| ABH1: | alpha‐ketoglutarate‐dependent dioxygenase 1 or AlkB Homolog 1 |
| ACP: | 3‐amino‐3‐carboxypropyl |
| ADAR: | adenosine deaminase acting on RNA |
| ADAT: | adenosine deaminase acting on tRNA |
| AHK3: | histidine kinase 3 |
| AHK4: | histidine kinase 4 |
| AID: | activation‐induced cytidine deaminase |
| ALKB: | alpha‐ketoglutarate‐dependent dioxygenase |
| ALKBH1: | alkylated DNA repair protein (AlkB) homolog 1 |
| ALKBH3: | alkylated DNA repair protein (AlkB) homolog 3 |
| ALKBH5: | alkylated DNA repair protein (AlkB) homolog 5 |
| ALKBH8: | alkylated DNA repair protein (AlkB) homolog 8 |
| AML: | acute myeloid leukemia |
| ArcS/arcTGT: | archaeosine synthase |
| AroD: | 3‐dehydroquinate dehydratase |
| Atm1: | mitochondrial iron–sulfur clusters transporter |
| BMT5/6: | 25S rRNA (uridine(2634)‐N 3)‐methyltransferases 5 and 6 |
| Bud23: | rRNA methyltransferase and ribosome maturation factor |
| c‐di‐GMP: | cyclic di‐guanosine monophosphate |
| CDK5RAP1: | cyclin‐dependent kinase 5 regulatory subunit associated protein 1 |
| CDKAL1: | threonylcarbamoyladenosine tRNA methythiotransferase or cyclin‐dependent kinase (CDK) 5‐regulatory subunit associated protein 1 like 1 |
| cDNA: | complementary DNA |
| CDS: | coding sequence |
| Cfr: | chloramphenicol‐florfenicol resistance |
| CMC: | N‐cyclohexyl‐N′‐(2‐morpholinoethyl)‐carbodiimide |
| CMCT: | N‐cyclohexyl‐N′‐(2‐morpholinoethyl)‐carbodiimide metho‐p‐toluenesulphonate |
| c‐myc: | cellular avian myelocytomatosis viral oncogene homolog |
| CmoABM: | carboxy‐S‐adenosyl‐L‐methionine synthase A, B, or M |
| COG1738: | conserved protein domain 1738 |
| CRE1: | cytokinin response element 1 |
| CsdAE: | cysteine desulfurase A or E |
| Ctu1‐2: | cytoplasmic tRNA 2‐thiolation proteins 1 or 2 |
| DDX6: | DEAD‐box helicase 6 |
| Dim1: | dimethyladenosine transferase 1 |
| DKC1: | dyskerin pseudouridine synthase 1 |
| DNMT3A: | DNA methyltransferase 3 alpha or DNA (cytosine‐5‐)‐methyltransferase 3 alpha |
| dpCoA: | 3′‐dephospho‐coenzyme A |
| DROSHA: | double‐stranded RNA‐specific endoribonuclease |
| DTWD1‐2: | DTW (aspartate‐threonine‐tryptophan) domain‐containing proteins 1 or 2 |
| Dus: | dihydrouridine synthase |
| Dus1‐4p: | dihydrouridine synthase proteins 1–4 |
| DusABC: | dihydrouridine synthase A, B, or C |
| eEF1A: | eukaryotic elongation factor 1A |
| EF‐Tu: | elongation factor thermo unstable |
| EGFR: | epidermal growth factor receptor |
| eIF3H: | eukaryotic translation initiation factor 3 subunit H |
| eL41: | eukaryotic ribosomal protein L41 |
| Elp1‐6: | Elongator proteins 1–6 |
| Emg1: | N 1‐specific pseudouridine methyltransferase |
| FICC‐seq: | fluorouracil‐induced‐catalytic‐crosslinking‐sequencing |
| FMN: | flavin mononucleotide |
| FTO: | fat mass and obesity‐associated related |
| Fur: | ferric uptake regulator |
| GAT‐QueC: | glutamine amidotransferase class‐II‐7‐cyano‐7‐deazaguanine synthase fusion protein |
| GCD: | tRNA (adenine‐N 1‐)‐methyltransferase |
| Gcd10p/Gcd14p: | tRNA (adenine‐N 1‐)‐methyltransferases 10 and 14 proteins or tRNA (adenine(58)‐N(1))‐methyltransferase noncatalytic subunit Trm6 and Trm61 |
| GidA: | uridine 5‐carboxymethylaminomethyl modification enzyme |
| GluQRS: | glutamyl‐Q tRNA(Asp) synthetase |
| GRIA2: | glutamate ionotropic receptor alpha‐amino 3‐hydroxy‐5‐methyl‐4‐isoxazole propionate (AMPA) type subunit 2 |
| GTPBP3: | guanosine triphosphate binding protein 3 |
| H/ACA: | H‐ and ACA‐box‐containing small nucleolar RNA |
| HER2+: | human epidermal growth factor receptor 2 positive |
| hDus2p: | human dihydrouridine synthase protein 2 |
| hnRNP: | heterogeneous nuclear ribonucleoprotein |
| hTRMT10A or B: | human tRNA methyltransferase 10 A or B |
| IGF2BP: | insulin‐like growth factor 2 mRNA‐binding protein |
| IPP: | isopentenyl pyrophosphate |
| IscS: | iron–sulfur cluster S or cysteine desulfurase |
| IscU: | iron–sulfur cluster assembly enzyme |
| Isu1/2: | iron–sulfur cluster assembly proteins 1 and 2 |
| KEOPS: | kinase, putative endopeptidase and other proteins of small size |
| KsgA: | rRNA adenine dimethyltransferase or ribosomal RNA small subunit methyltransferase A |
| L7Ae: | 50S ribosomal protein |
| LC–MS: | liquid chromatography–mass spectrometry |
| MALAT1: | metastasis‐associated lung adenocarcinoma transcript 1 |
| MAT2A: | methionine adenosyltransferase 2A |
| MELAS: | mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke‐like episodes |
| MERRF: | myoclonus epilepsy associated with ragged‐red fibers |
| METTL: | methyltransferase‐like protein |
| METTL2: | methyltransferase‐like protein 2 |
| METTL3/14: | methyltransferase‐like proteins 3 and 14 |
| METTL5: | methyltransferase‐like protein 5 |
| METTL6: | methyltransferase‐like protein 6 |
| METTL8: | methyltransferase‐like protein 8 |
| METTL15: | methyltransferase‐like protein 15 |
| METTL16: | methyltransferase‐like protein 16 |
| MiaA: | tRNA delta(2)‐isopentenylpyrophosphate transferase A or tRNA dimethylallyltransferase A |
| MiaB: | tRNA delta(2)‐isopentenylpyrophosphate transferase B or tRNA dimethylallyltransferase B |
| MiaE: | tRNA delta(2)‐isopentenylpyrophosphate transferase E or tRNA dimethylallyltransferase E |
| miR/miRNA: | microRNA |
| MK2: | MAPK activated protein kinase 2 or mitogen‐activated protein kinase‐activated protein kinase 2 or MAPKAPK2 |
| MLASA: | mitochondrial myopathy and sideroblastic anemia |
| MnmACEGH: | tRNA‐specific 2‐thiouridylase A, C, E, G, or H |
| MnmC(m): | tRNA‐specific 2‐thiouridylase C, methyltransferase domain |
| MnmC(o): | tRNA‐specific 2‐thiouridylase C, oxidoreductase domain |
| Moco: | molybdenum cofactor |
| Mod5: | tRNA isopentenyltransferase 1 |
| MtaB: | threonylcarbamoyladenosine tRNA methylthiotransferase or TcdA |
| mTOR: | mammalian target of rapamycin |
| MTO1: | mitochondrial tRNA translation optimization 1 |
| MTU1: | mitochondrial tRNA‐specific 2‐thiouridylase 1 or TRMU |
| NAD+: | nicotinamide adenine dinucleotide (oxidized form) |
| NADH: | nicotinamide adenine dinucleotide (reduced form) |
| NAP57: | nucleolar and coiled‐body phosphoprotein 57 or dyskerin |
| NAT10: | N‐acetyltransferase 10 |
| Ncs6: | cytoplasmic tRNA 2‐thiolation protein 1 |
| Nep1/Emg1: | N 1‐specific pseudouridine methyltransferase |
| NFS1: | mitochondrial cysteine desulfurase |
| NifZ: | nitrogen fixation protein |
| Nm: | 2′‐O‐methyl mark |
| NML: | nucleomethylin |
| NOP56: | nucleolar protein 56 |
| NOP58: | nucleolar protein 58 |
| NRF2: | nuclear factor erythroid 2 like 2 |
| NSUN: | nucleolar protein 22/Sun domain RNA methyltransferase |
| Nt: | Nucleotide |
| Opa1: | optic atrophy 1 |
| P body: | processing body |
| PAR: | poly(ADP‐ribose) |
| PAR‐CLIP: | photoactivatable ribonucleoside‐enhanced crosslinking and immunoprecipitation |
| PCIF1: | phosphorylated C‐terminal domain‐interacting factor 1 |
| PKR: | interferon‐inducible double‐stranded RNA‐activated protein kinase or eIF‐2A protein kinase 2 |
| pri‐miRNA: | primary microRNA transcripts |
| PRC2: | polycomb responsive complex 2 |
| PRPP: | phosphoribosylpyrophosphate |
| PrrC: | anticodon nuclease |
| PRRC2A: | proline‐rich coiled‐coil 2A |
| PTC: | peptidyl transferase center |
| Pus: | pseudouridine synthase |
| Pus1p: | pseudouridine synthase 1 protein |
| Pus10: | pseudouridine synthase 10 |
| QueA: | S‐adenosyl‐l‐methionine‐dependent tRNA ribosyltransferase‐isomerase |
| QueCDE: | 7‐cyano‐7‐deazaguanine synthase, 6‐carboxy‐5,6,7,8‐tetrahydropterine synthase, and 7‐carboxy‐7‐deazaguanine synthase |
| QueF: | NADPH‐dependent 7‐cyano‐7‐deazaguanine reductase |
| QueF‐like: | similar to NADPH‐dependent 7‐cyano‐7‐deazaguanine reductase |
| QueG: | epoxyqueuosine reductase |
| QueH: | epoxyqueuosine reductase |
| QueT: | queuosine precursor transporter |
| RaSEA: | radical SAM enzyme for archaeosine formation |
| Rit1: | ribosylation of initiator tRNA 1 |
| RlhA: | 23S rRNA 5‐hydroxycytidine C2501 synthase |
| RlmA: | ribosomal RNA large subunit methyltransferase A or 23S rRNA (guanine(745)‐N(1))‐methyltransferase |
| RlmC: | ribosomal RNA large subunit methyltransferase C or 23S rRNA (uracil(747)‐C(5))‐methyltransferase |
| RlmD: | ribosomal RNA large subunit methyltransferase D or 23S rRNA (uracil(1939)‐C(5))‐methyltransferase |
| RlmF: | ribosomal RNA large subunit methyltransferase F |
| RlmFO: | ribosomal RNA large subunit methyltransferase FO or methylenetetrahydrofolate‐tRNA‐(uracil‐5‐)‐methyltransferase |
| RlmG: | ribosomal RNA large subunit methyltransferase G |
| RlmH: | ribosomal RNA large subunit methyltransferase H |
| RlmJ: | ribosomal RNA large subunit methyltransferase J |
| RlmL: | ribosomal RNA large subunit methyltransferase L |
| RlmN: | 23S rRNA m2A2503 methyltransferase/tRNA or dual‐specificity RNA methyltransferase |
| RluA: | ribosomal large subunit pseudouridine synthase A or dual‐specificity RNA pseudouridine synthase |
| RluD: | ribosomal large subunit pseudouridine synthase D |
| RNMT: | RNA guanine‐7 methyltransferase |
| RRF: | ribosome release factor |
| RsmA: | ribosomal RNA small subunit methyltransferase A |
| RsmC: | ribosomal RNA small subunit methyltransferase C |
| RsmD: | ribosomal RNA small subunit methyltransferase D |
| RsmE: | ribosomal RNA small subunit methyltransferase E |
| RsmH: | ribosomal RNA small subunit methyltransferase H |
| RsmI: | ribosomal RNA small subunit methyltransferase I |
| RsuA: | ribosomal small subunit pseudouridine synthase A |
| SAH: | S‐adensoyl‐L‐homocysteine |
| SAM: | S‐adenosyl‐L‐methionine |
| SCARLET: | site‐specific cleavage and radioactive labeling followed by ligation‐assisted extraction and thin‐layer chromatography |
| SCM‐SAH: | S‐carboxy‐S‐adenosyl‐L‐homocysteine |
| SELEX: | systematic evolution of ligands by exponential enrichment |
| SelU: | tRNA 2‐selenouridine synthase |
| snoRNA: | small nucleolar RNA |
| snoRNP: | small nucleolar ribonucleo protein |
| SNP: | single nucleotide polymorphism |
| snR35: | small nucleolar RNA 35 |
| snRNA: | small nuclear RNA |
| snRNP: | small nuclear ribonucleoprotein |
| SNU13: | small nuclear ribonucleoprotein 13 or 15.5K |
| SOS: | inducible DNA repair system |
| SRA: | steroid receptor RNA activator |
| T: | thymidine |
| Tad1p: | tRNA‐specific adenosine deaminase 1 protein |
| Tad2p: | tRNA‐specific adenosine deaminase 2 protein |
| Tad3p: | tRNA‐specific adenosine deaminase 3 protein |
| TadA: | tRNA‐specific adenosine deaminase |
| Tan1: | tRNA acetyltransferase 1 |
| TapT: | tRNA aminocarboxypropyltransferase |
| Taw1‐3: | SAM‐dependent tRNA 4‐demethylwyosine synthases 1–3 |
| Taw22: | SAM‐dependent tRNA 4‐demethylwyosine synthase 22 |
| TAZ: | tafazzin |
| TCD1/2: | threonylcarbamoyladenosine dehydratase 1 or 2 |
| TcdA: | threonylcarbamoyladenosine dehydratase A |
| Tcs1/2: | threonylcarbamoyladenylate synthase 1 or 2 |
| TermY: | tRNA m1Ψ54‐methyltransferase |
| TET: | ten‐eleven translocation methylcytosine dioxygenase |
| TET1: | ten‐eleven translocation methylcytosine dioxygenase 1 |
| Tgs1: | trimethylguanosine synthase 1 |
| TGT: | queuine tRNA‐ribosyltransferase |
| ThiI: | tRNA sulfurtransferase |
| TiaS: | tRNAIle‐agmatidine synthetase |
| TilS: | tRNAIle‐lysidine synthetase |
| Tit1: | tRNA isopentenyltransferase 1 |
| tmRNA: | transfer‐messenger RNA |
| TOR: | target of rapamycin |
| TP53: | tumor protein P53 |
| TPA: | 12‐O‐tetradecanoylphorbol‐13‐acetate |
| TPP: | thiamin pyrophosphate |
| TrhOP: | metallophos domain‐containing protein O or P |
| TRIT1: | tRNA isopentenyltransferase 1 |
| Trm‐G10: | tRNA (guanine‐10‐N 2)‐dimethyltransferase |
| Trm1: | tRNA methyltransferase 1 |
| Trm1p: | tRNA methyltransferase 1 protein |
| TRM4B: | tRNA cytosine‐C5‐methyltransferase |
| Trm5: | tRNA methyltransferase 5 |
| Trm6‐Trm61: | tRNA methyltransferases 6 and 61 |
| Trm8p/Trm82p: | tRNA (guanine‐N 7‐)‐methyltransferase |
| Trm9/Trm112: | tRNA (carboxymethyluridine(34)‐5‐O)‐methyltransferase protein |
| Trm10: | tRNA (guanine(9)‐N 1)‐methyltransferase |
| Trm11p/112p: | tRNA (guanine(10)‐N 2)‐methyltransferase |
| Trm140: | tRNA(Thr) (cytosine(32)‐N 3)‐methyltransferase |
| TrmA: | tRNA/tmRNA (uracil‐C5)‐methyltransferase |
| TrmD: | tRNA (guanine‐N 1‐)‐methyltransferase |
| TrmFO: | methylenetetrahydrofolate‐tRNA‐(uracil‐5‐)‐methyltransferase |
| TrmI: | tRNA m1A58/m7G46 methyltransferase |
| TrmM: | tRNA (adenosine(37)‐N 6)‐methyltransferase or YfiC or TrmN6 |
| TrmO: | tRNA methyltransferase O or tRNA (adenine(37)‐N 6‐methyltransferase |
| TrmU: | tRNA 5‐methylaminomethyl‐2‐thiouridylate methyltransferase |
| TRMT: | tRNA methyltransferase |
| TRMT1: | tRNA methyltransferase 1 or tRNA (guanine(26)‐N(2))‐dimethyltransferase |
| TRMT10: | tRNA methyltransferase 10 |
| TRMT2A: | tRNA methyltransferase 2A or tRNA (uracil‐5‐)‐methyltransferase |
| TRMT6: | tRNA methyltransferase 6 or tRNA (adenine(58)‐N(1))‐methyltransferase |
| TRMT12: | tRNA methyltransferase 12 homolog or tRNA wybutosine‐synthesizing protein 2 homolog |
| TRMT61A: | tRNA methyltransferase 61A or tRNA (adenine(58)‐N(1))‐methyltransferase |
| TRMT61B: | tRNA methyltransferase 61B or tRNA (adenine(58)‐N(1))‐methyltransferase |
| TRMT112: | tRNA methyltransferase 112 |
| TruA: | tRNA pseudouridine synthase A or Pus1 |
| TruB: | tRNA pseudouridine synthase B or Pus4 |
| TruD: | tRNA pseudouridine synthase D or Pus7 |
| TtcA: | tRNA‐cytidine‐32 2‐sulfurtransferase |
| TsaBCDE: | tRNA adenosine(37) threonylcarbamoyltransferase complex, dimerization subunit type 1; threonylcarbamoyladenylate synthase; tRNA adenosine(37) threonylcarbamoyltransferase complex, transferase subunit; tRNA adenosine(37) threonylcarbamoyltransferase complex, ATPase subunit type 1 |
| TsaC2: | threonylcarbamoyladenylate synthase |
| Tsr3: | acp transferase ribosome maturation factor |
| TuaA: | tRNA U47 acp transferase A or YfiP |
| Tum1: | thiosulfate sulfurtransferase |
| Tus: | sulfur carrier protein or Moa |
| TYW1‐5: | SAM‐dependent tRNA 4‐demethylwyosine synthases 1–5 |
| UTR: | untranslated region |
| WBSCR22: | Willams–Beuren syndrome chromosomal region 22 protein |
| WTAP: | Wilms Tumor 1‐Associating Protein |
| X‐DC: | X‐linked dyskeratosis congenita |
| YbbB: | tRNA 2‐selenouridine/geranyl‐2‐thiouridine synthase |
| YbeA: | m3Ψ synthase or RlmH |
| YhhQ: | queuosine precursor transporter |
| YrvO: | cysteine desulfurase |
| YTH: | YT521‐B protein domain |
| YTHDF1‐3: | YTH N 6‐methyladenosine RNA binding proteins 1–3 |
| ZCCHC4: | zinc finger CCHC‐type containing 4 |
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