Methylation of the 18S rRNA at Position G1575. Mol Cell Biol 22493060
Yamagishi M Isolation of temperature-sensitive mutants for mRNA capping enzyme in Saccharomyces cerevisiae. Mol Gen Genet 7500935
Itoh N Messenger RNA guanylyltransferase from Saccharomyces cerevisiae. Large scale purification, subunit functions, and subcellular localization. J Biol Chem 3029058
Gu M Structure of the Saccharomyces cerevisiae Cet1-Ceg1 mRNA capping apparatus. Structure 20159466
Takase Y The essential interaction between yeast mRNA capping enzyme subunits is not required for triphosphatase function in vivo. Mol Cell Biol 11094081
Savage DF Molecular determinants of dihydrouridine synthase activity. FEBS Lett 16962594
Blaise M Crystal structure of glutamyl-queuosine tRNAAsp synthetase complexed with L-glutamate: structural elements mediating tRNA-independent activation of glutamate and glutamylation of tRNAAsp anticodon. J Mol Biol 18602926
Huang Y Structural insights into mechanisms of the small RNA methyltransferase HEN1. Nature 19812675
Vilkaitis G Kinetic and functional analysis of the small RNA methyltransferase HEN1: the catalytic domain is essential for preferential modification of duplex RNA. RNA 20705645
Li J Methylation protects miRNAs and siRNAs from a 3'-end uridylation activity in Arabidopsis. Curr Biol 16111943
Yu B Methylation as a crucial step in plant microRNA biogenesis. Science 15705854
Yu B siRNAs compete with miRNAs for methylation by HEN1 in Arabidopsis. Nucleic Acids Res 20448024
Yang Z HEN1 recognizes 21-24 nt small RNA duplexes and deposits a methyl group onto the 2' OH of the 3' terminal nucleotide. Nucleic Acids Res 16449203
Bodi Z Yeast targets for mRNA methylation. Nucleic Acids Res 20421205
Chimnaronk S Snapshots of dynamics in synthesizing N(6)-isopentenyladenosine at the tRNA anticodon. Biochemistry 19435325
Seif E RNA-protein mutually induced fit: structure of Escherichia coli isopentenyl-tRNA transferase in complex with tRNA(Phe). J Biol Chem 19158097
Moore JA Escherichia coli dimethylallyl diphosphate:tRNA dimethylallyltransferase: a binding mechanism for recombinant enzyme. Biochemistry 9012675
Pierrel F Enzymatic modification of tRNAs: MiaB is an iron-sulfur protein. J Biol Chem 11882645
Waller JC Evidence that the folate-dependent proteins YgfZ and MnmEG have opposing effects on growth and on activity of the iron-sulfur enzyme MiaB. J Bacteriol 22081392
Anantharaman V TRAM, a predicted RNA-binding domain, common to tRNA uracil methylation and adenine thiolation enzymes. FEMS Microbiol Lett 11313137
Armengod ME Enzymology of tRNA modification in the bacterial MnmEG pathway. Biochimie 22386868
Tolerico LH Saccharomyces cerevisiae Mod5p-II contains sequences antagonistic for nuclear and cytosolic locations. Genetics 9872948
Lamichhane TN Plasticity and diversity of tRNA anticodon determinants of substrate recognition by eukaryotic A37 isopentenyltransferases. RNA 21873461
Feder M Molecular phylogenetics of the RrmJ/fibrillarin superfamily of ribose 2'-O-methyltransferases. Gene 12527203
Sirum-Connolly K Implications of a functional large ribosomal RNA with only three modified nucleotides. Biochimie 7541254
Noma A Mechanistic characterization of the sulfur-relay system for eukaryotic 2-thiouridine biogenesis at tRNA wobble positions. Nucleic Acids Res 19151091
Huang B A genome-wide screen identifies genes required for formation of the wobble nucleoside 5-methoxycarbonylmethyl-2-thiouridine in Saccharomyces cerevisiae. RNA 18755837
Nakai Y Thio-modification of yeast cytosolic tRNA requires a ubiquitin-related system that resembles bacterial sulfur transfer systems. J Biol Chem 18664566
Thomas SR Structural insight into the functional mechanism of Nep1/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis. Nucleic Acids Res 21087996
Brand RC Biosynthesis of a hypermodified nucleotide in Saccharomyces carlsbergensis 17S and HeLa-cell 18S ribosomal ribonucleic acid. Biochem J 629754
Pavlopoulou A Phylogenetic analysis of the eukaryotic RNA (cytosine-5)-methyltransferases. Genomics 19135144
King MY RNA methyltransferases utilize two cysteine residues in the formation of 5-methylcytosine. Biochemistry 12220187
Yang C Psi35 in the branch site recognition region of U2 small nuclear RNA is important for pre-mRNA splicing in Saccharomyces cerevisiae. J Biol Chem 15611063
Lin Y X-ray structures of U2 snRNA-branchpoint duplexes containing conserved pseudouridines. Biochemistry 18435545
Decatur WA Different mechanisms for pseudouridine formation in yeast 5S and 5.8S rRNAs. Mol Cell Biol 18332121
Urban A RNA sequence and two-dimensional structure features required for efficient substrate modification by the Saccharomyces cerevisiae RNA:{Psi}-synthase Pus7p. J Biol Chem 19114708
Reader JS Identification of four genes necessary for biosynthesis of the modified nucleoside queuosine. J Biol Chem 14660578
Liu M Methylation of 23S rRNA nucleotide G745 is a secondary function of the RlmAI methyltransferase. RNA 15388872
Persaud C Mutagenesis of the modified bases, m(5)U1939 and psi2504, in Escherichia coli 23S rRNA. Biochem Biophys Res Commun 20067766
Osterman IA Methylated 23S rRNA nucleotide m2G1835 of Escherichia coli ribosome facilitates subunit association. Biochimie 21237242
Ero R Identification of pseudouridine methyltransferase in Escherichia coli. RNA 18755836
Ero R Specificity and kinetics of 23S rRNA modification enzymes RlmH and RluD. RNA 20817755
Motorin Y 5-methylcytosine in RNA: detection, enzymatic formation and biological functions. Nucleic Acids Res 20007150
Wang KT Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA. Nucleic Acids Res 22362734
Zhang Q Radical-mediated enzymatic methylation: a tale of two SAMS. Acc Chem Res 22097883
Grove TL Cfr and RlmN contain a single [4Fe-4S] cluster, which directs two distinct reactivities for S-adenosylmethionine: methyl transfer by SN2 displacement and radical generation. J Am Chem Soc 21916495
Ofengand J Pseudouridines and pseudouridine synthases of the ribosome. Cold Spring Harb Symp Quant Biol 12762017
Mizutani K Crystal structures of the catalytic domains of pseudouridine synthases RluC and RluD from Escherichia coli. Biochemistry 15078091
Huang L Identification of two Escherichia coli pseudouridine synthases that show multisite specificity for 23S RNA. Biochemistry 9843401
Del Campo M Crystal structure of the catalytic domain of RluD, the only rRNA pseudouridine synthase required for normal growth of Escherichia coli. RNA 14730022
Leppik M Substrate specificity of the pseudouridine synthase RluD in Escherichia coli. FEBS J 17937767
Sivaraman J Crystal structure of the RluD pseudouridine synthase catalytic module, an enzyme that modifies 23S rRNA and is essential for normal cell growth of Escherichia coli. J Mol Biol 14659742
Alian A Crystal structure of an RluF-RNA complex: a base-pair rearrangement is the key to selectivity of RluF for U2604 of the ribosome. J Mol Biol 19298824
Schmitt E Structural bases for 16 S rRNA methylation catalyzed by ArmA and RmtB methyltransferases. J Mol Biol 19303884
Boehringer D Structural insights into methyltransferase KsgA function in 30S ribosomal subunit biogenesis. J Biol Chem 22308031
Desai PM Site-directed mutants of 16S rRNA reveal important RNA domains for KsgA function and 30S subunit assembly. Biochemistry 21142019
Connolly K Mechanistic insight into the ribosome biogenesis functions of the ancient protein KsgA. Mol Microbiol 18990185
O'Farrell HC Control of substrate specificity by a single active site residue of the KsgA methyltransferase. Biochemistry 22142337
Poldermans B Studies on the function of two adjacent N6,N6-dimethyladenosines near the 3' end of 16 S ribosomal RNA of Escherichia coli. III. Purification and properties of the methylating enzyme and methylase-30 S interactions. J Biol Chem 383712
Poldermans B Studies on the function of two adjacent N6,N6-dimethyladenosines near the 3' end of 16S ribosomal RNA of Escherichia coli. IV. The effect of the methylgroups on ribosomal subunit interaction. Nucleic Acids Res 6986611
Lafontaine D The DIM1 gene responsible for the conserved m6(2)Am6(2)A dimethylation in the 3'-terminal loop of 18 S rRNA is essential in yeast. J Mol Biol 8064863
Park AK Comprehensive phylogenetic analysis of evolutionarily conserved rRNA adenine dimethyltransferase suggests diverse bacterial contributions to the nucleus-encoded plastid proteome. Mol Phylogenet Evol 19017544
Vanrobays E Dim2p, a KH-domain protein required for small ribosomal subunit synthesis. RNA 15037774
Lafontaine DL Yeast 18S rRNA dimethylase Dim1p: a quality control mechanism in ribosome synthesis? Mol Cell Biol 9528805
Weitzmann C A paradigm for local conformational control of function in the ribosome: binding of ribosomal protein S19 to Escherichia coli 16S rRNA in the presence of S7 is required for methylation of m2G966 and blocks methylation of m5C967 by their respective methyltransferases. Nucleic Acids Res 1766869
Sergeeva OV Properties of small rRNA methyltransferase RsmD: Mutational and kinetic study. RNA 22535590
Cubrilo S The aminoglycoside resistance methyltransferase Sgm impedes RsmF methylation at an adjacent rRNA nucleotide in the ribosomal A site. RNA 19509304
Benitez-Paez A Regulation of expression and catalytic activity of Escherichia coli RsmG methyltransferase. RNA 22337945
Mikheil DM Deletion of gene encoding methyltransferase (gidB) confers high-level antimicrobial resistance in Salmonella. J Antibiot (Tokyo) 22318332
Guymon R Influence of phylogeny on posttranscriptional modification of rRNA in thermophilic prokaryotes: the complete modification map of 16S rRNA of Thermus thermophilus. Biochemistry 16605256
Sivaraman J Structure of the 16S rRNA pseudouridine synthase RsuA bound to uracil and UMP. Nat Struct Biol 11953756
El Yacoubi B The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA. Nucleic Acids Res 19287007
Lin CA The Sua5 protein is essential for normal translational regulation in yeast. Mol Cell Biol 19884342
Jackman JE Doing it in reverse: 3'-to-5' polymerization by the Thg1 superfamily. RNA 22456265
Ozanick SG Conserved amino acids in each subunit of the heteroligomeric tRNA m1A58 Mtase from Saccharomyces cerevisiae contribute to tRNA binding. Nucleic Acids Res 17932071
Guelorget A Structural comparison of tRNA m(1)A58 methyltransferases revealed different molecular strategies to maintain their oligomeric architecture under extreme conditions. BMC Struct Biol 22168821
Sasarman F The 2-thiouridylase function of the human MTU1 (TRMU) enzyme is dispensable for mitochondrial translation. Hum Mol Genet 21890497
Harris KA YrdC exhibits properties expected of a subunit for a tRNA threonylcarbamoyl transferase. RNA 21775474
Deutsch C Biosynthesis of threonylcarbamoyl adenosine (t6A), a universal tRNA nucleoside. J Biol Chem 22378793
Brachat A Analysis of deletion phenotypes and GFP fusions of 21 novel Saccharomyces cerevisiae open reading frames. Yeast 10649453
Ishitani R Crystal structure of archaeosine tRNA-guanine transglycosylase. J Mol Biol 12054814
Ishitani R Alternative tertiary structure of tRNA for recognition by a posttranscriptional modification enzyme. Cell 12732145
Christian T Catalysis by the second class of tRNA(m1G37) methyl transferase requires a conserved proline. Biochemistry 16768442
Goto-Ito S Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation. Nat Struct Mol Biol 19749755
Kuratani M Crystal structure and mutational study of a unique SpoU family archaeal methylase that forms 2'-O-methylcytidine at position 56 of tRNA. J Mol Biol 18068186
Renalier MH The Cm56 tRNA modification in archaea is catalyzed either by a specific 2'-O-methylase, or a C/D sRNP. RNA 15987815
Walbott H The crystal structure of Pyrococcus abyssi tRNA (uracil-54, C5)-methyltransferase provides insights into its tRNA specificity. Nucleic Acids Res 18653523
Urbonavicius J Acquisition of a bacterial RumA-type tRNA(uracil-54, C5)-methyltransferase by Archaea through an ancient horizontal gene transfer. Mol Microbiol 18069966
Hecker A The universal Kae1 protein and the associated Bud32 kinase (PRPK), a mysterious protein couple probably essential for genome maintenance in Archaea and Eukarya. Biochem Soc Trans 19143597
Haile JD The activity of an ancient atypical protein kinase is stimulated by ADP-ribose in vitro. Arch Biochem Biophys 21527241
Facchin S Structure-function analysis of yeast piD261/Bud32, an atypical protein kinase essential for normal cell life. Biochem J 12023889
Henras AK Cbf5p, the putative pseudouridine synthase of H/ACA-type snoRNPs, can form a complex with Gar1p and Nop10p in absence of Nhp2p and box H/ACA snoRNAs. RNA 15388873
Liang B Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA. Nat Struct Mol Biol 19478803
Mao DY Atomic structure of the KEOPS complex: an ancient protein kinase-containing molecular machine. Mol Cell 18951093
Downey M A genome-wide screen identifies the evolutionarily conserved KEOPS complex as a telomere regulator. Cell 16564010
Jain R Active site mapping and substrate specificity of bacterial Hen1, a manganese-dependent 3' terminal RNA ribose 2'O-methyltransferase. RNA 21205839
Mui Chan C Structural and biochemical insights into 2'-O-methylation at the 3'-terminal nucleotide of RNA by Hen1. Proc Natl Acad Sci U S A 19822745
Jain R Bacterial Hen1 is a 3' terminal RNA ribose 2'-O-methyltransferase component of a bacterial RNA repair cassette. RNA 20007328
Zhang C Probing the substrate specificity of the bacterial Pnkp/Hen1 RNA repair system using synthetic RNAs. RNA 22190744
Chan CM Reconstituting bacterial RNA repair and modification in vitro. Science 19815768
Hecker A An archaeal orthologue of the universal protein Kae1 is an iron metalloprotein which exhibits atypical DNA-binding properties and apurinic-endonuclease activity in vitro. Nucleic Acids Res 17766251
Srinivasan M The highly conserved KEOPS/EKC complex is essential for a universal tRNA modification, t6A. EMBO J 21183954
El Yacoubi B A role for the universal Kae1/Qri7/YgjD (COG0533) family in tRNA modification. EMBO J 21285948
Daugeron MC Gcn4 misregulation reveals a direct role for the evolutionary conserved EKC/KEOPS in the t6A modification of tRNAs. Nucleic Acids Res 21459853
Hecker A Structure of the archaeal Kae1/Bud32 fusion protein MJ1130: a model for the eukaryotic EKC/KEOPS subcomplex. EMBO J 19172740
Anton BP Functional characterization of the YmcB and YqeV tRNA methylthiotransferases of Bacillus subtilis. Nucleic Acids Res 20472640
Hernandez HL MiaB, a bifunctional radical-S-adenosylmethionine enzyme involved in the thiolation and methylation of tRNA, contains two essential [4Fe-4S] clusters. Biochemistry 17407324
Pierrel F MiaB protein from Thermotoga maritima. Characterization of an extremely thermophilic tRNA-methylthiotransferase. J Biol Chem 12766153
Atta M S-Adenosylmethionine-dependent radical-based modification of biological macromolecules. Curr Opin Struct Biol 20951571
Golovko A Identification of a tRNA isopentenyltransferase gene from Arabidopsis thaliana. Plant Mol Biol 11999372
Miyawaki K Roles of Arabidopsis ATP/ADP isopentenyltransferases and tRNA isopentenyltransferases in cytokinin biosynthesis. Proc Natl Acad Sci U S A 17062755
Golovko A Cloning of a human tRNA isopentenyl transferase. Gene 11111046
Arragain S Identification of eukaryotic and prokaryotic methylthiotransferase for biosynthesis of 2-methylthio-N6-threonylcarbamoyladenosine in tRNA. J Biol Chem 20584901
Wei FY Deficit of tRNA(Lys) modification by Cdkal1 causes the development of type 2 diabetes in mice. J Clin Invest 21841312
Wurm JP Backbone resonance assignments of the 48 kDa dimeric putative 18S rRNA-methyltransferase Nep1 from Methanocaldococcus jannaschii. Biomol NMR Assign 19779849
Wurm JP The ribosome assembly factor Nep1 responsible for Bowen-Conradi syndrome is a pseudouridine-N1-specific methyltransferase. Nucleic Acids Res 20047967
Auxilien S Specificity shifts in the rRNA and tRNA nucleotide targets of archaeal and bacterial m5U methyltransferases. RNA 21051506
Oberto J Qri7/OSGEPL, the mitochondrial version of the universal Kae1/YgjD protein, is essential for mitochondrial genome maintenance. Nucleic Acids Res 19578062
Douthwaite S Interaction of the tylosin-resistance methyltransferase RlmA II at its rRNA target differs from the orthologue RlmA I. J Mol Biol 18406425
Lebars I Recognition elements in rRNA for the tylosin resistance methyltransferase RlmA(II). J Mol Biol 17673230
Douthwaite S The tylosin-resistance methyltransferase RlmA(II) (TlrB) modifies the N-1 position of 23S rRNA nucleotide G748. J Mol Biol 15046978
Desmolaize B A single methyltransferase YefA (RlmCD) catalyses both m5U747 and m5U1939 modifications in Bacillus subtilis 23S rRNA. Nucleic Acids Res 21824914
Niu L Cloning and characterization of the 23S RNA pseudouridine 2633 synthase from Bacillus subtilis. Biochemistry 9888802
Tu C Structural basis for binding of RNA and cofactor by a KsgA methyltransferase. Structure 19278652
Richter U A mitochondrial rRNA dimethyladenosine methyltransferase in Arabidopsis. Plant J 19929881
Cotney J Evidence for an early gene duplication event in the evolution of the mitochondrial transcription factor B family and maintenance of rRNA methyltransferase activity in human mtTFB1 and mtTFB2. J Mol Evol 17031457
O'Farrell HC Binding of adenosine-based ligands to the MjDim1 rRNA methyltransferase: implications for reaction mechanism and drug design. Biochemistry 20163168
Demirci H Structural rearrangements in the active site of the Thermus thermophilus 16S rRNA methyltransferase KsgA in a binary complex with 5'-methylthioadenosine. J Mol Biol 19285505
Ochi K Inactivation of KsgA, a 16S rRNA methyltransferase, causes vigorous emergence of mutants with high-level kasugamycin resistance. Antimicrob Agents Chemother 19001112
Demirci H Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus. RNA 20558545
Demirci H Crystal structure of the Thermus thermophilus 16 S rRNA methyltransferase RsmC in complex with cofactor and substrate guanosine. J Biol Chem 18667428
Kumar A Structural and functional characterization of Rv2966c protein reveals an RsmD-like methyltransferase from Mycobacterium tuberculosis and the role of its N-terminal domain in target recognition. J Biol Chem 21474448
Gregory ST Structural and functional studies of the Thermus thermophilus 16S rRNA methyltransferase RsmG. RNA 19622680
Kuratani M Crystal structure of Sulfolobus tokodaii Sua5 complexed with L-threonine and AMPPNP. Proteins 21538543
Agari Y X-ray crystal structure of a hypothetical Sua5 protein from Sulfolobus tokodaii strain 7. Proteins 18004774
Kuratani M Crystal structure of tRNA adenosine deaminase (TadA) from Aquifex aeolicus. J Biol Chem 15677468
Losey HC Crystal structure of Staphylococcus aureus tRNA adenosine deaminase TadA in complex with RNA. Nat Struct Mol Biol 16415880
Reuter K Sequence analysis and overexpression of the Zymomonas mobilis tgt gene encoding tRNA-guanine transglycosylase: purification and biochemical characterization of the enzyme. J Bacteriol 7665516
Romier C Crystal structure of tRNA-guanine transglycosylase: RNA modification by base exchange. EMBO J 8654383
Gradler U Mutagenesis and crystallographic studies of Zymomonas mobilis tRNA-guanine transglycosylase to elucidate the role of serine 103 for enzymatic activity. FEBS Lett 10413112
Awai T Substrate tRNA recognition mechanism of a multisite-specific tRNA methyltransferase, Aquifex aeolicus Trm1, based on the X-ray crystal structure. J Biol Chem 21844194
Awai T 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 19491098
Ihsanawati Crystal structure of tRNA N2,N2-guanosine dimethyltransferase Trm1 from Pyrococcus horikoshii. J Mol Biol 18789948
Kuratani M Crystal structure of Methanocaldococcus jannaschii Trm4 complexed with sinefungin. J Mol Biol 20600111
Gabant G THUMP from archaeal tRNA:m22G10 methyltransferase, a genuine autonomously folding domain. Nucleic Acids Res 16687654
Armengaud J N2-methylation of guanosine at position 10 in tRNA is catalyzed by a THUMP domain-containing, S-adenosylmethionine-dependent methyltransferase, conserved in Archaea and Eukaryota. J Biol Chem 15210688
Benitez-Paez A YibK is the 2'-O-methyltransferase TrmL that modifies the wobble nucleotide in Escherichia coli tRNA(Leu) isoacceptors. RNA 20855540
Roovers M The open reading frame TTC1157 of Thermus thermophilus HB27 encodes the methyltransferase forming N(2)-methylguanosine at position 6 in tRNA. RNA 22337946
Phannachet K Conformational change of pseudouridine 55 synthase upon its association with RNA substrate. Nucleic Acids Res 14990747
Handford JI Conserved network of proteins essential for bacterial viability. J Bacteriol 19376873
Hashimoto C Effects on transcription of mutations in ygjD, yeaZ, and yjeE genes, which are involved in a universal tRNA modification in Escherichia coli. J Bacteriol 21873492
Aydin I Structural analysis of the essential resuscitation promoting factor YeaZ suggests a mechanism of nucleotide regulation through dimer reorganization. PLoS One 21858042
Xu Q Structure of an essential bacterial protein YeaZ (TM0874) from Thermotoga maritima at 2.5 A resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun 20944216
Fu TM The structure of the hypothetical protein smu.1377c from Streptococcus mutans suggests a role in tRNA modification. Acta Crystallogr Sect F Struct Biol Cryst Commun 20606270
Karst JC The ATPase activity of an 'essential' Bacillus subtilis enzyme, YdiB, is required for its cellular function and is modulated by oligomerization. Microbiology 19246765
Mangat CS Known bioactive small molecules probe the function of a widely conserved but enigmatic bacterial ATPase, YjeE. Chem Biol 19101473
Brown ED Conserved P-loop GTPases of unknown function in bacteria: an emerging and vital ensemble in bacterial physiology. Biochem Cell Biol 16333325
Qian Q The methyl group of the N6-methyl-N6-threonylcarbamoyladenosine in tRNA of Escherichia coli modestly improves the efficiency of the tRNA. J Bacteriol 9537379
Phillips G Biosynthesis of 7-deazaguanosine-modified tRNA nucleosides: a new role for GTP cyclohydrolase I. J Bacteriol 18931107
McCarty RM The deazapurine biosynthetic pathway revealed: in vitro enzymatic synthesis of PreQ(0) from guanosine 5'-triphosphate in four steps. Biochemistry 19354300
Gaur R Genetic analysis identifies a function for the queC (ybaX) gene product at an initial step in the queuosine biosynthetic pathway in Escherichia coli. J Bacteriol 16199558
Cicmil N Crystal structure of QueC from Bacillus subtilis: an enzyme involved in preQ1 biosynthesis. Proteins 18491386
McCarty RM Escherichia coli QueD is a 6-carboxy-5,6,7,8-tetrahydropterin synthase. Biochemistry 19231875
Phillips G Functional promiscuity of the COG0720 family. ACS Chem Biol 21999246
Cicmil N Crystallization and preliminary X-ray characterization of queD from Bacillus subtilis, an enzyme involved in queuosine biosynthesis. Acta Crystallogr Sect F Struct Biol Cryst Commun 18259064
Sekiya T Identification of BMP and activin membrane-bound inhibitor (BAMBI), an inhibitor of transforming growth factor-beta signaling, as a target of the beta-catenin pathway in colorectal tumor cells. J Biol Chem 14660579
Lee BW Mechanistic studies of Bacillus subtilis QueF, the nitrile oxidoreductase involved in queuosine biosynthesis. Biochemistry 17929836
Droogmans L Cloning and characterization of tRNA (m1A58) methyltransferase (TrmI) from Thermus thermophilus HB27, a protein required for cell growth at extreme temperatures. Nucleic Acids Res 12682365
Barraud P Crystal structure of Thermus thermophilus tRNA m1A58 methyltransferase and biophysical characterization of its interaction with tRNA. J Mol Biol 18262540
Varshney U Mycobacterium tuberculosis Rv2118c codes for a single-component homotetrameric m1A58 tRNA methyltransferase. Nucleic Acids Res 14960715
Gupta A Crystal structure of Rv2118c: an AdoMet-dependent methyltransferase from Mycobacterium tuberculosis H37Rv. J Mol Biol 11554794
Pastore C 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 22065580
Fu D Human AlkB homolog ABH8 Is a tRNA methyltransferase required for wobble uridine modification and DNA damage survival. Mol Cell Biol 20308323
van den Born E ALKBH8-mediated formation of a novel diastereomeric pair of wobble nucleosides in mammalian tRNA. Nat Commun 21285950
Fu Y The AlkB domain of mammalian ABH8 catalyzes hydroxylation of 5-methoxycarbonylmethyluridine at the wobble position of tRNA. Angew Chem Int Ed Engl 20583019
Noma A Actin-binding protein ABP140 is a methyltransferase for 3-methylcytidine at position 32 of tRNAs in Saccharomyces cerevisiae. RNA 21518805
D'Silva S A domain of the actin binding protein Abp140 is the yeast methyltransferase responsible for 3-methylcytidine modification in the tRNA anti-codon loop. RNA 21518804
Zegers I Crystal structure of Bacillus subtilis TrmB, the tRNA (m7G46) methyltransferase. Nucleic Acids Res 16600901
Songe-Moller L Mammalian ALKBH8 possesses tRNA methyltransferase activity required for the biogenesis of multiple wobble uridine modifications implicated in translational decoding. Mol Cell Biol 20123966
Huang B An early step in wobble uridine tRNA modification requires the Elongator complex. RNA 15769872
Yamada-Okabe T Isolation and characterization of a human cDNA for mRNA 5'-capping enzyme. Nucleic Acids Res 9512541
Tsukamoto T Cloning and characterization of two human cDNAs encoding the mRNA capping enzyme. Biochem Biophys Res Commun 9473487
Pillutla RC Recombinant human mRNA cap methyltransferase binds capping enzyme/RNA polymerase IIo complexes. J Biol Chem 9705270
Chu C Structure of the guanylyltransferase domain of human mRNA capping enzyme. Proc Natl Acad Sci U S A 21636784
Tsukamoto T Cloning and characterization of three human cDNAs encoding mRNA (guanine-7-)-methyltransferase, an mRNA cap methylase. Biochem Biophys Res Commun 9790902
Saha N Characterization of human, Schizosaccharomyces pombe, and Candida albicans mRNA cap methyltransferases and complete replacement of the yeast capping apparatus by mammalian enzymes. J Biol Chem 10347220
Wen Y Cap methyltransferase selective binding and methylation of GpppG-RNA are stimulated by importin-alpha. Genes Dev 11114884
Shafer B Human mRNA cap methyltransferase: alternative nuclear localization signal motifs ensure nuclear localization required for viability. Mol Cell Biol 15767670
Gonatopoulos-Pournatzis T RAM/Fam103a1 is required for mRNA cap methylation. Mol Cell 22099306
Hausmann S Genetic and biochemical analysis of yeast and human cap trimethylguanosine synthase: functional overlap of 2,2,7-trimethylguanosine caps, small nuclear ribonucleoprotein components, pre-mRNA splicing factors, and RNA decay pathways. J Biol Chem 18775984
Monecke T Structure analysis of the conserved methyltransferase domain of human trimethylguanosine synthase TGS1. Acta Crystallogr D Biol Crystallogr 19307714
Belanger F Characterization of hMTr1, a human Cap1 2'-O-ribose methyltransferase. J Biol Chem 20713356
Haline-Vaz T The human interferon-regulated ISG95 protein interacts with RNA polymerase II and shows methyltransferase activity. Biochem Biophys Res Commun 18533109
Monecke T Structural basis for m7G-cap hypermethylation of small nuclear, small nucleolar and telomerase RNA by the dimethyltransferase TGS1. Nucleic Acids Res 19386620
Werner M 2'-O-ribose methylation of cap2 in human: function and evolution in a horizontally mobile family. Nucleic Acids Res 21310715
Jeronimo C Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme. Mol Cell 17643375
Xue Y A capping-independent function of MePCE in stabilizing 7SK snRNA and facilitating the assembly of 7SK snRNP. Nucleic Acids Res 19906723
Gu M Insights into the structure, mechanism, and regulation of scavenger mRNA decapping activity. Mol Cell 15068804
Liu H The scavenger mRNA decapping enzyme DcpS is a member of the HIT family of pyrophosphatases. EMBO J 12198172
Kwasnicka DA Coordinate expression of NADPH-dependent flavin reductase, Fre-1, and Hint-related 7meGMP-directed hydrolase, DCS-1. J Biol Chem 12871939
Wang Z Functional link between the mammalian exosome and mRNA decapping. Cell 11747811
van Dijk E DcpS can act in the 5'-3' mRNA decay pathway in addition to the 3'-5' pathway. Proc Natl Acad Sci U S A 14523240
Liu SW Functional analysis of mRNA scavenger decapping enzymes. RNA 15273322
Treede I The avilamycin resistance determinants AviRa and AviRb methylate 23S rRNA at the guanosine 2535 base and the uridine 2479 ribose. Mol Microbiol 12828631
Mosbacher TG Crystal structure of the avilamycin resistance-conferring methyltransferase AviRa from Streptomyces viridochromogenes. J Mol Biol 12742024
Weitnauer G An ATP-binding cassette transporter and two rRNA methyltransferases are involved in resistance to avilamycin in the producer organism Streptomyces viridochromogenes Tu57. Antimicrob Agents Chemother 11181344
Mosbacher TG Structure and function of the antibiotic resistance-mediating methyltransferase AviRb from Streptomyces viridochromogenes. J Mol Biol 15581897
Monod M Sequence and properties of pIM13, a macrolide-lincosamide-streptogramin B resistance plasmid from Bacillus subtilis. J Bacteriol 3087948
Zhong P Substrate requirements for ErmC' methyltransferase activity. J Bacteriol 7543473
Gath A Family background of children with Down's syndrome and of children with a similar degree of mental retardation. Br J Psychiatry 2946350
Maravic G Alanine-scanning mutagenesis of the predicted rRNA-binding domain of ErmC' redefines the substrate-binding site and suggests a model for protein-RNA interactions. Nucleic Acids Res 12907737
Bussiere DE Crystal structure of ErmC', an rRNA methyltransferase which mediates antibiotic resistance in bacteria. Biochemistry 9585521
Schluckebier G The 2.2 A structure of the rRNA methyltransferase ErmC' and its complexes with cofactor and cofactor analogs: implications for the reaction mechanism. J Mol Biol 10366505
Trieu-Cuot P Nucleotide sequence of the erythromycin resistance gene of the conjugative transposon Tn1545. Nucleic Acids Res 2163525
Yu L Solution structure of an rRNA methyltransferase (ErmAM) that confers macrolide-lincosamide-streptogramin antibiotic resistance. Nat Struct Biol 9187657
Bercot B Plasmid-mediated 16S rRNA methylases among extended-spectrum beta-lactamase-producing Enterobacteriaceae isolates. Antimicrob Agents Chemother 18838598
Bibb MJ Nucleotide sequences encoding and promoting expression of three antibiotic resistance genes indigenous to Streptomyces. Mol Gen Genet 2987648
Dunstan MS Structure of the thiostrepton resistance methyltransferase.S-adenosyl-L-methionine complex and its interaction with ribosomal RNA. J Biol Chem 19369248
Bechthold A Overexpression of the thiostrepton-resistance gene from Streptomyces azureus in Escherichia coli and characterization of recognition sites of the 23S rRNA A1067 2'-methyltransferase in the guanosine triphosphatase center of 23S ribosomal RNA. Eur J Biochem 7925357
Husain N Structural basis for the methylation of G1405 in 16S rRNA by aminoglycoside resistance methyltransferase Sgm from an antibiotic producer: a diversity of active sites in m7G methyltransferases. Nucleic Acids Res 20194115
Kojic M Cloning and characterization of an aminoglycoside resistance determinant from Micromonospora zionensis. J Bacteriol 1447159
Savic M Critical residues for cofactor binding and catalytic activity in the aminoglycoside resistance methyltransferase Sgm. J Bacteriol 18586937
Yang H Crystallization and preliminary crystallographic analysis of nosiheptide-resistance methyltransferase from Streptomyces actuosus in complex with SAM. Acta Crystallogr Sect F Struct Biol Cryst Commun 20445264
Goto-Ito S Crystal structure of archaeal tRNA(m(1)G37)methyltransferase aTrm5. Proteins 18384044
Pitsch S. Reliable Chemical Synthesis of Oligoribonucleotides (RNA) with 2′-O-[(Triisopropylsilyl)oxy]methyl(2′-O-tom)-Protected Phosphoramidites Helvetica Chimica Acta 10.1002/1522-2675(20011219)84:12<3773::AID-HLCA377
Chaix C. The use of labilebaseprotectinggroups in oligoribonucleotidesynthesis Tetrahedron Letters 10.1016/S0040-4039(01)80326-9
Reddy M.P. Methylaminedeprotectionprovidesincreasedyield of oligoribonucleotides Tetrahedron Letters 10.1016/0040-4039(95)01953-F
Bogdan F. M. The Synthesis of Allyl- and Ailyioxycarbonyl-Protected RNA Phosphoramidites. Useful Reagents for Solid-Phase Synthesis of RNAs with Base-Labile Modifications Tetrahedron Letters 10.1016/S0040-4039(98)00157-9
Karpeisky A. 2′-O-Methyl Thiomethyl Modifications in Hammerhead Ribozymes Nucleosides and Nucleotides 10.1080/07328319708006114
Reddy M.P. Ultrafast Cleavage and Deprotection of Oligonucleotides Synthesis and Use of CAc Derivatives Nucleosides and Nucleotides 10.1080/07328319708006236
Martin P. Ein neuer Zugang zu 2’-O-Alkylribonucleosiden und Eigenschaften deren Oligonucleotide Helvetica Chimica Acta 10.1002/hlca.19950780219
Bhattacharya B. K. A Facile Synthesis of the Phosphoramidites of 2-N-Methyl-2′- deoxy (or 2′-O-allyl)-ψ-isocytidine, 1, 3-Dimethyl-2′-deoxy-ψ-uridine and N1- Methyl-2′-O-allyl-ψ-uridine as Synthons Suitable for Oligonuc Nucleosides and Nucleotides 10.1080/15257779408009476
Ohgi T A new RNA synthetic method with a 2'-O-(2-cyanoethoxymethyl) protecting group. Org Lett 16048321
Hyde RM Antiviral amphipathic oligo- and polyribonucleotides: analogue development and biological studies. J Med Chem 12723951
Shohda K Synthesis and properties of 2'-O-methyl-2-thiouridine and oligoribonucleotides containing 2'-O-methyl-2-thiouridine. Bioorg Med Chem Lett 10969970
Porcher S. Synthesis of modified nucleosides for the incorporation into tRNAs
Porcher S. Chemical Approach for the Study of the ‘Kissing Complex’ of Moloney murine leukaemia Virus Helvetica Chimica Acta 10.1002/hlca.200890133
Atta M The methylthiolation reaction mediated by the Radical-SAM enzymes. Biochim Biophys Acta 22178611
Takeda H Identification of Aquifex aeolicus tRNA (m2(2G26) methyltransferase gene. Nucleic Acids Res Suppl. 12903189
Mitsui T Fluorescent properties of an unnatural nucleobase, 2-amino-6-(2-thienyl)purine, in DNA and RNA fragments. Nucleic Acids Symp Ser (Oxf) 17150745
Awai T Aquifex aeolicus Trm1[tRNA (m2(2)G26) methyltransferase] has a novel recognition mechanism of the substrate RNA. Nucleic Acids Symp Ser (Oxf) 17150754
Motorin Y RNA nucleotide methylation. Wiley Interdiscip Rev RNA 21823225
McDonald MK The Handling of the Mechanistic Probe 5-Fluorouridine by the Pseudouridine Synthase TruA and Its Consistency with the Handling of the Same Probe by the Pseudouridine Synthases TruB and RluA. Biochemistry 21142053
O'Farrell HC Crystal structure of KsgA, a universally conserved rRNA adenine dimethyltransferase in Escherichia coli. J Mol Biol 15136037
Chikwana VM Structural Basis of Biological Nitrile Reduction. J Biol Chem 22787148
Duan J Structural mechanism of substrate RNA recruitment in H/ACA RNA-guided pseudouridine synthase. Mol Cell 19481523
Kagawa N cAMP-dependent transcription of the human CYP21B (P-450C21) gene requires a cis-regulatory element distinct from the consensus cAMP-regulatory element. J Biol Chem 2162843
Muller S Identification of determinants in the protein partners aCBF5 and aNOP10 necessary for the tRNA:Psi55-synthase and RNA-guided RNA:Psi-synthase activities. Nucleic Acids Res 17704128
Gurha P Differential roles of archaeal box H/ACA proteins in guide RNA-dependent and independent pseudouridine formation. RNA Biol 17993784
Blaby IK Pseudouridine formation in archaeal RNAs: The case of Haloferax volcanii. RNA 21628430
Torabi N Variants in SUP45 and TRM10 underlie natural variation in translation termination efficiency in Saccharomyces cerevisiae. PLoS Genet 21829385
Noma A Expanding role of the jumonji C domain as an RNA hydroxylase. J Biol Chem 20739293
Kato M Crystal structure of a novel JmjC-domain-containing protein, TYW5, involved in tRNA modification. Nucleic Acids Res 20972222
Walbott H The H/ACA RNP assembly factor SHQ1 functions as an RNA mimic. Genes Dev 22085966
Sakuno T Decapping reaction of mRNA requires Dcp1 in fission yeast: its characterization in different species from yeast to human. J Biochem 15671491
Hausmann S An essential function of Saccharomyces cerevisiae RNA triphosphatase Cet1 is to stabilize RNA guanylyltransferase Ceg1 against thermal inactivation. J Biol Chem 11463793
Kasprzak JM Molecular evolution of dihydrouridine synthases. BMC Bioinformatics 22741570
Rider LW Mechanism of dihydrouridine synthase 2 from yeast and the importance of modifications for efficient tRNA reduction. J Biol Chem 19139092
Chen C Elongator complex influences telomeric gene silencing and DNA damage response by its role in wobble uridine tRNA modification. PLoS Genet 21912530
Otero G Elongator, a multisubunit component of a novel RNA polymerase II holoenzyme for transcriptional elongation. Mol Cell 10024884
Galimand M Intrinsic resistance to aminoglycosides in Enterococcus faecium is conferred by the 16S rRNA m5C1404-specific methyltransferase EfmM. RNA 21159796
Rottman FM N6-adenosine methylation in mRNA: substrate specificity and enzyme complexity. Biochimie 7748945
Leach RA Expression of the mRNA (N6-adenosine)-methyltransferase S-adenosyl-L-methionine binding subunit mRNA in cultured cells. Int J Biochem Cell Biol 11470232
Bokar JA Purification and cDNA cloning of the AdoMet-binding subunit of the human mRNA (N6-adenosine)-methyltransferase. RNA 9409616
Maas S Identification and characterization of a human tRNA-specific adenosine deaminase related to the ADAR family of pre-mRNA editing enzymes. Proc Natl Acad Sci U S A 10430867
Liu J The human tRNA(m(2)(2)G(26))dimethyltransferase: functional expression and characterization of a cloned hTRM1 gene. Nucleic Acids Res 10982862
Brzezicha B 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 17071714
Squires JE Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA. Nucleic Acids Res 22344696
Squires JE Function and detection of 5-methylcytosine in eukaryotic RNA. Epigenomics 22122054
Goll MG Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2. Science 16424344
Dong A Structure of human DNMT2, an enigmatic DNA methyltransferase homolog that displays denaturant-resistant binding to DNA. Nucleic Acids Res 11139614
Benitez-Paez A The Escherichia coli RlmN methyltransferase is a dual-specificity enzyme that modifies both rRNA and tRNA and controls translational accuracy. RNA 22891362
Yanagawa H A novel minimum ribozyme with oxidoreduction activity. Biochemistry 2271669
Kupfer PA Synthesis, base pairing properties and trans-lesion synthesis by reverse transcriptases of oligoribonucleotides containing the oxidatively damaged base 5-hydroxycytidine. Nucleic Acids Res 21852326
Dumelin CE Discovery and biological characterization of geranylated RNA in bacteria. Nat Chem Biol 22983156
Chen P A gain of function mutation in a protein mediates production of novel modified nucleosides. EMBO J 15861125
Kim IY Escherichia coli mutant SELD enzymes. The cysteine 17 residue is essential for selenophosphate formation from ATP and selenide. J Biol Chem 1527085
Veres Z Selenophosphate synthetase. Enzyme properties and catalytic reaction. J Biol Chem 8144648
Lacourciere GM Biosynthesis of selenophosphate. Biofactors 10609888
Li X A human mitochondrial GTP binding protein related to tRNA modification may modulate phenotypic expression of the deafness-associated mitochondrial 12S rRNA mutation. Mol Cell Biol 12370316
Kitamura A Characterization and structure of the Aquifex aeolicus protein DUF752: a bacterial tRNA-methyltransferase (MnmC2) functioning without the usually fused oxidase domain (MnmC1). J Biol Chem 23091054
McCusker KP Covalent Intermediate in the Catalytic Mechanism of the Radical S-Adenosyl-l-methionine Methyl Synthase RlmN Trapped by Mutagenesis. J Am Chem Soc 23088750
Auxilien S The Human tRNA m ( 5) C methyltransferase Misu is multisite-specific. RNA Biol 22995836
Xhemalce B Human RNA Methyltransferase BCDIN3D Regulates MicroRNA Processing. Cell 23063121
Hamdane D FAD/Folate-Dependent tRNA Methyltransferase: Flavin as a new methyl-transfer agent. J Am Chem Soc 23157377
Bousquet-Antonelli C Rrp8p is a yeast nucleolar protein functionally linked to Gar1p and involved in pre-rRNA cleavage at site A2. RNA 10864042
Leulliot N The box H/ACA RNP assembly factor Naf1p contains a domain homologous to Gar1p mediating its interaction with Cbf5p. J Mol Biol 17612558
Agarwala SD RNA methylation by the MIS complex regulates a cell fate decision in yeast. PLoS Genet 22685417
Ollagnier-de-Choudens S SufA/IscA: reactivity studies of a class of scaffold proteins involved in [Fe-S] cluster assembly. J Biol Inorg Chem 15278785
Lundgren HK Structural alterations of the cysteine desulfurase IscS of Salmonella enterica serovar Typhimurium reveal substrate specificity of IscS in tRNA thiolation. J Bacteriol 16585765
Saito H Cloning and mapping of a human novel cDNA (NHP2L1) that encodes a protein highly homologous to yeast nuclear protein NHP2. Cytogenet Cell Genet 8978773
Kiss T Biogenesis and intranuclear trafficking of human box C/D and H/ACA RNPs. Cold Spring Harb Symp Quant Biol 17381323
Muhlenhoff U Functional characterization of the eukaryotic cysteine desulfurase Nfs1p from Saccharomyces cerevisiae. J Biol Chem 15220327
Pandey A Isd11p protein activates the mitochondrial cysteine desulfurase Nfs1p protein. J Biol Chem 21908622
Koo BK Structure of H/ACA RNP protein Nhp2p reveals cis/trans isomerization of a conserved proline at the RNA and Nop10 binding interface. J Mol Biol 21708174
Peifer C Yeast Rrp8p, a novel methyltransferase responsible for m1A 645 base modification of 25S rRNA. Nucleic Acids Res 23180764
Yamagami R The tRNA recognition mechanism of folate/FAD-dependent tRNA methyltransferase (TrmFO). J Biol Chem 23095745
Guy MP Yeast Trm7 interacts with distinct proteins for critical modifications of the tRNAPhe anticodon loop. RNA 22912484
Zheng G ALKBH5 Is a Mammalian RNA Demethylase that Impacts RNA Metabolism and Mouse Fertility. Mol Cell 23177736
Thalhammer A Human AlkB homologue 5 is a nuclear 2-oxoglutarate dependent oxygenase and a direct target of hypoxia-inducible factor 1alpha (HIF-1alpha). PLoS One 21264265
Tkaczuk KL Trm13p, the tRNA:Xm4 modification enzyme from Saccharomyces cerevisiae is a member of the Rossmann-fold MTase superfamily: prediction of structure and active site. J Mol Model 19697067
Sorensen MA Over expression of a tRNA(Leu) isoacceptor changes charging pattern of leucine tRNAs and reveals new codon reading. J Mol Biol 16236318
Griffey RH 15N-labeled tRNA. Identification of 4-thiouridine in Escherichia coli tRNASer1 and tRNATyr2 by 1H-15N two-dimensional NMR spectroscopy. J Biol Chem 3638307
Fislage M Crystal structures of the tRNA:m2G6 methyltransferase Trm14/TrmN from two domains of life. Nucleic Acids Res 22362751
Schweizer MP The isolation and characterization of N-[9-(beta-D-ribofuranosyl)-purin-6-ylcarbamoyl]glycine from yeast transfer RNA. Biochem Biophys Res Commun 5503779
Patton JR Pseudouridine modification in Caenorhabditis elegans spliceosomal snRNAs: unique modifications are found in regions involved in snRNA-snRNA interactions. BMC Mol Biol 16236171
Meier UT Pseudouridylation goes regulatory. EMBO J 21206510
Wu G U2 snRNA is inducibly pseudouridylated at novel sites by Pus7p and snR81 RNP. EMBO J 21131909
Patton JR Caenorhabditis elegans pseudouridine synthase 1 activity in vivo: tRNA is a substrate, but not U2 small nuclear RNA. Biochem J 12597772
Chujo T Trmt61B is a methyltransferase responsible for 1-methyladenosine at position 58 of human mitochondrial tRNAs. RNA 23097428
Miyauchi K A cyclic form of N(6)-threonylcarbamoyladenosine as a widely distributed tRNA hypermodification. Nat Chem Biol 23242255
Vilardo E A subcomplex of human mitochondrial RNase P is a bifunctional methyltransferase--extensive moonlighting in mitochondrial tRNA biogenesis. Nucleic Acids Res 23042678
Ishida K Pseudouridine at position 55 in tRNA controls the contents of other modified nucleotides for low-temperature adaptation in the extreme-thermophilic eubacterium Thermus thermophilus. Nucleic Acids Res 21097467
Larsen LH Identification and characterization of the Thermus thermophilus 5-methylcytidine (m5C) methyltransferase modifying 23 S ribosomal RNA (rRNA) base C1942. J Biol Chem 22711535
Savic M Determination of the target nucleosides for members of two families of 16S rRNA methyltransferases that confer resistance to partially overlapping groups of aminoglycoside antibiotics. Nucleic Acids Res 19589804
Pioszak AA Structures of a putative RNA 5-methyluridine methyltransferase, Thermus thermophilus TTHA1280, and its complex with S-adenosyl-L-homocysteine. Acta Crystallogr Sect F Struct Biol Cryst Commun 16511182
Shisler KA Emerging themes in radical SAM chemistry. Curr Opin Struct Biol 23141873
Golovina AY The last rRNA methyltransferase of E. coli revealed: the yhiR gene encodes adenine-N6 methyltransferase specific for modification of A2030 of 23S ribosomal RNA. RNA 22847818
Matsugi J Characterization of a B. subtilis minor isoleucine tRNA deduced from tDNA having a methionine anticodon CAT. J Biochem 8743586
Yamazaki S Characterization of a whole set of tRNA molecules in an aerobic hyper-thermophilic Crenarchaeon, Aeropyrum pernix K1. DNA Res 16769697
Randau L The complete set of tRNA species in Nanoarchaeum equitans. FEBS Lett 15893316
Wang C Loss of a universal tRNA feature. J Bacteriol 17172343
Esseiva AC Mitochondrial tRNA import in Toxoplasma gondii. J Biol Chem 15280394
Sunny Sharma Identification of a novel methyltransferase, Bmt2, responsible for the N-1-methyl-adenosine base modification of 25S rRNA in Saccharomyces cerevisiae Nucleic Acids Res 23558746
Plotnikova A Mechanistic insights into small RNA recognition and modification by the HEN1 methyltransferase. Biochem J 23621770
Fu Y FTO-mediated formation of N(6)-hydroxymethyladenosine and N(6)-formyladenosine in mammalian RNA. Nat Commun 23653210
Jia G N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat Chem Biol 22002720
Han Z Crystal structure of the FTO protein reveals basis for its substrate specificity. Nature 20376003
Kim J Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function. Nature 23676670
Byrne RT S-Adenosyl-S-carboxymethyl-L-homocysteine: a novel cofactor found in the putative tRNA-modifying enzyme CmoA. Acta Crystallogr D Biol Crystallogr 23695253
Voorhees RM The structural basis for specific decoding of AUA by isoleucine tRNA on the ribosome. Nat Struct Mol Biol 23542153
Kamalampeta R tRNA binding, positioning and modification by the pseudouridine synthase Pus10. J Mol Biol 23743107
Liu RJ The tRNA recognition mechanism of the minimalist SPOUT methyltransferase, TrmL. Nucleic Acids Res 23804755
Swinehart WE Unexpected expansion of tRNA substrate recognition by the yeast m1G9 methyltransferase Trm10. RNA 23793893
Christian T Conservation of structure and mechanism by Trm5 enzymes. RNA 23887145
Hori H Identification and characterization of tRNA (Gm18) methyltransferase from Thermus thermophilus HB8: domain structure and conserved amino acid sequence motifs. Genes Cells 11918670
Hori H Substrate recognition of tRNA (Guanosine-2'-)-methyltransferase from Thermus thermophilus HB27. J Biol Chem 9748240
Nureki O Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme. Structure 15062082
Ochi A The catalytic domain of topological knot tRNA methyltransferase (TrmH) discriminates between substrate tRNA and non-substrate tRNA via an induced-fit process. J Biol Chem 23867454
Chen M Structure of dihydrouridine synthase C (DusC) from Escherichia coli. Acta Crystallogr Sect F Struct Biol Cryst Commun 23908023
Sharma S Yeast Nop2 and Rcm1 methylate C2870 and C2278 of the 25S rRNA, respectively. Nucleic Acids Res 23913415
Sardana R The methyltransferase adaptor protein Trm112 is involved in biogenesis of both ribosomal subunits. Mol Biol Cell 22956767
Punekar AS Structural and functional insights into the molecular mechanism of rRNA m6A methyltransferase RlmJ. Nucleic Acids Res 23945937
Noon KR Influence of temperature on tRNA modification in archaea: Methanococcoides burtonii (optimum growth temperature [Topt], 23 degrees C) and Stetteria hydrogenophila (Topt, 95 degrees C). J Bacteriol 12949100
Shao Z Crystal structure of tRNA m1G9 methyltransferase Trm10: insight into the catalytic mechanism and recognition of tRNA substrate Nucleic Acids Res. 24081582
Rodriguez V Structure-function analysis of human TYW2 enzyme required for the biosynthesis of a highly modified Wybutosine (yW) base in phenylalanine-tRNA. PLoS One 22761755
Ghosh SK A small RNA derived from RNA coactivator SRA blocks steroid receptor signaling via inhibition of Pus1p-mediated pseudouridylation of SRA: evidence of a novel RNA binding domain in the N-terminus of steroid receptors. Biochemistry 22998747
Sibert BS Pseudouridine synthase 1: a site-specific synthase without strict sequence recognition requirements. Nucleic Acids Res 22102571
Sibert BS Partial activity is seen with many substitutions of highly conserved active site residues in human Pseudouridine synthase 1. RNA 18648068
Patton JR Mitochondrial myopathy and sideroblastic anemia (MLASA): missense mutation in the pseudouridine synthase 1 (PUS1) gene is associated with the loss of tRNA pseudouridylation. J Biol Chem 15772074
Czudnochowski N In Human Pseudouridine Synthase 1 (hPus1), a C-Terminal Helical Insert Blocks tRNA from Binding in the Same Orientation as in the Pus1 Bacterial Homologue TruA, Consistent with Their Different Target Selectivities. J Mol Biol 23707380
Helm M The presence of modified nucleotides is required for cloverleaf folding of a human mitochondrial tRNA. Nucleic Acids Res 9512533
Suzuki T Taurine as a constituent of mitochondrial tRNAs: new insights into the functions of taurine and human mitochondrial diseases. EMBO J 12456664
Yasukawa T Wobble modification deficiency in mutant tRNAs in patients with mitochondrial diseases. FEBS Lett 15893315
Brule H Effect of a mutation in the anticodon of human mitochondrial tRNAPro on its post-transcriptional modification pattern. Nucleic Acids Res 9421512
Messmer M Tertiary network in mammalian mitochondrial tRNAAsp revealed by solution probing and phylogeny. Nucleic Acids Res 19767615
Kirino Y Acquisition of the wobble modification in mitochondrial tRNALeu(CUN) bearing the G12300A mutation suppresses the MELAS molecular defect. Hum Mol Genet 16446307
Jones CN A disease-causing point mutation in human mitochondrial tRNAMet rsults in tRNA misfolding leading to defects in translational initiation and elongation. J Biol Chem 18835817
Kim J Structural basis for hypermodification of the wobble uridine in tRNA by bifunctional enzyme MnmC. BMC Struct Biol 23617613
Chan CT Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins. Nat Commun 22760636
Liu J A METTL3-METTL14 complex mediates mammalian nuclear RNA N-adenosine methylation. Nat Chem Biol 24316715
Mandal D Identification and codon reading properties of 5-cyanomethyl uridine, a new modified nucleoside found in the anticodon wobble position of mutant haloarchaeal isoleucine tRNAs. RNA 24344322
Sharma S Identification of novel methyltransferases, Bmt5 and Bmt6, responsible for the m3U methylations of 25S rRNA in Saccharomyces cerevisiae. Nucleic Acids Res 24335083
Friedt J An arginine-aspartate network in the active site of bacterial TruB is critical for catalyzing pseudouridine formation. Nucleic Acids Res 24371284
Moukadiri I The output of the tRNA modification pathways controlled by the Escherichia coli MnmEG and MnmC enzymes depends on the growth conditions and the tRNA species. Nucleic Acids Res 24293650
Aik W Structure of human RNA N6-methyladenine demethylase ALKBH5 provides insights into its mechanisms of nucleic acid recognition and demethylation. Nucleic Acids Res 24489119
Buchhaupt M Partial Methylation at Am100 in 18S rRNA of Baker's Yeast Reveals Ribosome Heterogeneity on the Level of Eukaryotic rRNA Modification. PLoS One 24586927
Feng C Crystal Structures of Human RNA Demethylase Alkbh5 Reveal Basis for Substrate Recognition. J Biol Chem 24616105
Nilsen TW Molecular biology. Internal mRNA methylation finally finds functions. Science 24626918
Fislage M SAXS analysis of the tRNA-modifying enzyme complex MnmE/MnmG reveals a novel interaction mode and GTP-induced oligomerization. Nucleic Acids Res 24634441
Dunkle JA Molecular recognition and modification of the 30S ribosome by the aminoglycoside-resistance methyltransferase NpmA. Proc Natl Acad Sci U S A 24717845
Kuchino Y Initiator tRNAs from archaebacteria show common unique sequence characteristics. Nature 6178978
Liu N Probing N6-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA. RNA 24141618
Xu C Structures of human ALKBH5 demethylase reveal a unique binding mode for specific single stranded m6A RNA demethylation. J Biol Chem 24778178
Tomikawa C Distinct tRNA modifications in the thermo-acidophilic archaeon, Thermoplasma acidophilum. FEBS Lett 24076028
Young AP Radical mediated ring formation in the biosynthesis of the hypermodified tRNA base wybutosine. Curr Opin Chem Biol 23856057
Young AP Pyruvate is the source of the two carbons that are required for formation of the imidazoline ring of 4-demethylwyosine. Biochemistry 22026549
Perche-Letuvee P 4-Demethylwyosine synthase from Pyrococcus abyssi is a radical-S-adenosyl-L-methionine enzyme with an additional [4Fe-4S](+2) cluster that interacts with the pyruvate co-substrate. J Biol Chem 23043105
Suzuki T A complete landscape of post-transcriptional modifications in mammalian mitochondrial tRNAs. Nucleic Acids Res 24831542
Nagao A Biogenesis of glutaminyl-mt tRNAGln in human mitochondria. Proc Natl Acad Sci U S A 19805282
Yokogawa T A novel cloverleaf structure found in mammalian mitochondrial tRNA(Ser) (UCN). Nucleic Acids Res 1840673
Auxilien S Archease from Pyrococcus abyssi improves substrate specificity and solubility of a tRNA m5C methyltransferase. J Biol Chem 17470432
Phillips G Discovery and characterization of an amidinotransferase involved in the modification of archaeal tRNA. J Biol Chem 20129918
Lauhon CT Mechanism of N6-threonylcarbamoyladenonsine (t(6)A) biosynthesis: isolation and characterization of the intermediate threonylcarbamoyl-AMP. Biochemistry 23072323
Heyman T Yeast serine isoacceptor tRNAs: variations of their content as a function of growth conditions and primary structure of the minor tRNA(Ser)GCU. FEBS Lett 8033992
Sauerwald A N6-Acetyladenosine: a new modified nucleoside from Methanopyrus kandleri tRNA. FEBS Lett 15907485
Lartigue C The flavoprotein Mcap0476 (RlmFO) catalyzes m5U1939 modification in Mycoplasma capricolum 23S rRNA. Nucleic Acids Res 24939895
Somme J Characterization of two homologous 2'-O-methyltransferases showing different specificities for their tRNA substrates. RNA 24951554
Shanmugam R The Dnmt2 RNA methyltransferase homolog of Geobacter sulfurreducens specifically methylates tRNA-Glu. Nucleic Acids Res 24711368
Bouvier D TtcA a new tRNA-thioltransferase with an Fe-S cluster. Nucleic Acids Res 24914049
Gillis D TRMT10A dysfunction is associated with abnormalities in glucose homeostasis, short stature and microcephaly. J Med Genet 25053765
Ito S A single acetylation of 18S rRNA is essential for biogenesis of the small ribosomal subunit in Saccharomyces cerevisiae. J Biol Chem 25086048
Kuiper EG Binding Induced RNA Conformational Changes Control Substrate Recognition and Catalysis by the Thiostrepton-resistance Methyltransferase (Tsr). J Biol Chem 25086036
Lee KW Assignment of 2'-O-methyltransferases to Modification Sites on the Mammalian Mitochondrial Large Subunit 16S rRNA. J Biol Chem 25074936
Kimura S Discovery of the beta-barrel-type RNA methyltransferase responsible for N6-methylation of N6-threonylcarbamoyladenosine in tRNAs. Nucleic Acids Res 25063302
Urbonavicius J Biosynthesis of wyosine derivatives in tRNA(Phe) of Archaea: role of a remarkable bifunctional tRNA(Phe):m1G/imG2 methyltransferase. RNA 24837075
Gigova A A cluster of methylations in the domain IV of 25S rRNA is required for ribosome stability. RNA 25125595
Moon HJ Trm4 and Nsun2 RNA:mC Methyltransferases Form Metabolite-Dependent, Covalent Adducts with Previously Methylated RNA. Biochemistry 25375641
Yuan S Methylation by NSun2 represses the levels and function of microRNA 125b. Mol Cell Biol 25047833
Tominaga T Structure of Saccharomyces cerevisiae mitochondrial Qri7 in complex with AMP. Acta Crystallogr F Struct Biol Commun 25084372
Letoquart J 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 25489090
Wurth L Hypermethylated-capped selenoprotein mRNAs in mammals. Nucleic Acids Res 25013170
Zhao X FTO-dependent demethylation of N6-methyladenosine regulates mRNA splicing and is required for adipogenesis. Cell Res 25412662
Wei Y Crystal and solution structures of methyltransferase RsmH provide basis for methylation of C1402 in 16S rRNA. J Struct Biol 22561317
Zhao M Purification, crystallization and preliminary crystallographic analysis of the 16S rRNA methyltransferase RsmI from Escherichia coli. Acta Crystallogr F Struct Biol Commun 25195904
Hamdane D Dynamics of RNA modification by a multi-site-specific tRNA methyltransferase. Nucleic Acids Res 25217588
Guelorget A Insights into the hyperthermostability and unusual region-specificity of archaeal Pyrococcus abyssi tRNA m1A57/58 methyltransferase. Nucleic Acids Res 20483913
Ito S Human NAT10 is an ATP-dependent RNA acetyltransferase responsible for N4-acetylcytidine formation in 18S rRNA. J Biol Chem 25411247
Taoka M RNA Cytidine Acetyltransferase of Small-Subunit Ribosomal RNA: Identification of Acetylation Sites and the Responsible Acetyltransferase in Fission Yeast, Schizosaccharomyces pombe. PLoS One 25402480
Huet T Steroid receptor RNA activator (SRA) modification by the human pseudouridine synthase 1 (hPus1p): RNA binding, activity, and atomic model. PLoS One 24722331
Glatt S Structure of the Kti11/Kti13 Heterodimer and Its Double Role in Modifications of tRNA and Eukaryotic Elongation Factor 2. Structure 25543256
Sun J Solution structure of Kti11p from Saccharomyces cerevisiae reveals a novel zinc-binding module. Biochemistry 15952786
Reddy DM Structure determination of two new amino acid-containing derivatives of adenosine from tRNA of thermophilic bacteria and archaea. Nucleic Acids Res 1280806
Schosserer M Methylation of ribosomal RNA by NSUN5 is a conserved mechanism modulating organismal lifespan. Nat Commun 25635753
Sharma S Yeast Kre33 and human NAT10 are conserved 18S rRNA cytosine acetyltransferases that modify tRNAs assisted by the adaptor Tan1/THUMPD1. Nucleic Acids Res 25653167
Glasser AL Presence and coding properties of 2'-O-methyl-5-carbamoylmethyluridine (ncm5Um) in the wobble position of the anticodon of tRNA(Leu) (U*AA) from brewer's yeast. FEBS Lett 1468572
Guy MP Conservation of an intricate circuit for crucial modifications of the tRNAPhe anticodon loop in eukaryotes. RNA 25404562
Szweykowska-Kulinska Z Intron-dependent formation of pseudouridines in the anticodon of Saccharomyces cerevisiae minor tRNA(Ile). EMBO J 7925304
Kim J Determinants of the CmoB carboxymethyl transferase utilized for selective tRNA wobble modification. Nucleic Acids Res 25855808
Tyagi K Protein degradation and dynamic tRNA thiolation fine-tune translation at elevated temperatures. Nucleic Acids Res 25870413
Johansson MJ Eukaryotic wobble uridine modifications promote a functionally redundant decoding system. Mol Cell Biol 18332122
Wittwer AJ Selenium-containing tRNA(Glu) and tRNA(Lys) from Escherichia coli: purification, codon specificity and translational activity. Biofactors 2679651
Kim S The Structure of Escherichia coli TcdA (Also Known As CsdL) Reveals a Novel Topology and Provides Insight into the tRNA Binding Surface Required for N-Threonylcarbamoyladenosine Dehydratase Activity. J Mol Biol 26101842
Lopez-Estepa M The crystal structure and small-angle X-ray analysis of CsdL/TcdA reveal a new tRNA binding motif in the MoeB/E1 superfamily. PLoS One 25897750
Bou-Nader C An extended dsRBD is required for post-transcriptional modification in human tRNAs. Nucleic Acids Res 26429968
Shaheen R Mutation in WDR4 impairs tRNA m(7)G46 methylation and causes a distinct form of microcephalic primordial dwarfism. Genome Biol 26416026
Finer-Moore J Crystal Structure of the Human tRNA mA58 Methyltransferase-tRNA Complex: Refolding of Substrate tRNA allows Access to the Methylation Target. J Mol Biol 26470919
Letoquart J Insights into molecular plasticity in protein complexes from Trm9-Trm112 tRNA modifying enzyme crystal structure. Nucleic Acids Res 26438534
Militello KT A map of 5-methylcytosine residues in Trypanosoma brucei tRNA revealed by sodium bisulfite sequencing. Mol Biochem Parasitol 24389163
Sakai Y Biogenesis and growth phase-dependent alteration of 5-methoxycarbonylmethoxyuridine in tRNA anticodons Nucleic Acids Res. 26681692
Kawamura T Multisite-specific archaeosine tRNA-guanine transglycosylase (ArcTGT) from Thermoplasma acidophilum, a thermo-acidophilic archaeon. Nucleic Acids Res. 26721388
Sitao Yin Substrate Recognition and Modification by the Nosiheptide Resistance Methyltransferase PLoS One. 4409310
Takuma H Substrate tRNA recognition mechanism of eubacterial tRNA (m1A58) methyltransferase (TrmI). J Biol Chem. 25593312
Patil A Translational infidelity-induced protein stress results from a deficiency in Trm9-catalyzed tRNA modifications. RNA Biol. 22832247
Lin CJ An extensive allelic series of Drosophila kae1 mutants reveals diverse and tissue-specific requirements for t6A biogenesis RNA 26516084
Müller M Dynamic modulation of Dnmt2-dependent tRNA methylation by the micronutrient queuine. Nucleic Acids Res. 26424849
Ramírez V Loss of a Conserved tRNA Anticodon Modification Perturbs Plant Immunity. PLoS Genet. 26492405
Kellner S Profiling of RNA modifications by multiplexed stable isotope labelling. Chem Commun (Camb). 24567952
Su D Quantitative analysis of ribonucleoside modifications in tRNA by HPLC-coupled mass spectrometry. Nat Protoc 24625781
Kellner S Absolute and relative quantification of RNA modifications via biosynthetic isotopomers. Nucleic Acids Res 25129236
Pendleton KE The U6 snRNA m6A Methyltransferase METTL16 Regulates SAM Synthetase Intron Retention Cell 28525753
Haag S NSUN6 is a human RNA methyltransferase that catalyzes formation of m5C72 in specific tRNAs. RNA 26160102
Long T Sequence-specific and Shape-selective RNA Recognition by the Human RNA 5-Methylcytosine Methyltransferase NSun6. J Biol Chem 27703015
Liu RJ Structural basis for substrate binding and catalytic mechanism of a human RNA:m5C methyltransferase NSun6. Nucleic Acids Res 28531330
Xu L Three distinct 3-methylcytidine (m(3)C) methyltransferases modify tRNA and mRNA in mice and humans. J Biol Chem 28655767
Metodiev MD NSUN4 is a dual function mitochondrial protein required for both methylation of 12S rRNA and coordination of mitoribosomal assembly. PLoS Genet. 24516400
Spåhr H Structure of the human MTERF4-NSUN4 protein complex that regulates mitochondrial ribosome biogenesis. Proc Natl Acad Sci U S A 22949673
Cámara Y MTERF4 regulates translation by targeting the methyltransferase NSUN4 to the mammalian mitochondrial ribosome. Cell Metab. 21531335
McCulloch V A human mitochondrial transcription factor is related to RNA adenine methyltransferases and binds S-adenosylmethionine. Mol Cell Biol. 11809803
Metodiev MD Methylation of 12S rRNA is necessary for in vivo stability of the small subunit of the mammalian mitochondrial ribosome. Cell Metab. 19356719
Rorbach J MRM2 and MRM3 are involved in biogenesis of the large subunit of the mitochondrial ribosome. Mol Biol Cell 25009282
Zaganelli S The Pseudouridine Synthase RPUSD4 Is an Essential Component of Mitochondrial RNA Granules. J Biol Chem 28082677
Antonicka H A pseudouridine synthase module is essential for mitochondrial protein synthesis and cell viability. EMBO Rep. 27974379
Nakano S, Suzuki T, Kawarada L, Iwata H, Asano K, NSUN3 methylase initiates 5-formylcytidine biogenesis in human mitochondrial tRNA(Met). Nat Chem Biol. 27214402
Van Haute L Deficient methylation and formylation of mt-tRNA(Met) wobble cytosine in a patient carrying mutations in NSUN3. Nat Commun. 27356879
Haag S NSUN3 and ABH1 modify the wobble position of mt-tRNAMet to expand codon recognition in mitochondrial translation. ENBO J. 27497299
Chen YC Characterization of the human tRNA-guanine transglycosylase: confirmation of the heterodimeric subunit structure. RNS 20354154
Shaheen R A homozygous truncating mutation in PUS3 expands the role of tRNA modification in normal cognition. Hum Genet. 27055666
Mundus J Identification of the methyltransferase targeting C2499 in Deinococcus radiodurans 23S ribosomal RNA. Extremophiles 26590840
Zhong S MTA is an Arabidopsis messenger RNA adenosine methylase and interacts with a homolog of a sex-specific splicing factor. Plant Cell 18505803
Růžička K Identification of factors required for m(6) A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI. New Phytol. 28503769
Guan-Zheng Luo Unique Features of the m6A Methylome in Arabidopsis thaliana Nat Commun. 25430002
Byeong-il Kang Identification of 2-methylthio cyclic N6-threonylcarbamoyladenosine (ms2ct6A) as a novel RNA modification at position 37 of tRNAs Nucleic Acids Research 5389704
Ntokou E Biochemical and Computational Analysis of the Substrate Specificities of Cfr and RlmN Methyltransferases PLoS One 26700482
Van Laer B Structural and functional insights into tRNA binding and adenosine N1-methylation by an archaeal Trm10 homologue. Nucleic Acids Res. 26673726
Deng W Trm9-Catalyzed tRNA Modifications Regulate Global Protein Expression by Codon-Biased Translation PLoS Genet. 26670883
Shoji T RlmCD-mediated U747 methylation promotes efficient G748 methylation by methyltransferase RlmAII in 23S rRNA in Streptococcus pneumoniae; interplay between two rRNA methylations responsible for telithr Nucleic Acids Res 26365244
Liu RJ tRNA recognition by a bacterial tRNA Xm32 modification enzyme from the SPOUT methyltransferase superfamily. Nucleic Acids Res. 26202969
Zhou M Identification of determinants for tRNA substrate recognition by Escherichia coli C/U34 2'-O-methyltransferase. RNA Biol. 26106808
Zorbas C The human 18S rRNA base methyltransferases DIMT1L and WBSCR22-TRMT112 but not rRNA modification are required for ribosome biogenesis. Mol Biol Cell 25851604
Nagao A Hydroxylation of a conserved tRNA modification establishes non-universal genetic code in echinoderm mitochondria. Nat Struct Mol Biol 28783151
Dal Magro C A vastly increased chemical variety of RNA modifications that includes a thioacetal structure Angew. Chem. Int. Ed. 29624844
Kawarada L ALKBH1 is an RNA dioxygenase responsible for cytoplasmic and mitochondrial tRNA modifications. Nucleic Acids Res 28472312
Hawkes NA Purification and characterization of the human elongator complex. J Biol Chem 11714725
Schlieker CD A functional proteomics approach links the ubiquitin-related modifier Urm1 to a tRNA modification pathway. Proc Natl Acad Sci U S A 19017811
Guzzi N Pseudouridylation of tRNA-Derived Fragments Steers Translational Control in Stem Cells. Cell 29628141
Fleming IM A tRNA methyltransferase paralog is important for ribosome stability and cell division in Trypanosoma brucei. Sci Rep 26888608
Schaub M RNA editing by adenosine deaminases generates RNA and protein diversity. Biochimie 12457566
Ramser J A splice site mutation in the methyltransferase gene FTSJ1 in Xp11.23 is associated with non-syndromic mental retardation in a large Belgian family (MRX9). J Med Genet 15342698
Freude K Mutations in the FTSJ1 gene coding for a novel S-adenosylmethionine-binding protein cause nonsyndromic X-linked mental retardation. Am J Hum Genet 15162322
Xu J Solution structure of Urm1 and its implications for the origin of protein modifiers. Proc Natl Acad Sci U S A 16864801
Matthies A Molybdenum cofactor biosynthesis in humans: identification of a persulfide group in the rhodanese-like domain of MOCS3 by mass spectrometry. Biochemistry 15910006
Biederbick A Role of human mitochondrial Nfs1 in cytosolic iron-sulfur protein biogenesis and iron regulation. Mol Cell Biol 16847322
Tong WH Distinct iron-sulfur cluster assembly complexes exist in the cytosol and mitochondria of human cells. EMBO J 11060020
Wan LC Proteomic analysis of the human KEOPS complex identifies C14ORF142 as a core subunit homologous to yeast Gon7. Nucleic Acids Res 27903914
Costessi A The human EKC/KEOPS complex is recruited to Cullin2 ubiquitin ligases by the human tumour antigen PRAME. PLoS One 22912744
Edvardson S tRNA N6-adenosine threonylcarbamoyltransferase defect due to KAE1/TCS3 (OSGEP) mutation manifest by neurodegeneration and renal tubulopathy. Eur J Hum Genet 28272532
Facchin S Functional homology between yeast piD261/Bud32 and human PRPK: both phosphorylate p53 and PRPK partially complements piD261/Bud32 deficiency. FEBS Lett 12914926
Abe Y Cloning and characterization of a p53-related protein kinase expressed in interleukin-2-activated cytotoxic T-cells, epithelial tumor cell lines, and the testes. J Biol Chem 11546806
Miyoshi A Identification of CGI-121, a novel PRPK (p53-related protein kinase)-binding protein. Biochem Biophys Res Commun 12659830
Huber SM 2'-O-Methyl-5-hydroxymethylcytidine: A Second Oxidative Derivative of 5-Methylcytidine in RNA. J Am Chem Soc 28107630
Ryu H Identification of a novel tRNA wobble uridine modifying activity in the biosynthesis of 5-methoxyuridine. Nucleic Acids Res 29982645
Simonova A LC/MS analysis and deep sequencing reveal the accurate RNA composition in the HIV-1 virion. Sci Rep 31213632
A Beghini RNA hyperediting and alternative splicing of hematopoietic cell phosphatase (PTPN6) gene in acute myeloid leukemia. Hum Mol Genet 11001933
Pauli C Site-specific methylation of 18S ribosomal RNA by SNORD42A is required for acutemyeloid leukemia cell proliferation. Blood 32097467
Gillian I Rice Mutations in ADAR1 cause Aicardi-Goutières syndrome associated with a type I interferon signature. Nat Genet 23001123
Daniele Hasler The Alazami Syndrome-Associated Protein LARP7 Guides U6 Small Nuclear RNA Modification and Contributes to Splicing Robustness. Mol Cell 32017898
Li H FTO is involved in Alzheimer&#39;s disease by targeting TSC1-mTOR-Tau signaling. Biochem Biophys Res Commun 29501742
Keller L The obesity related gene, FTO, interacts with APOE, and is associated withAlzheimer&#39;s disease risk: a prospective cohort study. J Alzheimers Dis 21098976
Reitz C Genetic variants in the Fat and Obesity Associated (FTO) gene and risk ofAlzheimer&#39;s disease. Arch Biochem Biophys 23251365
Min Han Abnormality of m6A mRNA Methylation Is Involved in Alzheimer's Disease. Front Neurosci 32184705
Maas S Underediting of glutamate receptor GluR-B mRNA in malignant gliomas. Proc Natl Acad Sci U S A 11717408
Donnelly CJ Aberrant RNA homeostasis in amyotrophic lateral sclerosis: potential for newtherapeutic targets? Arch Biochem Biophys 25531686
Zia Choudhry Association between obesity-related gene FTO and ADHD. Obesity (Silver Spring) 23512716
Bhalla T Control of human potassium channel inactivation by editing of a small mRNA hairpin. Nat Struct Mol Biol 15361858
Jie Han METTL3 promote tumor proliferation of bladder cancer by accelerating pri-miR221/222 maturation in m6A-dependent manner. Mol Cancer 31228940
Maosheng Cheng The mA methyltransferase METTL3 promotes bladder cancer progression via AFF4/NF-κB/MYC signaling network. Oncogene 30659266
Fan Yang Dynamic mA mRNA methylation reveals the role of METTL3-mA-CDCP1 signaling axis in chemical carcinogenesis. Oncogene 30796352
Chaohui Gu Mettl14 inhibits bladder TIC self-renewal and bladder tumorigenesis through N-methyladenosine of Notch1. Mol Cancer 31760940
Lin-Jian Wang Wilms' tumour 1-associating protein inhibits endothelial cell angiogenesis by m6A-dependent epigenetic silencing of desmoplakin in brain arteriovenous malformation. J Cell Mol Med 32281240
Ho AJ A commonly carried allele of the obesity-related FTO gene is associated with reducedbrain volume in the healthy elderly. Proc Natl Acad Sci USA 20404173
Zhen Wei Topological Characterization of Human and Mouse mC Epitranscriptome Revealed by Bisulfite Sequencing. Int J Genomics 30009162
Debora Fumagalli Principles Governing A-to-I RNA Editing in the Breast Cancer Transcriptome. Cell Rep 26440892
Marcel V p53 acts as a safeguard of translational control by regulating fibrillarin and rRNAmethylation in cancer. Cancer Cell 24029231
Cai X HBXIP-elevated methyltransferase METTL3 promotes the progression of breast cancervia inhibiting tumor suppressor let-7g. Cancer Lett 29174803
Nate J Fry N-methyladenosine contributes to cellular phenotype in a genetically-defined model of breast cancer progression. Oncotarget 30131850
Chuanzhao Zhang Hypoxia induces the breast cancer stem cell phenotype by HIF-dependent and ALKBH5-mediated m⁶A-demethylation of NANOG mRNA. Proc Natl Acad Sci U S A 27001847
Lianpin Wu Changes of N6-methyladenosine modulators promote breast cancer progression. BMC Cancer 30953473
Yi Niu RNA N6-methyladenosine demethylase FTO promotes breast tumor progression through inhibiting BNIP3. Mol Cancer 30922314
Carolyn M Klinge HNRNPA2/B1 is upregulated in endocrine-resistant LCC9 breast cancer cells and alters the miRNA transcriptome when overexpressed in MCF-7 cells. Sci Rep 31263129
Liwen Liu N6-methyladenosine-related Genomic Targets are Altered in Breast Cancer Tissue and Associated with Poor Survival. J Cancer 31632489
Wang H N6-methyladenosine METTL3 promotes the breast cancer progression via targetingBcl-2. Gene 31454538
Chen Z Transfer RNA demethylase ALKBH3 promotes cancer progression via induction oftRNA-derived small RNAs. Nucleic Acids Res 30541109
Jain M RNA editing of Filamin A pre-mRNA regulates vascular contraction and diastolic blood pressure EMBO J 30087110
Håkansson KEJ Genetic associations and regulation of expression indicate an independent role for14q32 snoRNAs in human cardiovascular disease. Cardiovasc Res 30544252
Shun Zhou FTO regulates the chemo-radiotherapy resistance of cervical squamous cell carcinoma (CSCC) by targeting β-catenin through mRNA demethylation. Mol Carcinog 29315835
Dongling Zou The mA eraser FTO facilitates proliferation and migration of human cervical cancer cells. Cancer Cell Int 31827395
Xiuli Wang Reduced mA mRNA methylation is correlated with the progression of human cervical cancer. Oncotarget 29228737
Chen W A-to-I RNA editing of BLCAP lost the inhibition to STAT3 activation in cervicalcancer. Oncotarget 28455960
Qingfei Jiang ADAR1 promotes malignant progenitor reprogramming in chronic myeloid leukemia. Proc Natl Acad Sci U S A 23275297
Ru Deng mA methyltransferase METTL3 suppresses colorectal cancer proliferation and migration through p38/ERK pathways. Onco Targets Ther 31239708
Chen X METTL14 Suppresses CRC Progression via Regulating N6-Methyladenosine-DependentPrimary miR-375 Processing. Mol Ther 31839484
Ting Li METTL3 facilitates tumor progression via an mA-IGF2BP2-dependent mechanism in colorectal carcinoma. Mol Cancer 31230592
Yujiro Nishizawa Oncogene c-Myc promotes epitranscriptome mA reader YTHDF1 expression in colorectal cancer. Oncotarget 29484125
Yang Bai YTHDF1 Regulates Tumorigenicity and Cancer Stem Cell-Like Activity in Human Colorectal Carcinoma. Front Oncol 31131257
Yingmin Wu mA-induced lncRNA RP11 triggers the dissemination of colorectal cancer cells via upregulation of Zeb1. Mol Cancer 30979372
Wen Peng Upregulated METTL3 promotes metastasis of colorectal Cancer via miR-1246/SPRED2/MAPK signaling pathway. J Exp Clin Cancer Res 31492150
Tanabe A RNA helicase YTHDC2 promotes cancer metastasis via the enhancement of the efficiencyby which HIF-1α mRNA is translated. Cancer Lett 26996300
Sae-Won Han RNA editing in RHOQ promotes invasion potential in colorectal cancer. J Exp Med 24663214
Maik Grohmann Alternative splicing and extensive RNA editing of human TPH2 transcripts. PLoS One 20126463
Chen SH RNA editing of apolipoprotein B mRNA. Sequence specificity determined by in vitrocoupled transcription editing. J Biol Chem 2324099
Fernando Jose Martinez Whole exome sequencing identifies a splicing mutation in NSUN2 as a cause of a Dubowitz-like syndrome. J Med Genet 22577224
Daphna Nachmani Germline NPM1 mutations lead to altered rRNA 2'-O-methylation and cause dyskeratosis congenita. Nat Genet 31570891
Jun Liu mA mRNA methylation regulates AKT activity to promote the proliferation and tumorigenicity of endometrial cancer. Nat Cell Biol 30154548
Li Fu RNA editing of drives early tumor invasion and metastasis in familial esophageal cancer. Proc Natl Acad Sci U S A 28533408
Tim Hon Man Chan A disrupted RNA editing balance mediated by ADARs (Adenosine DeAminases that act on RNA) in human hepatocellular carcinoma. Gut 23766440
Yuan-Bin Chen ADAR2 functions as a tumor suppressor via editing IGFBP7 in esophageal squamous cell carcinoma. Int J Oncol 28035363
Li Y Novel long noncoding RNA NMR promotes tumor progression via NSUN2 and BPTF inesophageal squamous cell carcinoma. Cancer Lett 29763634
Jun Zhang ALKBH5 promotes invasion and metastasis of gastric cancer by decreasing methylation of the lncRNA NEAT1. J Physiol Biochem 31290116
Sen Lin METTL3 Promotes the Proliferation and Mobility of Gastric Cancer Cells. Open Med (Wars) 30886897
Tong Liu Dysregulated N6-methyladenosine methylation writer METTL3 contributes to the proliferation and migration of gastric cancer. J Cell Physiol 31232471
Dong Xu FTO expression is associated with the occurrence of gastric cancer and prognosis. Oncol Rep 28849183
Yue Li Expression of Demethylase Genes, FTO and ALKBH1, Is Associated with Prognosis of Gastric Cancer. Dig Dis Sci 30637548
Zhang J [Knockdown of YTH N(6)-methyladenosine RNA binding protein 2 (YTHDF2) inhibitsproliferation and promotes apoptosis in MGC-803 gastric cancer cells]. Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi 29382422
Cheng Zhang Reduced m6A modification predicts malignant phenotypes and augmented Wnt/PI3K-Akt signaling in gastric cancer. Cancer Med 31243897
Zhao Y m1A Regulated Genes Modulate PI3K/AKT/mTOR and ErbB Pathways in GastrointestinalCancer. Transl Oncol 31352195
Zhang S m(6)A Demethylase ALKBH5 Maintains Tumorigenicity of Glioblastoma Stem-like Cells bySustaining FOXM1 Expression and Cell Proliferation Program. Cancer Cell 28344040
Ai-Hua Gong FoxM1 Drives a Feed-Forward STAT3-Activation Signaling Loop That Promotes the Self-Renewal and Tumorigenicity of Glioblastoma Stem-like Cells. Cancer Res 25832656
Cui Q m(6)A RNA Methylation Regulates the Self-Renewal and Tumorigenesis of GlioblastomaStem Cells. Cell Rep 28297667
Visvanathan A N⁶-Methyladenosine Landscape of Glioma Stem-Like Cells: METTL3 Is Essential for theExpression of Actively Transcribed Genes and Sustenance of the Oncogenic Signaling Genes (Basel) 30781903
A Visvanathan Essential role of METTL3-mediated mA modification in glioma stem-like cells maintenance and radioresistance. Oncogene 28991227
Du-Il Jin Expression and roles of Wilms' tumor 1-associating protein in glioblastoma. Cancer Sci 22957919
Zhuo Xi WTAP Expression Predicts Poor Prognosis in Malignant Glioma Patients. J Mol Neurosci 27370540
F Macari TRM6/61 connects PKCα with translational control through tRNAi(Met) stabilization: impact on tumorigenesis. Oncogene 26234676
Domenico Alessandro Silvestris Dynamic inosinome profiles reveal novel patient stratification and gender-specific differences in glioblastoma. Genome Biol 30760294
Sara Tomaselli Modulation of microRNA editing, expression and processing by ADAR2 deaminase in glioblastoma. Genome Biol 25582055
Lu L High tRNA Transferase NSUN2 Gene Expression is Associated with Poor Prognosis inHead and Neck Squamous Carcinoma. Cancer Invest 29775108
Sornjai W Hypermethylation of 28S ribosomal RNA in β-thalassemia trait carriers. Int J Biol Macromol 27765567
Mengnuo Chen RNA N6-methyladenosine methyltransferase-like 3 promotes liver cancer progression through YTHDF2-dependent posttranscriptional silencing of SOCS2. Hepatology 29171881
Yu Zhou Expression profiles and prognostic significance of RNA N6-methyladenosine-related genes in patients with hepatocellular carcinoma: evidence from independent datasets. Cancer Manag Res 31118805
Xinyao Lin RNA mA methylation regulates the epithelial mesenchymal transition of cancer cells and translation of Snail. Nat Commun 31061416
Jin-Zhao Ma METTL14 suppresses the metastatic potential of hepatocellular carcinoma by modulating N -methyladenosine-dependent primary MicroRNA processing. Hepatology 27774652
Zhe Yang MicroRNA-145 Modulates -Methyladenosine Levels by Targeting the 3'-Untranslated mRNA Region of the -Methyladenosine Binding YTH Domain Family 2 Protein. J Biol Chem 28104805
Jiajie Hou YTHDF2 reduction fuels inflammation and vascular abnormalization in hepatocellular carcinoma. Mol Cancer 31735169
Zhong L YTHDF2 suppresses cell proliferation and growth via destabilizing the EGFR mRNA inhepatocellular carcinoma. Cancer Lett 30423408
Zhao X Overexpression of YTHDF1 is associated with poor prognosis in patients withhepatocellular carcinoma. Cancer Biomark 29439311
Xiaoyu Cheng KIAA1429 regulates the migration and invasion of hepatocellular carcinoma by altering m6A modification of ID2 mRNA. Onco Targets Ther 31118692
Tian Lan KIAA1429 contributes to liver cancer progression through N6-methyladenosine-dependent post-transcriptional modification of GATA3. Mol Cancer 31856849
Yunhao Chen WTAP facilitates progression of hepatocellular carcinoma via m6A-HuR-dependent epigenetic silencing of ETS1. Mol Cancer 31438961
Xueliang Zuo M6A-mediated upregulation of LINC00958 increases lipogenesis and acts as a nanotherapeutic target in hepatocellular carcinoma. J Hematol Oncol 31915027
Xiuqing Dong CDK13 RNA Over-Editing Mediated by ADAR1 Associates with Poor Prognosis of Hepatocellular Carcinoma Patients. Cell Physiol Biochem 29996118
Yan-Ru Qin Adenosine-to-inosine RNA editing mediated by ADARs in esophageal squamous cell carcinoma. Cancer Res 24302582
Leilei Chen Recoding RNA editing of AZIN1 predisposes to hepatocellular carcinoma. Nat Med 23291631
Yamanaka S A novel translational repressor mRNA is edited extensively in livers containingtumors caused by the transgene expression of the apoB mRNA-editing enzyme. Genes Dev 9030685
Hua Su Transcriptome-wide map of mA circRNAs identified in a rat model of hypoxia mediated pulmonary hypertension. BMC Genomics 31931709
de Brouwer APM Variants in PUS7 Cause Intellectual Disability with Speech Delay, Microcephaly,Short Stature, and Aggressive Behavior. Am J Hum Genet 30526862
Julia Fischer Inactivation of the Fto gene protects from obesity. Nature 19234441
Li L Fat mass and obesity-associated (FTO) protein regulates adult neurogenesis. Hum Mol Genet 28398475
Ranad Shaheen PUS7 mutations impair pseudouridylation in humans and cause intellectual disability and microcephaly. Hum Genet 30778726
Huiwen Song METTL3 and ALKBH5 oppositely regulate mA modification of mRNA, which dictates the fate of hypoxia/reoxygenation-treated cardiomyocytes. Autophagy 30870073
Fengbiao Zhou AML1-ETO requires enhanced C/D box snoRNA/RNP formation to induce self-renewal and leukaemia. Nat Cell Biol 28650479
Congcong Sun The study of METTL3 and METTL14 expressions in childhood ETV6/RUNX1-positive acute lymphoblastic leukemia. Mol Genet Genomic Med 31429529
Chau-To Kwok Genetic alterations of mA regulators predict poorer survival in acute myeloid leukemia. J Hematol Oncol 28153030
Ly P Vu The N-methyladenosine (mA)-forming enzyme METTL3 controls myeloid differentiation of normal hematopoietic and leukemia cells. Nat Med 28920958
Li Z FTO Plays an Oncogenic Role in Acute Myeloid Leukemia as a N(6)-Methyladenosine RNADemethylase. Cancer Cell 28017614
Paris J Targeting the RNA m(6)A Reader YTHDF2 Selectively Compromises Cancer Stem Cells inAcute Myeloid Leukemia. Cell Stem Cell 31031138
Huang Y Small-Molecule Targeting of Oncogenic FTO Demethylase in Acute Myeloid Leukemia. Cancer Cell 30991027
Zhenrui Li Suppression of mA reader Ythdf2 promotes hematopoietic stem cell expansion. Cell Res 30065315
Weng H METTL14 Inhibits Hematopoietic Stem/Progenitor Differentiation and PromotesLeukemogenesis via mRNA m(6)A Modification. Cell Stem Cell 29290617
Wei Huang Determination of DNA and RNA Methylation in Circulating Tumor Cells by Mass Spectrometry. Anal Chem 26707930
C Anadón Gene amplification-associated overexpression of the RNA editing enzyme ADAR1 enhances human lung tumorigenesis. Oncogene 26640150
Du T An association study of the m6A genes with major depressive disorder in Chinese Hanpopulation. J Affect Disord 26047305
Z Samaan The protective effect of the obesity-associated rs9939609 A variant in fat mass- and obesity-associated gene on depression. Mol Psychiatry 23164817
Y Milaneschi The effect of FTO rs9939609 on major depression differs across MDD subtypes. Mol Psychiatry 24492350
Mina S Khella The Association Between the FTO rs9939609 Variant and Malignant Pleural Mesothelioma Risk: A Case-Control Study. Genet Test Mol Biomarkers 29260910
Seungwon Yang mA mRNA demethylase FTO regulates melanoma tumorigenicity and response to anti-PD-1 blockade. Nat Commun 31239444
Dahal U RNA m6A methyltransferase METTL3 regulates invasiveness of melanoma cells by matrixmetallopeptidase 2. Melanoma Res 30762711
Ruobing Jia mA modification suppresses ocular melanoma through modulating HINT2 mRNA translation. Mol Cancer 31722709
Motoko Watanabe Development of metachronous rectal cancers in a young man with dyskeratosis congenita: a case report. J Med Case Rep 31027506
Bykhovskaya Y Missense mutation in pseudouridine synthase 1 (PUS1) causes mitochondrial myopathyand sideroblastic anemia (MLASA). Am J Hum Genet 15108122
Elisa Lazzari Alu-dependent RNA editing of GLI1 promotes malignant regeneration in multiple myeloma. Nat Commun 29203771
Uwe Richter RNA modification landscape of the human mitochondrial tRNA regulates protein synthesis. Nat Commun 30262910
Elaine deLorimier Pseudouridine Modification Inhibits Muscleblind-like 1 (MBNL1) Binding to CCUG Repeats and Minimally Structured RNA through Reduced RNA Flexibility. J Biol Chem 28130447
Sandra Blanco Aberrant methylation of tRNAs links cellular stress to neuro-developmental disorders. EMBO J 25063673
Mukhopadhyay D C--&gt;U editing of neurofibromatosis 1 mRNA occurs in tumors that express both thetype II transcript and apobec-1, the catalytic subunit of the apolipoprotein BmRNA-editing enzyme. Am J Hum Genet 11727199
Lin S The m(6)A Methyltransferase METTL3 Promotes Translation in Human Cancer Cells. Mol Cell 27117702
Du M MiR-33a suppresses proliferation of NSCLC cells via targeting METTL3 mRNA. Biochem Biophys Res Commun 27856248
Junho Choe mRNA circularization by METTL3-eIF3h enhances translation and promotes oncogenesis. Nature 30232453
Dan Jin mA mRNA methylation initiated by METTL3 directly promotes YAP translation and increases YAP activity by regulating the MALAT1-miR-1914-3p-YAP axis to induce NSCLC drug resistance and metastasis. J Hematol Oncol 31818312
Hongsheng Wang N6-methyladenosine induced miR-143-3p promotes the brain metastasis of lung cancer via regulation of VASH1. Mol Cancer 31823788
Li J The m6A demethylase FTO promotes the growth of lung cancer cells by regulating them6A level of USP7 mRNA. Biochem Biophys Res Commun 30905413
Liu J m(6)A demethylase FTO facilitates tumor progression in lung squamous cell carcinomaby regulating MZF1 expression. Biochem Biophys Res Commun 29842885
Sheng H YTH domain family 2 promotes lung cancer cell growth by facilitating6-phosphogluconate dehydrogenase mRNA translation. Carcinogenesis 31504235
Chao Y ALKBH5-m(6)A-FOXM1 signaling axis promotes proliferation and invasion of lungadenocarcinoma cells under intermittent hypoxia. Biochem Biophys Res Commun 31677788
Zhu Z N(6)-methyladenosine ALKBH5 promotes non-small cell lung cancer progress byregulating TIMP3 stability. Gene 31927006
Michael P Guy Defects in tRNA Anticodon Loop 2'-O-Methylation Are Implicated in Nonsyndromic X-Linked Intellectual Disability due to Mutations in FTSJ1. Hum Mutat 26310293
Lu Qi Fat mass-and obesity-associated (FTO) gene variant is associated with obesity: longitudinal analyses in two cohort studies and functional test. Diabetes 18647953
Vladimir Babenko FTO haplotyping underlines high obesity risk for European populations. BMC Med Genomics 30871540
Scuteri A Genome-wide association scan shows genetic variants in the FTO gene are associatedwith obesity-related traits. PLoS Genet 17658951
Yunshu Wu Mettl3-mediated mA RNA methylation regulates the fate of bone marrow mesenchymal stem cells and osteoporosis. Nat Commun 30429466
Miao W The m6A methyltransferase METTL3 promotes osteosarcoma progression by regulating them6A level of LEF1. Biochem Biophys Res Commun 31253399
Woo HH Human ALKBH3-induced m(1)A demethylation increases the CSF-1 mRNA stability inbreast and ovarian cancer cells. Biochim Biophys Acta Gene Regul Mech 30342176
Kosuke Taketo The epitranscriptome m6A writer METTL3 promotes chemo- and radioresistance in pancreatic cancer cells. Int J Oncol 29345285
Jixiang Chen YTH domain family 2 orchestrates epithelial-mesenchymal transition/proliferation dichotomy in pancreatic cancer cells. Cell Cycle 29135329
Daniele Fanale Germline copy number variation in the YTHDC2 gene: does it have a role in finding a novel potential molecular target involved in pancreatic adenocarcinoma susceptibility? Expert Opin Ther Targets 24834797
Yuan He ALKBH5 Inhibits Pancreatic Cancer Motility by Decreasing Long Non-Coding RNA KCNK15-AS1 Methylation. Cell Physiol Biochem 30032148
Bo Tang mA demethylase ALKBH5 inhibits pancreatic cancer tumorigenesis by decreasing WIF-1 RNA methylation and mediating Wnt signaling. Mol Cancer 31906946
Xuechai Chen Down-Regulation of m6A mRNA Methylation Is Involved in Dopaminergic Neuronal Death. ACS Chem Neurosci 30835997
Wettengel J Harnessing human ADAR2 for RNA repair - Recoding a PINK1 mutation rescues mitophagy. Nucleic Acids Res 27907896
Chenyue Ding Increased N6-methyladenosine causes infertility is associated with FTO expression. J Cell Physiol 29384212
Jiangfeng Li Downregulation of N-methyladenosine binding YTHDF2 protein mediated by miR-493-3p suppresses prostate cancer by elevating N-methyladenosine levels. Oncotarget 29423080
Jiarong Cai RNA mA Methyltransferase METTL3 Promotes The Growth Of Prostate Cancer By Regulating Hedgehog Pathway. Onco Targets Ther 31806999
Richard T O'Neil Quantitative analysis of 5HT(2C) receptor RNA editing patterns in psychiatric disorders. Neurobiol Dis 21914481
Xiao Li The M6A methyltransferase METTL3: acting as a tumor suppressor in renal cell carcinoma. Oncotarget 29221190
Dongkui Gong The mA-suppressed P2RX6 activation promotes renal cancer cells migration and invasion through ATP-induced Ca influx modulating ERK1/2 phosphorylation and MMP9 signaling pathway. J Exp Clin Cancer Res 31159832
Changshui Zhuang N6-methyladenosine demethylase FTO suppresses clear cell renal cell carcinoma through a novel FTO-PGC-1α signalling axis. J Cell Mol Med 30648791
Jingyuan Tang Wilms' tumor 1-associating protein promotes renal cell carcinoma proliferation by regulating CDK2 mRNA stability. J Exp Clin Cancer Res 29482572
Ahmadreza Niavarani APOBEC3A is implicated in a novel class of G-to-A mRNA editing in WT1 transcripts. PLoS One 25807502
Brusa R Early-onset epilepsy and postnatal lethality associated with an editing-deficientGluR-B allele in mice. Science 7502080
Alessandro Barbon Acute spinal cord injury persistently reduces R/G RNA editing of AMPA receptors. J Neurochem 20456005
Svenja Kankowski A Novel RNA Editing Sensor Tool and a Specific Agonist Determine Neuronal Protein Expression of RNA-Edited Glycine Receptors and Identify a Genomic APOBEC1 Dimorphism as a New Genetic Risk Factor of Epilepsy. Front Mol Neurosci 29375302
Gonzales B The Treacher Collins syndrome (TCOF1) gene product is involved in pre-rRNAmethylation. Hum Mol Genet 15930015
Frayling TM A common variant in the FTO gene is associated with body mass index and predisposesto childhood and adult obesity. Science 17434869
Dario F De Jesus mA mRNA Methylation Regulates Human β-Cell Biology in Physiological States and in Type 2 Diabetes. Nat Metab 31867565
Oscar Franzén Global analysis of A-to-I RNA editing reveals association with common disease variants. PeerJ 29527417
Chen X 5-methylcytosine promotes pathogenesis of bladder cancer through stabilizing mRNAs Nat Cell Biol . 31358969
Shinichiro Akichika Cap-specific terminal -methylation of RNA by an RNA polymerase II-associated methyltransferase. Science 30467178
Hanxiao Sun Cap-specific, terminal N-methylation by a mammalian mAm methyltransferase. Cell Res 30487554
Konstantinos Boulias Identification of the mAm Methyltransferase PCIF1 Reveals the Location and Functions of mAm in the Transcriptome. Mol Cell 31279658
Erdem Sendinc PCIF1 Catalyzes m6Am mRNA Methylation to Regulate Gene Expression. Mol Cell 31279659
Nhan van Tran The human 18S rRNA m6A methyltransferase METTL5 is stabilized by TRMT112. Nucleic Acids Res 31328227
Valentina V Ignatova The rRNA mA methyltransferase METTL5 is involved in pluripotency and developmental programs. Genes Dev 32217665
Honghui Ma NMethyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation. Nat Chem Biol 30531910
Rita Pinto The human methyltransferase ZCCHC4 catalyses N6-methyladenosine modification of 28S ribosomal RNA. Nucleic Acids Res 31799605
Wendan Ren Structure and regulation of ZCCHC4 in mA-methylation of 28S rRNA. Nat Commun 31695039
Hao Chen METTL4 is an snRNA mAm methyltransferase that regulates RNA splicing. Cell Res 31913360
Ziyang Hao N-Deoxyadenosine Methylation in Mammalian Mitochondrial DNA. Mol Cell 32183942
Martin Müller Division of labour: tRNA methylation by the NSun2 tRNA methyltransferases Trm4a and Trm4b in fission yeast. RNA Biol 30646830
Maria Becker Pmt1, a Dnmt2 homolog in Schizosaccharomyces pombe, mediates tRNA methylation in response to nutrient signaling. Nucleic Acids Res 23074192
J G Tokuhisa Chloroplast development at low temperatures requires a homolog of DIM1, a yeast gene encoding the 18S rRNA dimethylase. Plant Cell 9596631
Jun-Ichi Wachino RmtC introduces G1405 methylation in 16S rRNA and confers high-level aminoglycoside resistance on Gram-positive microorganisms. FEMS Microbiol Lett 20722735
Meisam Nosrati Functionally critical residues in the aminoglycoside resistance-associated methyltransferase RmtC play distinct roles in 30S substrate recognition. J Biol Chem 31594862
Alena Stsiapanava Crystal structure of ErmE - 23S rRNA methyltransferase in macrolide resistance. Sci Rep 31601908
I D Villsen ErmE methyltransferase recognizes features of the primary and secondary structure in a motif within domain V of 23 S rRNA. J Mol Biol 9973557
B Vester Domain V of 23S rRNA contains all the structural elements necessary for recognition by the ErmE methyltransferase. J Bacteriol 7961464
B Vester The conformation of 23S rRNA nucleotide A2058 determines its recognition by the ErmE methyltransferase. RNA 7489511
Jean-Michel Carter FICC-Seq: a method for enzyme-specified profiling of methyl-5-uridine in cellular RNA. Nucleic Acids Res 31361898
Marisa Pereira mU54 tRNA Hypomodification by Lack of TRMT2A Drives the Generation of tRNA-Derived Small RNAs. Int J Mol Sci 33799331
Christopher A Powell TRMT2B is responsible for both tRNA and rRNA mU-methylation in human mitochondria. RNA Biol 31948311
Ivan Laptev Mouse Trmt2B protein is a dual specific mitochondrial metyltransferase responsible for mU formation in both tRNA and rRNA. RNA Biol 31736397
Jahangir Alam Expression and analysis of the SAM-dependent RNA methyltransferase Rsm22 from Saccharomyces cerevisiae. Acta Crystallogr D Struct Biol 34076597
Meijuan Zou The critical function of the plastid rRNA methyltransferase, CMAL, in ribosome biogenesis and plant development. Nucleic Acids Res 32095829
Lindsey Van Haute METTL15 introduces N4-methylcytidine into human mitochondrial 12S rRNA and is required for mitoribosome biogenesis. Nucleic Acids Res 31665743
Hao Chen The human mitochondrial 12S rRNA mC methyltransferase METTL15 is required for mitochondrial function. J Biol Chem 32371392
Ivan Laptev METTL15 interacts with the assembly intermediate of murine mitochondrial small ribosomal subunit to form m4C840 12S rRNA residue. Nucleic Acids Res 32573735
Jason D Arroyo A Genome-wide CRISPR Death Screen Identifies Genes Essential for Oxidative Phosphorylation. Cell Metab 27667664
Shaoni Mukhopadhyay Mammalian nuclear TRUB1, mitochondrial TRUB2, and cytoplasmic PUS10 produce conserved pseudouridine 55 in different sets of tRNA. RNA 33023933
Modi Safra TRUB1 is the predominant pseudouridine synthase acting on mammalian mRNA via a predictable and conserved code. Genome Res 28073919
Xue-Ling Mao Mutually exclusive substrate selection strategy by human m3C RNA transferases METTL2A and METTL6. Nucleic Acids Res 34268557
Nikoletta A Gkatza Cytosine-5 RNA methylation links protein synthesis to cell metabolism. PLoS Biol 31199786
Xiaotian Zhang The tRNA methyltransferase NSun2 stabilizes p16INK⁴ mRNA by methylating the 3'-untranslated region of p16. Nat Commun 22395603
Abdulrahim A Sajini Loss of 5-methylcytosine alters the biogenesis of vault-derived small RNAs to coordinate epidermal differentiation. Nat Commun 31186410
Jinghui Song Differential roles of human PUS10 in miRNA processing and tRNA pseudouridylation. Nat Chem Biol 31819270
Manisha Deogharia The human ortholog of archaeal Pus10 produces pseudouridine 54 in select tRNAs where its recognition sequence contains a modified residue. RNA 30530625
Zuxiao Yang Functional organization of box C/D RNA-guided RNA methyltransferase. Nucleic Acids Res 32297938
Xiaodan Liu Structural insights into dimethylation of 12S rRNA by TFB1M: indispensable role in translation of mitochondrial genes and mitochondrial function. Nucleic Acids Res 31251801
Dan Bar-Yaacov Mitochondrial 16S rRNA Is Methylated by tRNA Methyltransferase TRMT61B in All Vertebrates. PLoS Biol 27631568
Nathan W Howell Distinct substrate specificities of the human tRNA methyltransferases TRMT10A and TRMT10B. RNA 31292261
Y Nagayoshi Loss of Ftsj1 perturbs codon-specific translation efficiency in the brain and is associated with X-linked intellectual disability. Sci Adv 33771871
J M Lentini 1 METTL8 is required for 3-methylcytosine modification in human mitochondrial tRNAs
Konstantin A Ivanov Multiple enzymatic activities associated with severe acute respiratory syndrome coronavirus helicase. J Virol 15140959
Liming Yan Cryo-EM Structure of an Extended SARS-CoV-2 Replication and Transcription Complex Reveals an Intermediate State in Cap Synthesis. Cell 33232691
Souradeep Basu Identifying SARS-CoV-2 antiviral compounds by screening for small molecule inhibitors of Nsp14 RNA cap methyltransferase. Biochem J 34198328
Sheng Lin Crystal structure of SARS-CoV-2 nsp10 bound to nsp14-ExoN domain reveals an exoribonuclease with both structural and functional integrity. Nucleic Acids Res 33956156
Aliakbar Khalili Yazdi A High-Throughput Radioactivity-Based Assay for Screening SARS-CoV-2 nsp10-nsp16 Complex. SLAS Discov 33874769
Christopher Piccirillo Functional characterization of the mammalian mRNA decapping enzyme hDcp2. RNA 12923261
Erwin van Dijk Human Dcp2: a catalytically active mRNA decapping enzyme located in specific cytoplasmic structures. EMBO J 12486012
Man-Gen Song Multiple mRNA decapping enzymes in mammalian cells. Mol Cell 21070968
S Kramer The ApaH-like phosphatase TbALPH1 is the major mRNA decapping enzyme of trypanosomes PLoS Pathog 28628654
L Clemmesen Local cerebral glucose consumption during ethanol withdrawal in the rat: effects of single and multiple episodes and previous convulsive seizures. Brain Res 3401759
S Onesti The crystal structure of the lysyl-tRNA synthetase (LysU) from Escherichia coli. Structure 7735833
Daniel J Luciano Stresses that Raise NpA Levels Induce Protective Nucleoside Tetraphosphate Capping of Bacterial RNA. Mol Cell 31178354
Yaqing Zhang Extensive 5'-surveillance guards against non-canonical NAD-caps of nuclear mRNAs in yeast. Nat Commun 33139726
Ewa Grudzien-Nogalska "NAD-capQ" detection and quantitation of NAD caps. RNA 30045887
Xinfu Jiao Identification of a quality-control mechanism for mRNA 5'-end capping. Nature 20802481
S R AbdelRaheim The NADH diphosphatase encoded by the Saccharomyces cerevisiae NPY1 nudix hydrolase gene is located in peroxisomes. Arch Biochem Biophys 11361135
Xinfu Jiao 5' End Nicotinamide Adenine Dinucleotide Cap in Human Cells Promotes RNA Decay through DXO-Mediated deNADding. Cell 28283058
Ewa Grudzien-Nogalska Structural and mechanistic basis of mammalian Nudt12 RNA deNADding. Nat Chem Biol 31101919
F Picard-Jean 2'-O-methylation of the mRNA cap protects RNAs from decapping and degradation by DXO PLoS One 29601584
Petra Krafcikova Structural analysis of the SARS-CoV-2 methyltransferase complex involved in RNA cap creation bound to sinefungin. Nat Commun 32709887
Monica Rosas-Lemus High-resolution structures of the SARS-CoV-2 2'--methyltransferase reveal strategies for structure-based inhibitor design. Sci Signal 32994211
Yujiro Nishizawa Oncogene c-Myc promotes epitranscriptome mA reader YTHDF1 expression in colorectal cancer. Oncotarget 29484125
Y Bai YTHDF1 Regulates Tumorigenicity and Cancer Stem Cell-Like Activity in Human Colorectal Carcinoma Front Oncol. 31131257
S Lin METTL3 Promotes the Proliferation and Mobility of Gastric Cancer Cells Open Med (Wars) 30886897
Tong Liu Dysregulated N6-methyladenosine methylation writer METTL3 contributes to the proliferation and migration of gastric cancer. J Cell Physiol 31232471
Dong Xu FTO expression is associated with the occurrence of gastric cancer and prognosis. Oncol Rep 28849183
Yue Li Expression of Demethylase Genes, FTO and ALKBH1, Is Associated with Prognosis of Gastric Cancer. Dig Dis Sci 30637548
Abhirami Visvanathan N⁶-Methyladenosine Landscape of Glioma Stem-Like Cells: METTL3 Is Essential for the Expression of Actively Transcribed Genes and Sustenance of the Oncogenic Signaling. Genes (Basel) 30781903
A Visvanathan Essential role of METTL3-mediated mA modification in glioma stem-like cells maintenance and radioresistance. Oncogene 28991227
Du-Il Jin Expression and roles of Wilms' tumor 1-associating protein in glioblastoma. Cancer Sci 22957919
Zhuo Xi WTAP Expression Predicts Poor Prognosis in Malignant Glioma Patients. J Mol Neurosci 27370540
X Zhao Overexpression of YTHDF1 is associated with poor prognosis in patients with hepatocellular carcinoma Cancer Biomark . 29439311
Y Zhou Expression profiles and prognostic significance of RNA N6-methyladenosine-related genes in patients with hepatocellular carcinoma: evidence from independent datasets Cancer Manag Res. 31118805
Z Samaan The protective effect of the obesity-associated rs9939609 A variant in fat mass- and obesity-associated gene on depression. Mol Psychiatry 23164817
Y Milaneschi The effect of FTO rs9939609 on major depression differs across MDD subtypes. Mol Psychiatry 24492350
Qiyao Zhang Overview of distinct 5-methylcytosine profiles of messenger RNA in human hepatocellular carcinoma and paired adjacent non-tumor tissues. J Transl Med 32571340
Yuanbo Hu NSUN2 modified by SUMO-2/3 promotes gastric cancer progression and regulates mRNA m5C methylation. Cell Death Dis 34504059
Ruimeng Yang The RNA methyltransferase NSUN6 suppresses pancreatic cancer development by regulating cell proliferation. EBioMedicine 33418496
Liuhong Shi N1-methyladenosine profiling of long non-coding RNA in colorectal cancer. IUBMB Life 34314547
Rosaura Esteve-Puig Epigenetic loss of m1A RNA demethylase ALKBH3 in Hodgkin lymphoma targets collagen, conferring poor clinical outcome. Blood 32915956

Copyright © Genesilico - All rights reserved
If you have any advice or suggestions for corrections or improvements, please contact: Andrea Cappannini - lp.vog.bcmii@ininnappaca