FAIRsharing.3qh2tg; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:52.339479

modomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:52.339479

Other names: modomics

MODOMICS is the first comprehensive database system for biology of RNA modification. It integrates information about the chemical structure of modified nucleosides, their localization in RNA sequences, pathways of their biosynthesis and enzymes that carry out the respective reactions (together with their protein cofactors). Also included are the protein sequences, the structure data (if available), selected references from scientific literature, and links to other databases allowing to obtain comprehensive information about individual modified residues and proteins involved in their biosynthesis.

Webpage:

http://modomics.genesilico.pl/

Publications:

Publications
More detailed information about this field from each metasource.

MODOMICS: a database of RNA modification pathways--2013 update
PMID: 23118484
metasource: Fairsharing.org
version: FAIRsharing.org: MODOMICS; MODOMICS; DOI: https://doi.org/10.25504/FAIRsharing.3qh2tg; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

MODOMICS: a database of RNA modification pathways. 2008 update
PMID: 18854352
metasource: Fairsharing.org
version: FAIRsharing.org: MODOMICS; MODOMICS; DOI: https://doi.org/10.25504/FAIRsharing.3qh2tg; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

MODOMICS: a database of RNA modification pathways
PMID: 16381833
metasource: Fairsharing.org
version: FAIRsharing.org: MODOMICS; MODOMICS; DOI: https://doi.org/10.25504/FAIRsharing.3qh2tg; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

MODOMICS: An Operational Guide to the Use of the RNA Modification Pathways Database
PMID: 33835459
metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:52.339479

http://dx.doi.org/10.1093/nar/gks1007
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

MODOMICS: a database of RNA modification pathways--2013 update PubMed citations: 519.

519 articles citing: MODOMICS: a database of RNA modification pathways--2013 update

A multiplex platform for small RNA sequencing elucidates multifaceted tRNA stress response and translational regulation. PMID:35513407
The plant epitranscriptome: revisiting pseudouridine and 2'-O-methyl RNA modifications. PMID:35445501
Multi-omics approaches for biomarker discovery in early ovarian cancer diagnosis. PMID:35439677
Modified mRNA-Based Vaccines Against Coronavirus Disease 2019. PMID:35438579
Accurate quantification of 3'-terminal 2'-O-methylated small RNAs by utilizing oxidative deep sequencing and stem-loop RT-qPCR. PMID:35416629
Epitranscriptomic Reprogramming Is Required to Prevent Stress and Damage from Acetaminophen. PMID:35327975
Application of m6A and TME in Predicting the Prognosis and Treatment of Clear Cell Renal Cell Carcinoma. PMID:35281520
Distinct Roles of m5C RNA Methyltransferase NSUN2 in Major Gynecologic Cancers. PMID:35280737
Decreased RNA m6A methylation enhances the process of the epithelial mesenchymal transition and vasculogenic mimicry in glioblastoma. PMID:35261810
Directed Evolution Pipeline for the Improvement of Orthogonal Translation Machinery for Genetic Code Expansion at Sense Codons. PMID:35252113
"Superwobbling" and tRNA-34 Wobble and tRNA-37 Anticodon Loop Modifications in Evolution and Devolution of the Genetic Code. PMID:35207539
Profiling Selective Packaging of Host RNA and Viral RNA Modification in SARS-CoV-2 Viral Preparations. PMID:35186917
Looking for the skeleton in the closet-rare genetic diagnoses in patients with diabetes and skeletal manifestations. PMID:35137278
RNA modifications stabilize the tertiary structure of tRNAfMet by locally increasing conformational dynamics. PMID:35137185
Targeting PUS7 suppresses tRNA pseudouridylation and glioblastoma tumorigenesis. PMID:35121864
Comprehensive Analysis of Differentially Expressed Profiles of mRNA N6-Methyladenosine in Colorectal Cancer. PMID:35087827
Spectroscopic and Computational Investigation of the Epoxyqueuosine Reductase QueG Reveals Intriguing Similarities with the Reductive Dehalogenase PceA. PMID:35061353
Cancer stem cells: a major culprit of intra-tumor heterogeneity. PMID:35018226
Demethylase FTO promotes mechanical stress induced osteogenic differentiation of BMSCs with up-regulation of HIF-1α. PMID:35006515
N6-Methyladenosine Modifications in the Female Reproductive System: Roles in Gonad Development and Diseases. PMID:35002524
Modulation of Phase Separation by RNA: A Glimpse on N6-Methyladenosine Modification. PMID:34957114
TCF4 and HuR mediated-METTL14 suppresses dissemination of colorectal cancer via N6-methyladenosine-dependent silencing of ARRDC4. PMID:34916487
Epitranscriptomics of cardiovascular diseases (Review). PMID:34791505
AI applications in functional genomics. PMID:34765093
Target-Specific Profiling of RNA m5C Methylation Level Using Amplicon Sequencing. PMID:34694621
Regulation and Site-Specific Covalent Labeling of NSUN2 via Genetic Encoding Expansion. PMID:34680884
Dynamic changes in tRNA modifications and abundance during T cell activation. PMID:34642250
Modifications of the human tRNA anticodon loop and their associations with genetic diseases. PMID:34605973
RNA N6 -methyladenosine modification in the lethal teamwork of cancer stem cells and the tumor immune microenvironment: Current landscape and therapeutic potential. PMID:34586737
METTL14-Mediated miR-30c-1-3p Maturation Represses the Progression of Lung Cancer via Regulation of MARCKSL1 Expression. PMID:34586620
The Importance of the Epi-Transcriptome in Translation Fidelity. PMID:34564313
BERT-m7G: A Transformer Architecture Based on BERT and Stacking Ensemble to Identify RNA N7-Methylguanosine Sites from Sequence Information. PMID:34484416
Evolution of Methyltransferase-Like (METTL) Proteins in Metazoa: A Complex Gene Family Involved in Epitranscriptomic Regulation and Other Epigenetic Processes. PMID:34480573
A novel view on an old drug, 5-fluorouracil: an unexpected RNA modifier with intriguing impact on cancer cell fate. PMID:34409299
Application of Modified mRNA in Somatic Reprogramming to Pluripotency and Directed Conversion of Cell Fate. PMID:34360910
Transcriptome-wide m6A profiling reveals mRNA post-transcriptional modification of boar sperm during cryopreservation. PMID:34344298
Chemical tagging for sensitive determination of uridine modifications in RNA. PMID:34123281
Structural model of the M7G46 Methyltransferase TrmB in complex with tRNA. PMID:34006170
Small RNAs are modified with N-glycans and displayed on the surface of living cells. PMID:34004145
Role of N6-methyl-adenosine modification in mammalian embryonic development. PMID:33999093
Inosine in Biology and Disease. PMID:33921764
Convergence of mammalian RQC and C-end rule proteolytic pathways via alanine tailing. PMID:33909987
A Bayesian hierarchical model for analyzing methylated RNA immunoprecipitation sequencing data. PMID:33833899
SMITER-A Python Library for the Simulation of LC-MS/MS Experiments. PMID:33799543
Molecular mechanism of RNase R substrate sensitivity for RNA ribose methylation. PMID:33788943
Modeling multi-species RNA modification through multi-task curriculum learning. PMID:33744973
Replacing thymine with a strongly pairing fifth Base: A combined quantum mechanics and molecular dynamics study. PMID:33738080
Mettl14-mediated m6A modification modulates neuron apoptosis during the repair of spinal cord injury by regulating the transformation from pri-mir-375 to miR-375. PMID:33706799
Characterizing RNA Pseudouridylation by Convolutional Neural Networks. PMID:33631424
The m6A methylome of SARS-CoV-2 in host cells. PMID:33510385
tsRNAs: Novel small molecules from cell function and regulatory mechanism to therapeutic targets. PMID:33507586
Terpene Chain Length Affects the Base Pairing Discrimination of S-geranyl-2-thiouridine in RNA Duplex. PMID:33319183
NOP10 predicts lung cancer prognosis and its associated small nucleolar RNAs drive proliferation and migration. PMID:33288886
A substrate binding model for the KEOPS tRNA modifying complex. PMID:33277478
Crystal structure of the yeast heterodimeric ADAT2/3 deaminase. PMID:33272269
CIGAR-seq, a CRISPR/Cas-based method for unbiased screening of novel mRNA modification regulators. PMID:33251765
The epitranscriptome beyond m6A. PMID:33188361
The epitranscriptome in stem cell biology and neural development. PMID:33065280
Nuclear metabolism and the regulation of the epigenome. PMID:33046909
Prader-Willi syndrome: reflections on seminal studies and future therapies. PMID:32961075
Hepatic FTO is dispensable for the regulation of metabolism but counteracts HCC development in vivo. PMID:32956847
Base pairing, structural and functional insights into N4-methylcytidine (m4C) and N4,N4-dimethylcytidine (m42C) modified RNA. PMID:32941619
Alkylative damage of mRNA leads to ribosome stalling and rescue by trans translation in bacteria. PMID:32940602
Records of RNA locations in living yeast revealed through covalent marks. PMID:32907940
tRNA-modifying enzyme mutations induce codon-specific mistranslation and protein aggregation in yeast. PMID:32893724
Toward Developing Therapies against Corona Virus: Synthesis and Anti-Avian Influenza Virus Activity of Novel Cytosine Thioglycoside Analogues. PMID:32832758
Epigenetic loss of the transfer RNA-modifying enzyme TYW2 induces ribosome frameshifts in colon cancer. PMID:32778592
Fat mass and obesity-associated protein promotes the tumorigenesis and development of liver cancer. PMID:32724383
Bioinformatics approaches for deciphering the epitranscriptome: Recent progress and emerging topics. PMID:32670500
Probing the diversity and regulation of tRNA modifications. PMID:32663792
Prediction of m5C Modifications in RNA Sequences by Combining Multiple Sequence Features. PMID:32645685
Amino Acid Modified RNA Bases as Building Blocks of an Early Earth RNA-Peptide World. PMID:32573861
Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping. PMID:32555463
METTL14-mediated N6-methyladenosine modification of SOX4 mRNA inhibits tumor metastasis in colorectal cancer. PMID:32552762
New twists on long noncoding RNAs: from mobile elements to motile cancer cells. PMID:32522127
Comparative tRNA sequencing and RNA mass spectrometry for surveying tRNA modifications. PMID:32514182
Novel Biallelic NSUN3 Variants Cause Early-Onset Mitochondrial Encephalomyopathy and Seizures. PMID:32488845
Detection and quantification of glycosylated queuosine modified tRNAs by acid denaturing and APB gels. PMID:32439717
Prebiotic Nucleoside Synthesis: The Selectivity of Simplicity. PMID:32428355
BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks. PMID:32423472
Functional characterization of the human tRNA methyltransferases TRMT10A and TRMT10B. PMID:32392304
Genome-wide analysis revealed novel molecular features and evolution of Anti-codons in cyanobacterial tRNAs. PMID:32346324
Targeting mitochondrial and cytosolic substrates of TRIT1 isopentenyltransferase: Specificity determinants and tRNA-i6A37 profiles. PMID:32324744
METTL14 promotes the migration and invasion of breast cancer cells by modulating N6‑methyladenosine and hsa‑miR‑146a‑5p expression. PMID:32323801
Novel insight into the regulatory roles of diverse RNA modifications: Re-defining the bridge between transcription and translation. PMID:32303268
Germline Elongator mutations in Sonic Hedgehog medulloblastoma. PMID:32296180
The nature of the purine at position 34 in tRNAs of 4-codon boxes is correlated with nucleotides at positions 32 and 38 to maintain decoding fidelity. PMID:32266934
Mapping and editing of nucleic acid modifications. PMID:32257049
MTA, an RNA m6A Methyltransferase, Enhances Drought Tolerance by Regulating the Development of Trichomes and Roots in Poplar. PMID:32252292
Proteomic and interactomic insights into the molecular basis of cell functional diversity. PMID:32235894
Analysis of mitochondrial m1A/G RNA modification reveals links to nuclear genetic variants and associated disease processes. PMID:32221480
Two genomes, one cell: Mitochondrial-nuclear coordination via epigenetic pathways. PMID:32217072
Malignant Evaluation and Clinical Prognostic Values of m6A RNA Methylation Regulators in Glioblastoma. PMID:32211315
The guide sRNA sequence determines the activity level of box C/D RNPs. PMID:32202498
The emerging roles of N6-methyladenosine (m6A) deregulation in liver carcinogenesis. PMID:32111216
The critical function of the plastid rRNA methyltransferase, CMAL, in ribosome biogenesis and plant development. PMID:32095829
The Arabidopsis TRM61/TRM6 complex is a bona fide tRNA N1-methyladenosine methyltransferase. PMID:32095811
Ribonucleic Acid Sequence Characterization by Negative Electron Transfer Dissociation Mass Spectrometry. PMID:32091202
Elongator Subunit 3 (Elp3) Is Required for Zebrafish Trunk Development. PMID:32023806
TRMT2B is responsible for both tRNA and rRNA m5U-methylation in human mitochondria. PMID:31948311
Arabidopsis TRM5 encodes a nuclear-localised bifunctional tRNA guanine and inosine-N1-methyltransferase that is important for growth. PMID:31756231
Antibiotic Resistance and Epigenetics: More to It than Meets the Eye. PMID:31740560
RNAm5CPred: Prediction of RNA 5-Methylcytosine Sites Based on Three Different Kinds of Nucleotide Composition. PMID:31726390
High-resolution ion mobility spectrometry-mass spectrometry of isomeric/isobaric ribonucleotide variants. PMID:31697854
Epitranscriptomic marks: Emerging modulators of RNA virus gene expression. PMID:31694072
RNA Regulators in Leukemia and Lymphoma. PMID:31615866
Development and validation of monoclonal antibodies against N6-methyladenosine for the detection of RNA modifications. PMID:31577817
Germline NPM1 mutations lead to altered rRNA 2'-O-methylation and cause dyskeratosis congenita. PMID:31570891
Detection of internal N7-methylguanosine (m7G) RNA modifications by mutational profiling sequencing. PMID:31504776
Modulating Mistranslation Potential of tRNASer in Saccharomyces cerevisiae. PMID:31484688
Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis. PMID:31439691
Structural and Energetic Effects of O2'-Ribose Methylation of Protonated Pyrimidine Nucleosides. PMID:31435890
Pseudouridine synthase 7 impacts Candida albicans rRNA processing and morphological plasticity. PMID:31364194
m1A Regulated Genes Modulate PI3K/AKT/mTOR and ErbB Pathways in Gastrointestinal Cancer. PMID:31352195
Structural insights into dimethylation of 12S rRNA by TFB1M: indispensable role in translation of mitochondrial genes and mitochondrial function. PMID:31251801
Identification and Quantification of Modified Nucleosides in Saccharomyces cerevisiae mRNAs. PMID:31243956
RNA m6A methylation regulates the epithelial mesenchymal transition of cancer cells and translation of Snail. PMID:31061416
METTL1 Promotes let-7 MicroRNA Processing via m7G Methylation. PMID:31031083
N1-Methyladenosine detection with CRISPR-Cas13a/C2c2. PMID:30996876
Recent Developments in mRNA-Based Protein Supplementation Therapy to Target Lung Diseases. PMID:30905577
Transcriptome-wide profiling of multiple RNA modifications simultaneously at single-base resolution. PMID:30872485
Regulation of transposable elements by DNA modifications. PMID:30867571
Emerging Role of Eukaryote Ribosomes in Translational Control. PMID:30862090
Incorporation of an Epigenetic Evaluation into Safety Assessment: What we First Need to Know. PMID:30740577
The Elongator subunit Elp3 is a non-canonical tRNA acetyltransferase. PMID:30733442
Bisulfite-free and base-resolution analysis of 5-methylcytidine and 5-hydroxymethylcytidine in RNA with peroxotungstate. PMID:30723849
Validation of a Metabolite Panel for a More Accurate Estimation of Glomerular Filtration Rate Using Quantitative LC-MS/MS. PMID:30647123
The RNA degradosome promotes tRNA quality control through clearance of hypomodified tRNA. PMID:30622183
Global analysis of tRNA and translation factor expression reveals a dynamic landscape of translational regulation in human cancers. PMID:30588513
Lifestyle modifications: coordinating the tRNA epitranscriptome with codon bias to adapt translation during stress responses. PMID:30587213
Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis. PMID:30559359
AtTrm5a catalyses 1-methylguanosine and 1-methylinosine formation on tRNAs and is important for vegetative and reproductive growth in Arabidopsis thaliana. PMID:30508117
Neuroepigenetic mechanisms underlying fear extinction: emerging concepts. PMID:30506235
N 6-Methyladenosine modification: a novel pharmacological target for anti-cancer drug development. PMID:30505654
FMRP Interacts with C/D Box snoRNA in the Nucleus and Regulates Ribosomal RNA Methylation. PMID:30469012
Inosine induces context-dependent recoding and translational stalling. PMID:30462291
Visualizing the Role of 2'-OH rRNA Methylations in the Human Ribosome Structure. PMID:30366442
Emerging function of N6-methyladenosine in cancer. PMID:30344705
Analysis of impact metrics for the Protein Data Bank. PMID:30325351
tRNA epitranscriptomics and biased codon are linked to proteome expression in Plasmodium falciparum. PMID:30287681
Interaction of rRNA with mRNA and tRNA in Translating Mammalian Ribosome: Functional Implications in Health and Disease. PMID:30261607
Landscape of the complete RNA chemical modifications in the human 80S ribosome. PMID:30202881
Uridine Depletion and Chemical Modification Increase Cas9 mRNA Activity and Reduce Immunogenicity without HPLC Purification. PMID:30195789
A novel malic acid-enhanced method for the analysis of 5-methyl-2'-deoxycytidine, 5-hydroxymethyl-2'-deoxycytidine, 5-methylcytidine and 5-hydroxymethylcytidine in human urine using hydrophilic interaction liquid chromatography-tandem mass spectrometry. PMID:30193624
Identification of the minimal bacterial 2'-deoxy-7-amido-7-deazaguanine synthesis machinery. PMID:30159947
Elongator mutation in mice induces neurodegeneration and ataxia-like behavior. PMID:30097576
TYW1: A Radical SAM Enzyme Involved in the Biosynthesis of Wybutosine Bases. PMID:30097090
Facile Solid-Phase Synthesis and Assessment of Nucleoside Analogs as Inhibitors of Bacterial UDP-Sugar Processing Enzymes. PMID:30080379
Direct quantification of 3' terminal 2'-O-methylation of small RNAs by RT-qPCR. PMID:30076204
Imbalance learning for the prediction of N6-Methylation sites in mRNAs. PMID:30068294
Formation and determination of the oxidation products of 5-methylcytosine in RNA. PMID:30034689
Novel insights on m6A RNA methylation in tumorigenesis: a double-edged sword. PMID:30031372
A rationale for tRNA modification circuits in the anticodon loop. PMID:30026310
Identification of a novel tRNA wobble uridine modifying activity in the biosynthesis of 5-methoxyuridine. PMID:29982645
Above the Epitranscriptome: RNA Modifications and Stem Cell Identity. PMID:29958477
Genome-Wide Analysis Reveals Ancestral Lack of Seventeen Different tRNAs and Clade-Specific Loss of tRNA-CNNs in Archaea. PMID:29930548
Epitranscriptomics of cancer. PMID:29900123
Structural insights into the stimulation of S. pombe Dnmt2 catalytic efficiency by the tRNA nucleoside queuosine. PMID:29892076
Turning Uridines around: Role of rRNA Pseudouridylation in Ribosome Biogenesis and Ribosomal Function. PMID:29874862
iRNA-3typeA: Identifying Three Types of Modification at RNA's Adenosine Sites. PMID:29858081
Structural and biochemical analysis of the dual-specificity Trm10 enzyme from Thermococcus kodakaraensis prompts reconsideration of its catalytic mechanism. PMID:29848639
Nuclear m6A reader YTHDC1 regulates alternative polyadenylation and splicing during mouse oocyte development. PMID:29799838
Biochemical and Structural Characterization of a Schiff Base in the Radical-Mediated Biosynthesis of 4-Demethylwyosine by TYW1. PMID:29792696
RNA-modifying proteins as anticancer drug targets. PMID:29773918
CO2-sensitive tRNA modification associated with human mitochondrial disease. PMID:29760464
Differentially abundant proteins associated with heterosis in the primary roots of popcorn. PMID:29758068
The structure of the TsaB/TsaD/TsaE complex reveals an unexpected mechanism for the bacterial t6A tRNA-modification. PMID:29741707
Transcriptome-Wide Annotation of m5C RNA Modifications Using Machine Learning. PMID:29720995
The Emerging Field of Epitranscriptomics in Neurodevelopmental and Neuronal Disorders. PMID:29707539
RNA N6-methyladenosine modification in cancers: current status and perspectives. PMID:29686311
A Brief Review on the Pathological Role of Decreased Blood Flow Affected in Retinitis Pigmentosa. PMID:29682340
MicroRNA MultiTool: A Software for Identifying Modified and Unmodified Human microRNA Using Mass Spectrometry. PMID:29657285
Recent Advances in Identification of RNA Modifications. PMID:29657273
Structure-function analysis of Sua5 protein reveals novel functional motifs required for the biosynthesis of the universal t6A tRNA modification. PMID:29650678
Lack of 2'-O-methylation in the tRNA anticodon loop of two phylogenetically distant yeast species activates the general amino acid control pathway. PMID:29596413
Deciphering the reading of the genetic code by near-cognate tRNA. PMID:29507244
SUMOylation of the m6A-RNA methyltransferase METTL3 modulates its function. PMID:29506078
The Role of Noncoding RNA Pseudouridylation in Nuclear Gene Expression Events. PMID:29473035
Heavy Chronic Intermittent Ethanol Exposure Alters Small Noncoding RNAs in Mouse Sperm and Epididymosomes. PMID:29472946
LET's sponge: How the lncRNA PFL promotes cardiac fibrosis. PMID:29463987
Modifications and functional genomics of human transfer RNA. PMID:29463900
Distinguishing RNA modifications from noise in epitranscriptome maps. PMID:29443978
Structural and evolutionary insights into ribosomal RNA methylation. PMID:29443970
Detecting RNA base methylations in single cells by in situ hybridization. PMID:29440632
The Effects of Ultraviolet Radiation on Nucleoside Modifications in RNA. PMID:29400945
Metabolic and chemical regulation of tRNA modification associated with taurine deficiency and human disease. PMID:29390138
Unique tRNA gene profile suggests paucity of nucleotide modifications in anticodons of a deep-sea symbiotic Spiroplasma. PMID:29390076
Positive-sense RNA viruses reveal the complexity and dynamics of the cellular and viral epitranscriptomes during infection. PMID:29373715
Rooted tRNAomes and evolution of the genetic code. PMID:29372672
Selective terminal methylation of a tRNA wobble base. PMID:29361055
Nutrient depletion and TOR inhibition induce 18S and 25S ribosomal RNAs resistant to a 5'-phosphate-dependent exonuclease in Candida albicans and other yeasts. PMID:29351732
Drugging tRNA aminoacylation. PMID:29345185
RFAthM6A: a new tool for predicting m6A sites in Arabidopsis thaliana. PMID:29340952
Tet protein function during Drosophila development. PMID:29324752
Unveiling structural and functional divergences of bacterial tRNA dihydrouridine synthases: perspectives on the evolution scenario. PMID:29294097
ALKBH5-dependent m6A demethylation controls splicing and stability of long 3'-UTR mRNAs in male germ cells. PMID:29279410
Reduced m6A mRNA methylation is correlated with the progression of human cervical cancer. PMID:29228737
Most m6A RNA Modifications in Protein-Coding Regions Are Evolutionarily Unconserved and Likely Nonfunctional. PMID:29228327
A hypertension-associated mitochondrial DNA mutation introduces an m1G37 modification into tRNAMet, altering its structure and function. PMID:29222331
Structural insight into the methyltransfer mechanism of the bifunctional Trm5. PMID:29214216
The fungal snoRNAome. PMID:29196413
MINTbase v2.0: a comprehensive database for tRNA-derived fragments that includes nuclear and mitochondrial fragments from all The Cancer Genome Atlas projects. PMID:29186503
Visualization of chemical modifications in the human 80S ribosome structure. PMID:29143818
The Dark Side of the Epitranscriptome: Chemical Modifications in Long Non-Coding RNAs. PMID:29125541
N6-Allyladenosine: A New Small Molecule for RNA Labeling Identified by Mutation Assay. PMID:29116772
Engineering of a DNA Polymerase for Direct m6 A Sequencing. PMID:29115744
Base-Resolution Mapping Reveals Distinct m1A Methylome in Nuclear- and Mitochondrial-Encoded Transcripts. PMID:29107537
MODOMICS: a database of RNA modification pathways. 2017 update. PMID:29106616
RNA Pseudouridylation in Physiology and Medicine: For Better and for Worse. PMID:29104216
RNA cytosine methyltransferase Nsun3 regulates embryonic stem cell differentiation by promoting mitochondrial activity. PMID:29103146
The m1A landscape on cytosolic and mitochondrial mRNA at single-base resolution. PMID:29072297
Biogenesis and iron-dependency of ribosomal RNA hydroxylation. PMID:29069499
Epitranscriptomic influences on development and disease. PMID:29061143
RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data. PMID:29040692
Profiling Cytidine Acetylation with Specific Affinity and Reactivity. PMID:29039931
Cdk5rap1-mediated 2-methylthio-N6-isopentenyladenosine modification is absent from nuclear-derived RNA species. PMID:28981754
Editing the Genome Without Double-Stranded DNA Breaks. PMID:28957631
Protein folding and tRNA biology. PMID:28944442
Experience-dependent neural plasticity, learning, and memory in the era of epitranscriptomics. PMID:28926184
Mechanistic features of the atypical tRNA m1G9 SPOUT methyltransferase, Trm10. PMID:28911116
Synthesis and Multiple Incorporations of 2'-O-Methyl-5-hydroxymethylcytidine, 5-Hydroxymethylcytidine and 5-Formylcytidine Monomers into RNA Oligonucleotides. PMID:28901692
The emerging complexity of the tRNA world: mammalian tRNAs beyond protein synthesis. PMID:28875994
Quantification of Pseudouridine Levels in Cellular RNA Pools with a Modified HPLC-UV Assay. PMID:28872587
QNB: differential RNA methylation analysis for count-based small-sample sequencing data with a quad-negative binomial model. PMID:28859631
The RNA modification landscape in human disease. PMID:28855326
mRNA pseudouridylation affects RNA metabolism in the parasite Toxoplasma gondii. PMID:28851751
The role of intracellular compartmentalization on tRNA processing and modification. PMID:28850002
A-to-I RNA editing - thinking beyond the single nucleotide. PMID:28820319
Celebrating wobble decoding: Half a century and still much is new. PMID:28812932
Editorial: RNA modifications - what to read first? PMID:28795877
Characterizing Expression and Processing of Precursor and Mature Human tRNAs by Hydro-tRNAseq and PAR-CLIP. PMID:28793268
TRMT1-Catalyzed tRNA Modifications Are Required for Redox Homeostasis To Ensure Proper Cellular Proliferation and Oxidative Stress Survival. PMID:28784718
The mitochondrial epitranscriptome: the roles of RNA modifications in mitochondrial translation and human disease. PMID:28752201
Novel ribonuclease activity of cusativin from Cucumis sativus for mapping nucleoside modifications in RNA. PMID:28730304
The t6A modification acts as a positive determinant for the anticodon nuclease PrrC, and is distinctively nonessential in Streptococcus mutans. PMID:28726545
Statistically robust methylation calling for whole-transcriptome bisulfite sequencing reveals distinct methylation patterns for mouse RNAs. PMID:28684555
The N6-Methyladenosine RNA modification in pluripotency and reprogramming. PMID:28683341
The m6A pathway facilitates sex determination in Drosophila. PMID:28675155
Three distinct 3-methylcytidine (m3C) methyltransferases modify tRNA and mRNA in mice and humans. PMID:28655767
AML1-ETO requires enhanced C/D box snoRNA/RNP formation to induce self-renewal and leukaemia. PMID:28650479
iRNA-PseColl: Identifying the Occurrence Sites of Different RNA Modifications by Incorporating Collective Effects of Nucleotides into PseKNC. PMID:28624191
Dynamic RNA Modifications in Gene Expression Regulation. PMID:28622506
The Evolution of Substrate Specificity by tRNA Modification Enzymes. PMID:28601226
Posttranscriptional RNA Pseudouridylation. PMID:28601221
The Importance of Being Modified: The Role of RNA Modifications in Translational Fidelity. PMID:28601219
Evolving Mistranslating tRNAs Through a Phenotypically Ambivalent Intermediate in Saccharomyces cerevisiae. PMID:28576863
Identification of an optimized 2'-O-methylated trinucleotide RNA motif inhibiting Toll-like receptors 7 and 8. PMID:28576825
Understanding RNA modifications: the promises and technological bottlenecks of the 'epitranscriptome'. PMID:28566301
Label-free, direct localization and relative quantitation of the RNA nucleobase methylations m6A, m5C, m3U, and m5U by top-down mass spectrometry. PMID:28549193
Epitranscriptomics: Toward A Better Understanding of RNA Modifications. PMID:28533024
Structural basis for substrate binding and catalytic mechanism of a human RNA:m5C methyltransferase NSun6. PMID:28531330
Nm-seq maps 2'-O-methylation sites in human mRNA with base precision. PMID:28504680
Identification of factors required for m6 A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI. PMID:28503769
Observing the fate of tRNA and its modifications by nucleic acid isotope labeling mass spectrometry: NAIL-MS. PMID:28488916
ALKBH1 is an RNA dioxygenase responsible for cytoplasmic and mitochondrial tRNA modifications. PMID:28472312
The Profile and Dynamics of RNA Modifications in Animals. PMID:28449301
Biochemical and structural characterization of oxygen-sensitive 2-thiouridine synthesis catalyzed by an iron-sulfur protein TtuA. PMID:28439027
Clostridioides difficile 630Δerm in silico and in vivo - quantitative growth and extensive polysaccharide secretion. PMID:28396843
tRNA Modifications: Impact on Structure and Thermal Adaptation. PMID:28375166
The 2'-O-methyladenosine nucleoside modification gene OsTRM13 positively regulates salt stress tolerance in rice. PMID:28369540
A fly view on the roles and mechanisms of the m6A mRNA modification and its players. PMID:28353398
High-Throughput Small RNA Sequencing Enhanced by AlkB-Facilitated RNA de-Methylation (ARM-Seq). PMID:28349464
In Silico Identification of RNA Modifications from High-Throughput Sequencing Data Using HAMR. PMID:28349463
A to I editing in disease is not fake news. PMID:28346055
Diverse Mechanisms of Sulfur Decoration in Bacterial tRNA and Their Cellular Functions. PMID:28327539
The central role of tRNA in genetic code expansion. PMID:28323071
Chemical and Conformational Diversity of Modified Nucleosides Affects tRNA Structure and Function. PMID:28300792
m6A RNA Methylation Regulates the Self-Renewal and Tumorigenesis of Glioblastoma Stem Cells. PMID:28297667
FUSION-Guided Hypothesis Development Leads to the Identification of N⁶,N⁶-Dimethyladenosine, a Marine-Derived AKT Pathway Inhibitor. PMID:28294973
Biosynthesis of Sulfur-Containing tRNA Modifications: A Comparison of Bacterial, Archaeal, and Eukaryotic Pathways. PMID:28287455
Regulation of Mammalian Mitochondrial Gene Expression: Recent Advances. PMID:28285835
Factors That Shape Eukaryotic tRNAomes: Processing, Modification and Anticodon-Codon Use. PMID:28282871
The modified base isopentenyladenosine and its derivatives in tRNA. PMID:28277934
Antibodies specific for nucleic acid modifications. PMID:28277931
tRNA N6-adenosine threonylcarbamoyltransferase defect due to KAE1/TCS3 (OSGEP) mutation manifest by neurodegeneration and renal tubulopathy. PMID:28272532
Modulation of the Proteostasis Machinery to Overcome Stress Caused by Diminished Levels of t6A-Modified tRNAs in Drosophila. PMID:28272317
mRNA N6-methyladenosine methylation of postnatal liver development in pig. PMID:28267806
Transfer RNA methyltransferases with a SpoU-TrmD (SPOUT) fold and their modified nucleosides in tRNA. PMID:28264529
Mapping Post-Transcriptional Modifications onto Transfer Ribonucleic Acid Sequences by Liquid Chromatography Tandem Mass Spectrometry. PMID:28241457
Editing and methylation at a single site by functionally interdependent activities. PMID:28230119
Sulfur Modifications of the Wobble U34 in tRNAs and their Intracellular Localization in Eukaryotic Cells. PMID:28218716
Detecting RNA modifications in the epitranscriptome: predict and validate. PMID:28216634
Next-Generation Sequencing-Based RiboMethSeq Protocol for Analysis of tRNA 2'-O-Methylation. PMID:28208788
Pseudouridine and N6-methyladenosine modifications weaken PUF protein/RNA interactions. PMID:28138061
Role of Pseudouridine Formation by Deg1 for Functionality of Two Glutamine Isoacceptor tRNAs. PMID:28134782
Human m6A writers: Two subunits, 2 roles. PMID:28121234
2'-O-Methyl-5-hydroxymethylcytidine: A Second Oxidative Derivative of 5-Methylcytidine in RNA. PMID:28107630
Stable Isotope Labeling for Improved Comparative Analysis of RNA Digests by Mass Spectrometry. PMID:28105550
C5-substituents of uridines and 2-thiouridines present at the wobble position of tRNA determine the formation of their keto-enol or zwitterionic forms - a factor important for accuracy of reading of guanosine at the 3΄-end of the mRNA codons. PMID:28088758
TRUB1 is the predominant pseudouridine synthase acting on mammalian mRNA via a predictable and conserved code. PMID:28073919
Transcriptome-Wide Mapping of RNA 5-Methylcytosine in Arabidopsis mRNAs and Noncoding RNAs. PMID:28062751
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160
Eukaryotic stand-alone pseudouridine synthases - RNA modifying enzymes and emerging regulators of gene expression? PMID:28045575
Cytosine-5 RNA Methylation Regulates Neural Stem Cell Differentiation and Motility. PMID:28041877
Mapping of Complete Set of Ribose and Base Modifications of Yeast rRNA by RP-HPLC and Mung Bean Nuclease Assay. PMID:28033325
Epitranscriptome sequencing technologies: decoding RNA modifications. PMID:28032622
S. cerevisiae Trm140 has two recognition modes for 3-methylcytidine modification of the anticodon loop of tRNA substrates. PMID:28003514
Beyond the Triplet Code: Context Cues Transform Translation. PMID:27984720
Genome recoding by tRNA modifications. PMID:27974624
The emerging biology of RNA post-transcriptional modifications. PMID:27937535
Structural and functional characterization of the TYW3/Taw3 class of SAM-dependent methyltransferases. PMID:27932585
Modification of orthogonal tRNAs: unexpected consequences for sense codon reassignment. PMID:27915288
Identification of 2-methylthio cyclic N6-threonylcarbamoyladenosine (ms2ct6A) as a novel RNA modification at position 37 of tRNAs. PMID:27913733
A hydantoin isoform of cyclic N6-threonylcarbamoyladenosine (ct6A) is present in tRNAs. PMID:27913732
Two for the price of one: RNA modification enzymes as chaperones. PMID:27911836
Tuning the ribosome: The influence of rRNA modification on eukaryotic ribosome biogenesis and function. PMID:27911188
Modified mRNA as a therapeutic tool to induce cardiac regeneration in ischemic heart disease. PMID:27911047
Determinants of tRNA Recognition by the Radical SAM Enzyme RlmN. PMID:27902775
RNA binding to APOBEC deaminases; Not simply a substrate for C to U editing. PMID:27869537
From profiles to function in epigenomics. PMID:27867193
Evolution of tRNAPhe:imG2 methyltransferases involved in the biosynthesis of wyosine derivatives in Archaea. PMID:27852927
RNA modification enzyme TruB is a tRNA chaperone. PMID:27849601
CoverageAnalyzer (CAn): A Tool for Inspection of Modification Signatures in RNA Sequencing Profiles. PMID:27834909
N6-Methyladenine: A Conserved and Dynamic DNA Mark. PMID:27826841
Post-transcriptional gene regulation by mRNA modifications. PMID:27808276
RNAcentral: a comprehensive database of non-coding RNA sequences. PMID:27794554
ALKBH1-Mediated tRNA Demethylation Regulates Translation. PMID:27745969
Molecular basis for cytoplasmic RNA surveillance by uridylation-triggered decay in Drosophila. PMID:27729457
Crystallographic study of the 2-thioribothymidine-synthetic complex TtuA-TtuB from Thermus thermophilus. PMID:27710943
Sequence-specific and Shape-selective RNA Recognition by the Human RNA 5-Methylcytosine Methyltransferase NSun6. PMID:27703015
Epigenetic inheritance of acquired traits through sperm RNAs and sperm RNA modifications. PMID:27694809
Mtu1-Mediated Thiouridine Formation of Mitochondrial tRNAs Is Required for Mitochondrial Translation and Is Involved in Reversible Infantile Liver Injury. PMID:27689697
Evolving insights into RNA modifications and their functional diversity in the brain. PMID:27669990
RNAs Containing Modified Nucleotides Fail To Trigger RIG-I Conformational Changes for Innate Immune Signaling. PMID:27651356
Mitochondrial 16S rRNA Is Methylated by tRNA Methyltransferase TRMT61B in All Vertebrates. PMID:27631568
Crystal structures of the bifunctional tRNA methyltransferase Trm5a. PMID:27629654
tRNA base methylation identification and quantification via high-throughput sequencing. PMID:27613580
Methionine on the rise: how mitochondria changed their codon usage. PMID:27578810
Viral cell biology: HIV RNA gets methylated. PMID:27572449
Reactive sulfur species regulate tRNA methylthiolation and contribute to insulin secretion. PMID:27568003
S-Geranyl-2-thiouridine wobble nucleosides of bacterial tRNAs; chemical and enzymatic synthesis of S-geranylated-RNAs and their physicochemical characterization. PMID:27566149
The physiology and habitat of the last universal common ancestor. PMID:27562259
Pseudouridine in the Anticodon of Escherichia coli tRNATyr(QΨA) Is Catalyzed by the Dual Specificity Enzyme RluF. PMID:27551044
Cognitive neuroepigenetics: the next evolution in our understanding of the molecular mechanisms underlying learning and memory? PMID:27512601
RAMPred: identifying the N(1)-methyladenosine sites in eukaryotic transcriptomes. PMID:27511610
Antibiotic resistance evolved via inactivation of a ribosomal RNA methylating enzyme. PMID:27496281
An integrated, structure- and energy-based view of the genetic code. PMID:27448410
The notorious R.N.A. in the spotlight - drug or target for the treatment of disease. PMID:27415589
Molecular biology: A surprise beginning for RNA. PMID:27383782
Deficient methylation and formylation of mt-tRNA(Met) wobble cytosine in a patient carrying mutations in NSUN3. PMID:27356879
Translating the epitranscriptome. PMID:27345446
The complete chemical structure of Saccharomyces cerevisiae rRNA: partial pseudouridylation of U2345 in 25S rRNA by snoRNA snR9. PMID:27325748
Structural and functional analyses of the archaeal tRNA m2G/m22G10 methyltransferase aTrm11 provide mechanistic insights into site specificity of a tRNA methyltransferase that contains common RNA-binding modules. PMID:27325738
Messenger RNA modifications: Form, distribution, and function. PMID:27313037
Synthesis, base pairing and structure studies of geranylated RNA. PMID:27307604
Illumina-based RiboMethSeq approach for mapping of 2'-O-Me residues in RNA. PMID:27302133
Profiling of 2'-O-Me in human rRNA reveals a subset of fractionally modified positions and provides evidence for ribosome heterogeneity. PMID:27257078
Going global: the new era of mapping modifications in RNA. PMID:27251302
Recent advances in dynamic m6A RNA modification. PMID:27249342
Gene- and genome-based analysis of significant codon patterns in yeast, rat and mice genomes with the CUT Codon UTilization tool. PMID:27245397
Guitar: An R/Bioconductor Package for Gene Annotation Guided Transcriptomic Analysis of RNA-Related Genomic Features. PMID:27239475
NSUN3 methylase initiates 5-formylcytidine biogenesis in human mitochondrial tRNA(Met). PMID:27214402
N (6)-Methyladenosine (m(6)A) Methylation in mRNA with A Dynamic and Reversible Epigenetic Modification. PMID:27179969
An updated human snoRNAome. PMID:27174936
Deciphering the epitranscriptome: A green perspective. PMID:27172004
N(6)-Methyladenosine: a conformational marker that regulates the substrate specificity of human demethylases FTO and ALKBH5. PMID:27156733
RNA modifications: what have we learned and where are we headed? PMID:27140282
RNA folding with hard and soft constraints. PMID:27110276
Nucleoside modifications in the regulation of gene expression: focus on tRNA. PMID:27094388
Base pairing and structural insights into the 5-formylcytosine in RNA duplex. PMID:27079978
A homozygous truncating mutation in PUS3 expands the role of tRNA modification in normal cognition. PMID:27055666
Sequence mapping of transfer RNA chemical modifications by liquid chromatography tandem mass spectrometry. PMID:27033178
tRNAmodpred: A computational method for predicting posttranscriptional modifications in tRNAs. PMID:27016142
From Prebiotics to Probiotics: The Evolution and Functions of tRNA Modifications. PMID:26985907
Mitochondria single nucleotide variation across six blood cell types. PMID:26956645
Nucleic Acid Modifications in Regulation of Gene Expression. PMID:26933737
Archaea box C/D enzymes methylate two distinct substrate rRNA sequences with different efficiency. PMID:26925607
Silent Polymorphisms: Can the tRNA Population Explain Changes in Protein Properties? PMID:26901226
SRAMP: prediction of mammalian N6-methyladenosine (m6A) sites based on sequence-derived features. PMID:26896799
Transcriptome-wide mapping reveals reversible and dynamic N(1)-methyladenosine methylome. PMID:26863410
The dynamic N(1)-methyladenosine methylome in eukaryotic messenger RNA. PMID:26863196
Global translational impacts of the loss of the tRNA modification t6A in yeast. PMID:26798630
Exploiting tRNAs to Boost Virulence. PMID:26797637
Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code. PMID:26791911
Cracking the epitranscriptome. PMID:26787305
Regulation of translation dynamic and neoplastic conversion by tRNA and their pieces. PMID:26779404
Bioengineering of noncoding RNAs for research agents and therapeutics. PMID:26763749
Global Epitranscriptomics Profiling of RNA Post-Transcriptional Modifications as an Effective Tool for Investigating the Epitranscriptomics of Stress Response. PMID:26733207
Multisite-specific archaeosine tRNA-guanine transglycosylase (ArcTGT) from Thermoplasma acidophilum, a thermo-acidophilic archaeon. PMID:26721388
Milk: an epigenetic amplifier of FTO-mediated transcription? Implications for Western diseases. PMID:26691922
Biogenesis and growth phase-dependent alteration of 5-methoxycarbonylmethoxyuridine in tRNA anticodons. PMID:26681692
Structural and functional insights into tRNA binding and adenosine N1-methylation by an archaeal Trm10 homologue. PMID:26673726
A mass spectrometry-based method for direct determination of pseudouridine in RNA. PMID:26673725
GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes. PMID:26673694
The Epitranscriptome and Innate Immunity. PMID:26658668
RNA epigenetics--chemical messages for posttranscriptional gene regulation. PMID:26625014
Immuno-Northern Blotting: Detection of RNA Modifications by Using Antibodies against Modified Nucleosides. PMID:26606401
Posttranscriptional methylation of transfer and ribosomal RNA in stress response pathways, cell differentiation, and cancer. PMID:26599292
Site-Directed RNA Editing in Vivo Can Be Triggered by the Light-Driven Assembly of an Artificial Riboprotein. PMID:26594902
The epitranscriptome in modulating spatiotemporal RNA translation in neuronal post-synaptic function. PMID:26582006
Nucleotide modifications within bacterial messenger RNAs regulate their translation and are able to rewire the genetic code. PMID:26578598
Chemical Modifications Mark Alternatively Spliced and Uncapped Messenger RNAs in Arabidopsis. PMID:26561561
tDRmapper: challenges and solutions to mapping, naming, and quantifying tRNA-derived RNAs from human small RNA-sequencing data. PMID:26530785
An extensive allelic series of Drosophila kae1 mutants reveals diverse and tissue-specific requirements for t6A biogenesis. PMID:26516084
Mass spectrometry of modified RNAs: recent developments. PMID:26501195
Loss of a Conserved tRNA Anticodon Modification Perturbs Plant Immunity. PMID:26492405
RMBase: a resource for decoding the landscape of RNA modifications from high-throughput sequencing data. PMID:26464443
Attomole quantification and global profile of RNA modifications: Epitranscriptome of human neural stem cells. PMID:26438536
New Insights into the Biological Role of Mammalian ADARs; the RNA Editing Proteins. PMID:26437436
An extended dsRBD is required for post-transcriptional modification in human tRNAs. PMID:26429968
Dynamic modulation of Dnmt2-dependent tRNA methylation by the micronutrient queuine. PMID:26424849
Mutation in WDR4 impairs tRNA m(7)G46 methylation and causes a distinct form of microcephalic primordial dwarfism. PMID:26416026
The reverse transcription signature of N-1-methyladenosine in RNA-Seq is sequence dependent. PMID:26365242
Structural Basis for the Discriminative Recognition of N6-Methyladenosine RNA by the Human YT521-B Homology Domain Family of Proteins. PMID:26318451
Removing roadblocks to deep sequencing of modified RNAs. PMID:26317237
Defects in tRNA Anticodon Loop 2'-O-Methylation Are Implicated in Nonsyndromic X-Linked Intellectual Disability due to Mutations in FTSJ1. PMID:26310293
A glyS T-box riboswitch with species-specific structural features responding to both proteinogenic and nonproteinogenic tRNAGly isoacceptors. PMID:26276802
The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle. PMID:26257709
Radical SAM-Mediated Methylation of Ribosomal RNA. PMID:26253978
A Platform for Discovery and Quantification of Modified Ribonucleosides in RNA: Application to Stress-Induced Reprogramming of tRNA Modifications. PMID:26253965
ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments. PMID:26237225
Biochemical and Spectroscopic Studies of Epoxyqueuosine Reductase: A Novel Iron-Sulfur Cluster- and Cobalamin-Containing Protein Involved in the Biosynthesis of Queuosine. PMID:26230193
Detection of RNA nucleoside modifications with the uridine-specific ribonuclease MC1 from Momordica charantia. PMID:26221047
tRNA recognition by a bacterial tRNA Xm32 modification enzyme from the SPOUT methyltransferase superfamily. PMID:26202969
Enhanced detection of post-transcriptional modifications using a mass-exclusion list strategy for RNA modification mapping by LC-MS/MS. PMID:26176336
RNA N6-methyladenosine methylation in post-transcriptional gene expression regulation. PMID:26159994
Simultaneous Quantification of Methylated Cytidine and Adenosine in Cellular and Tissue RNA by Nano-Flow Liquid Chromatography-Tandem Mass Spectrometry Coupled with the Stable Isotope-Dilution Method. PMID:26158405
An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies. PMID:26117545
Specificity and catalysis hardwired at the RNA-protein interface in a translational proofreading enzyme. PMID:26113036
Identification of determinants for tRNA substrate recognition by Escherichia coli C/U34 2'-O-methyltransferase. PMID:26106808
Transfer RNAs Mediate the Rapid Adaptation of Escherichia coli to Oxidative Stress. PMID:26090660
Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome. PMID:26075521
Widespread occurrence of N6-methyladenosine in bacterial mRNA. PMID:26068471
The Levels of a Universally Conserved tRNA Modification Regulate Cell Growth. PMID:26063805
MINT: software to identify motifs and short-range interactions in trajectories of nucleic acids. PMID:26024667
A mass spectrometry-based method for comprehensive quantitative determination of post-transcriptional RNA modifications: the complete chemical structure of Schizosaccharomyces pombe ribosomal RNAs. PMID:26013808
Profiling ribonucleotide modifications at full-transcriptome level: a step toward MS-based epitranscriptomics. PMID:25995446
Structure and mechanism of the T-box riboswitches. PMID:25959893
piRNAs from Pig Testis Provide Evidence for a Conserved Role of the Piwi Pathway in Post-Transcriptional Gene Regulation in Mammals. PMID:25950437
Intermolecular 'cross-torque': the N4-cytosine propargyl residue is rotated to the 'CH'-edge as a result of Watson-Crick interaction. PMID:25934805
The crystal structure and small-angle X-ray analysis of CsdL/TcdA reveal a new tRNA binding motif in the MoeB/E1 superfamily. PMID:25897750
A novel family of integrases associated with prophages and genomic islands integrated within the tRNA-dihydrouridine synthase A (dusA) gene. PMID:25883135
Protein degradation and dynamic tRNA thiolation fine-tune translation at elevated temperatures. PMID:25870413
Determinants of the CmoB carboxymethyl transferase utilized for selective tRNA wobble modification. PMID:25855808
A common tRNA modification at an unusual location: the discovery of wyosine biosynthesis in mitochondria. PMID:25845597
RoboOligo: software for mass spectrometry data to support manual and de novo sequencing of post-transcriptionally modified ribonucleic acids. PMID:25820423
Highly Predictive Reprogramming of tRNA Modifications Is Linked to Selective Expression of Codon-Biased Genes. PMID:25772370
tRNA biology in mitochondria. PMID:25734984
2-Thiouracil deprived of thiocarbonyl function preferentially base pairs with guanine rather than adenine in RNA and DNA duplexes. PMID:25690900
Formation and abundance of 5-hydroxymethylcytosine in RNA. PMID:25676849
Replacing uridine with 2-thiouridine enhances the rate and fidelity of nonenzymatic RNA primer extension. PMID:25654265
Wybutosine biosynthesis: structural and mechanistic overview. PMID:25629788
Diversity of the biosynthesis pathway for threonylcarbamoyladenosine (t(6)A), a universal modification of tRNA. PMID:25629598
Diversity in mechanism and function of tRNA methyltransferases. PMID:25626150
Two-subunit enzymes involved in eukaryotic post-transcriptional tRNA modification. PMID:25625329
The identification and characterization of non-coding and coding RNAs and their modified nucleosides by mass spectrometry. PMID:25616408
Pseudouridine: still mysterious, but never a fake (uridine)! PMID:25616362
Distribution and frequencies of post-transcriptional modifications in tRNAs. PMID:25611331
Post-transcriptional modifications are very important after all. PMID:25607350
Substrate tRNA recognition mechanism of eubacterial tRNA (m1A58) methyltransferase (TrmI). PMID:25593312
RNA-guided isomerization of uridine to pseudouridine--pseudouridylation. PMID:25590339
Profiling of cis-diol-containing nucleosides and ribosylated metabolites by boronate-affinity organic-silica hybrid monolithic capillary liquid chromatography/mass spectrometry. PMID:25585609
Transfer RNA methyltransferases from Thermoplasma acidophilum, a thermoacidophilic archaeon. PMID:25546389
An evolutionary approach uncovers a diverse response of tRNA 2-thiolation to elevated temperatures in yeast. PMID:25505025
Structure and function of dioxygenases in histone demethylation and DNA/RNA demethylation. PMID:25485134
Unique features of the m6A methylome in Arabidopsis thaliana. PMID:25430002
Expanded microbial genome coverage and improved protein family annotation in the COG database. PMID:25428365
Human NAT10 is an ATP-dependent RNA acetyltransferase responsible for N4-acetylcytidine formation in 18 S ribosomal RNA (rRNA). PMID:25411247
Conservation of an intricate circuit for crucial modifications of the tRNAPhe anticodon loop in eukaryotes. PMID:25404562
RNA cytidine acetyltransferase of small-subunit ribosomal RNA: identification of acetylation sites and the responsible acetyltransferase in fission yeast, Schizosaccharomyces pombe. PMID:25402480
Decomposition of RNA methylome reveals co-methylation patterns induced by latent enzymatic regulators of the epitranscriptome. PMID:25370990
Diverse cell stresses induce unique patterns of tRNA up- and down-regulation: tRNA-seq for quantifying changes in tRNA copy number. PMID:25348403
tRNA modifications regulate translation during cellular stress. PMID:25304425
Decreased N(6)-methyladenosine in peripheral blood RNA from diabetic patients is associated with FTO expression rather than ALKBH5. PMID:25303482
Dye label interference with RNA modification reveals 5-fluorouridine as non-covalent inhibitor. PMID:25300485
Prediction of uridine modifications in tRNA sequences. PMID:25272949
Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA. PMID:25219674
Crystal structure studies of RNA duplexes containing s(2)U:A and s(2)U:U base pairs. PMID:25188906
A single acetylation of 18 S rRNA is essential for biogenesis of the small ribosomal subunit in Saccharomyces cerevisiae. PMID:25086048
Binding induced RNA conformational changes control substrate recognition and catalysis by the thiostrepton resistance methyltransferase (Tsr). PMID:25086036
A modified dinucleotide motif specifies tRNA recognition by TLR7. PMID:25051971
Systematic identification of tRNAome and its dynamics in Lactococcus lactis. PMID:25040919
Role of RNA methyltransferases in tissue renewal and pathology. PMID:25014650
Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5' sites. PMID:24981863
A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package. PMID:24979058
Argonaute-dependent small RNAs derived from single-stranded, non-structured precursors. PMID:24959173
Remarkable acceleration of a DNA/RNA inter-strand functionality transfer reaction to modify a cytosine residue: the proximity effect via complexation with a metal cation. PMID:24957600
The flavoprotein Mcap0476 (RlmFO) catalyzes m5U1939 modification in Mycoplasma capricolum 23S rRNA. PMID:24939895
BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles. PMID:24931994
Methylated nucleosides in tRNA and tRNA methyltransferases. PMID:24904644
Biosynthesis of wyosine derivatives in tRNA(Phe) of Archaea: role of a remarkable bifunctional tRNA(Phe):m1G/imG2 methyltransferase. PMID:24837075
A complete landscape of post-transcriptional modifications in mammalian mitochondrial tRNAs. PMID:24831542
tRNADB-CE: tRNA gene database well-timed in the era of big sequence data. PMID:24822057
Predicting the minimal translation apparatus: lessons from the reductive evolution of mollicutes. PMID:24809820
Biosynthesis and functions of sulfur modifications in tRNA. PMID:24765101
Metabolic de-isotoping for improved LC-MS characterization of modified RNAs. PMID:24760295
Angiogenin-cleaved tRNA halves interact with cytochrome c, protecting cells from apoptosis during osmotic stress. PMID:24752898
Molecular recognition and modification of the 30S ribosome by the aminoglycoside-resistance methyltransferase NpmA. PMID:24717845
The Dnmt2 RNA methyltransferase homolog of Geobacter sulfurreducens specifically methylates tRNA-Glu. PMID:24711368
Crystal structure of a 4-thiouridine synthetase-RNA complex reveals specificity of tRNA U8 modification. PMID:24705700
The multifaceted roles of RNA binding in APOBEC cytidine deaminase functions. PMID:24664896
Gene expression regulation mediated through reversible m⁶A RNA methylation. PMID:24662220
A highly conserved family of domains related to the DNA-glycosylase fold helps predict multiple novel pathways for RNA modifications. PMID:24646681
Crystal structures of the novel cytosolic 5'-nucleotidase IIIB explain its preference for m7GMP. PMID:24603684
Partial methylation at Am100 in 18S rRNA of baker's yeast reveals ribosome heterogeneity on the level of eukaryotic rRNA modification. PMID:24586927
Nucleic acid oxidation in DNA damage repair and epigenetics. PMID:24580634
Structure of human RNA N⁶-methyladenine demethylase ALKBH5 provides insights into its mechanisms of nucleic acid recognition and demethylation. PMID:24489119
Transcriptome-wide target profiling of RNA cytosine methyltransferases using the mechanism-based enrichment procedure Aza-IP. PMID:24434802
Quantitative analysis of rRNA modifications using stable isotope labeling and mass spectrometry. PMID:24422502
A system of RNA modifications and biased codon use controls cellular stress response at the level of translation. PMID:24422464
High-performance liquid chromatography purification of chemically modified RNA aptamers. PMID:24373999
Posttranscriptional RNA Modifications: playing metabolic games in a cell's chemical Legoland. PMID:24315934
Retrograde transfer RNA nuclear import provides a new level of tRNA quality control in Saccharomyces cerevisiae. PMID:24297920
Characterizing 5-methylcytosine in the mammalian epitranscriptome. PMID:24286375
Method for site-specific detection of m6A nucleoside presence in RNA based on high-resolution melting (HRM) analysis. PMID:24265225
snOPY: a small nucleolar RNA orthological gene database. PMID:24148649
LigandRNA: computational predictor of RNA-ligand interactions. PMID:24145824
Unusual noncanonical intron editing is important for tRNA splicing in Trypanosoma brucei. PMID:24095278
Indigenous and acquired modifications in the aminoglycoside binding sites of Pseudomonas aeruginosa rRNAs. PMID:23948732
Functional assignment of KEOPS/EKC complex subunits in the biosynthesis of the universal t6A tRNA modification. PMID:23945934
Yeast Nop2 and Rcm1 methylate C2870 and C2278 of the 25S rRNA, respectively. PMID:23913415
The tRNA recognition mechanism of the minimalist SPOUT methyltransferase, TrmL. PMID:23804755
Unexpected expansion of tRNA substrate recognition by the yeast m1G9 methyltransferase Trm10. PMID:23793893
Emerging roles for ribonucleoprotein modification and remodeling in controlling RNA fate. PMID:23756094
Structural and mechanistic basis for enhanced translational efficiency by 2-thiouridine at the tRNA anticodon wobble position. PMID:23727144
Identification of a novel methyltransferase, Bmt2, responsible for the N-1-methyl-adenosine base modification of 25S rRNA in Saccharomyces cerevisiae. PMID:23558746
Purification, crystallization and preliminary crystallographic analysis of a 4-thiouridine synthetase-RNA complex. PMID:23545650
CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction. PMID:23435231
The 2013 Nucleic Acids Research Database Issue and the online molecular biology database collection. PMID:23203983
MODOMICS: a database of RNA modification pathways. 2008 update PubMed citations: 107.

107 articles citing: MODOMICS: a database of RNA modification pathways. 2008 update

Genome-Wide Identification of m6A Writers, Erasers and Readers in Poplar 84K. PMID:35741780
"Superwobbling" and tRNA-34 Wobble and tRNA-37 Anticodon Loop Modifications in Evolution and Devolution of the Genetic Code. PMID:35207539
RNA modifications stabilize the tertiary structure of tRNAfMet by locally increasing conformational dynamics. PMID:35137185
Epitranscriptomics of cardiovascular diseases (Review). PMID:34791505
Single-molecule RNA sequencing for simultaneous detection of m6A and 5mC. PMID:34588546
The Latest Research Progress of m6A Modification and Its Writers, Erasers, Readers in Infertility: A Review. PMID:34568313
SMITER-A Python Library for the Simulation of LC-MS/MS Experiments. PMID:33799543
tRNA-modifying enzyme mutations induce codon-specific mistranslation and protein aggregation in yeast. PMID:32893724
Epitranscriptomic systems regulate the translation of reactive oxygen species detoxifying and disease linked selenoproteins. PMID:31476365
Structural and Energetic Effects of O2'-Ribose Methylation of Protonated Pyrimidine Nucleosides. PMID:31435890
Ncl1-mediated metabolic rewiring critical during metabolic stress. PMID:31416893
Significant epitranscriptomes in heterogeneous cancer. PMID:31187550
Translational Control under Stress: Reshaping the Translatome. PMID:31026340
AtTrm5a catalyses 1-methylguanosine and 1-methylinosine formation on tRNAs and is important for vegetative and reproductive growth in Arabidopsis thaliana. PMID:30508117
Structural insight into the human mitochondrial tRNA purine N1-methyltransferase and ribonuclease P complexes. PMID:29880640
MicroRNA MultiTool: A Software for Identifying Modified and Unmodified Human microRNA Using Mass Spectrometry. PMID:29657285
Transcriptome-wide Analysis of Roles for tRNA Modifications in Translational Regulation. PMID:29198561
Effect of Population Size and Mutation Rate on the Evolution of RNA Sequences on an Adaptive Landscape Determined by RNA Folding. PMID:29104505
Quantification of Pseudouridine Levels in Cellular RNA Pools with a Modified HPLC-UV Assay. PMID:28872587
Lost in Translation: Defects in Transfer RNA Modifications and Neurological Disorders. PMID:28536502
Trm5 and TrmD: Two Enzymes from Distinct Origins Catalyze the Identical tRNA Modification, m¹G37. PMID:28335556
Modification of orthogonal tRNAs: unexpected consequences for sense codon reassignment. PMID:27915288
Determinants of tRNA Recognition by the Radical SAM Enzyme RlmN. PMID:27902775
NSUN3 and ABH1 modify the wobble position of mt-tRNAMet to expand codon recognition in mitochondrial translation. PMID:27497299
Cytosine methylation of tRNA-Asp by DNMT2 has a role in translation of proteins containing poly-Asp sequences. PMID:27462411
From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF. PMID:27114493
Multiple Layers of Stress-Induced Regulation in tRNA Biology. PMID:27023616
Silent Polymorphisms: Can the tRNA Population Explain Changes in Protein Properties? PMID:26901226
Exploiting tRNAs to Boost Virulence. PMID:26797637
Milk: an epigenetic amplifier of FTO-mediated transcription? Implications for Western diseases. PMID:26691922
A Platform for Discovery and Quantification of Modified Ribonucleosides in RNA: Application to Stress-Induced Reprogramming of tRNA Modifications. PMID:26253965
2'-O-Methylation within Bacterial RNA Acts as Suppressor of TLR7/TLR8 Activation in Human Innate Immune Cells. PMID:25823462
Highly Predictive Reprogramming of tRNA Modifications Is Linked to Selective Expression of Codon-Biased Genes. PMID:25772370
N6-adenosine methylation in MiRNAs. PMID:25723394
Diversity in mechanism and function of tRNA methyltransferases. PMID:25626150
Distribution and frequencies of post-transcriptional modifications in tRNAs. PMID:25611331
Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes. PMID:25540822
Emerging roles of tRNA in adaptive translation, signalling dynamics and disease. PMID:25534324
Role of tautomerism in RNA biochemistry. PMID:25516996
tRNA modifications regulate translation during cellular stress. PMID:25304425
Prediction of uridine modifications in tRNA sequences. PMID:25272949
The rise of regulatory RNA. PMID:24776770
Quantitative analysis of ribonucleoside modifications in tRNA by HPLC-coupled mass spectrometry. PMID:24625781
A system of RNA modifications and biased codon use controls cellular stress response at the level of translation. PMID:24422464
HAMR: high-throughput annotation of modified ribonucleotides. PMID:24149843
Structural insights of non-canonical U*U pair and Hoogsteen interaction probed with Se atom. PMID:24013566
Targeting folded RNA: a branched peptide boronic acid that binds to a large surface area of HIV-1 RRE RNA. PMID:23925474
tRNA tKUUU, tQUUG, and tEUUC wobble position modifications fine-tune protein translation by promoting ribosome A-site binding. PMID:23836657
Transcriptome-wide mapping of 5-methylcytidine RNA modifications in bacteria, archaea, and yeast reveals m5C within archaeal mRNAs. PMID:23825970
Unexpected expansion of tRNA substrate recognition by the yeast m1G9 methyltransferase Trm10. PMID:23793893
Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function. PMID:23676670
Evaluating the reproducibility of quantifying modified nucleosides from ribonucleic acids by LC-UV-MS. PMID:23500350
N6-methyl-adenosine (m6A) in RNA: an old modification with a novel epigenetic function. PMID:23453015
A rapid and sensitive non-radioactive method applicable for genome-wide analysis of Saccharomyces cerevisiae genes involved in small RNA biology. PMID:23417998
A novel method for detecting 7-methyl guanine reveals aberrant methylation levels in Huntington disease. PMID:23416183
RNA pseudouridylation: new insights into an old modification. PMID:23391857
Decoding in Candidatus Riesia pediculicola, close to a minimal tRNA modification set? PMID:23308034
Transcriptome-wide mapping of N(6)-methyladenosine by m(6)A-seq based on immunocapturing and massively parallel sequencing. PMID:23288318
In vitro biosynthesis of a universal t6A tRNA modification in Archaea and Eukarya. PMID:23258706
BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA. PMID:23203881
RNApathwaysDB--a database of RNA maturation and decay pathways. PMID:23155061
MODOMICS: a database of RNA modification pathways--2013 update. PMID:23118484
Trmt61B is a methyltransferase responsible for 1-methyladenosine at position 58 of human mitochondrial tRNAs. PMID:23097428
Characterization and structure of the Aquifex aeolicus protein DUF752: a bacterial tRNA-methyltransferase (MnmC2) functioning without the usually fused oxidase domain (MnmC1). PMID:23091054
A subcomplex of human mitochondrial RNase P is a bifunctional methyltransferase--extensive moonlighting in mitochondrial tRNA biogenesis. PMID:23042678
The architecture of eukaryotic translation. PMID:22965119
The Escherichia coli RlmN methyltransferase is a dual-specificity enzyme that modifies both rRNA and tRNA and controls translational accuracy. PMID:22891362
Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins. PMID:22760636
Molecular evolution of dihydrouridine synthases. PMID:22741570
RNA mediated Toll-like receptor stimulation in health and disease. PMID:22617878
Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. PMID:22575960
Identification of modifications in microbial, native tRNA that suppress immunostimulatory activity. PMID:22312113
RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction. PMID:22287623
The archaeal COG1901/DUF358 SPOUT-methyltransferase members, together with pseudouridine synthase Pus10, catalyze the formation of 1-methylpseudouridine at position 54 of tRNA. PMID:22274953
Of P and Z: mitochondrial tRNA processing enzymes. PMID:22137969
YhiQ is RsmJ, the methyltransferase responsible for methylation of G1516 in 16S rRNA of E. coli. PMID:22079366
Comprehensive survey and geometric classification of base triples in RNA structures. PMID:22053086
Identification and modeling of a phosphatase-like domain in a tRNA 2'-O-ribosyl phosphate transferase Rit1p. PMID:22030622
RNAcentral: A vision for an international database of RNA sequences. PMID:21940779
Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems. PMID:21890906
A toolbox for developing bioinformatics software. PMID:21803787
Identification of N6,N6-dimethyladenosine in transfer RNA from Mycobacterium bovis Bacille Calmette-Guérin. PMID:21694680
Potential for interdependent development of tRNA determinants for aminoacylation and ribosome decoding. PMID:21629262
Functional consequences of T-stem mutations in E. coli tRNAThrUGU in vitro and in vivo. PMID:21527672
ModeRNA: a tool for comparative modeling of RNA 3D structure. PMID:21300639
Pseudouridylation goes regulatory. PMID:21206510
A quantitative systems approach reveals dynamic control of tRNA modifications during cellular stress. PMID:21187895
The RNA Modification Database, RNAMDB: 2011 update. PMID:21071406
REPAIRtoire--a database of DNA repair pathways. PMID:21051355
Mechanism of N-methylation by the tRNA m1G37 methyltransferase Trm5. PMID:20980671
Crystal structure of a novel JmjC-domain-containing protein, TYW5, involved in tRNA modification. PMID:20972222
Fidelity in archaeal information processing. PMID:20871851
New archaeal methyltransferases forming 1-methyladenosine or 1-methyladenosine and 1-methylguanosine at position 9 of tRNA. PMID:20525789
Functional characterization of the YmcB and YqeV tRNA methylthiotransferases of Bacillus subtilis. PMID:20472640
RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures. PMID:20459631
Origin and evolution of peptide-modifying dioxygenases and identification of the wybutosine hydroxylase/hydroperoxidase. PMID:20423905
Human AlkB homolog ABH8 Is a tRNA methyltransferase required for wobble uridine modification and DNA damage survival. PMID:20308323
Combination of the loss of cmnm5U34 with the lack of s2U34 modifications of tRNALys, tRNAGlu, and tRNAGln altered mitochondrial biogenesis and respiration. PMID:20004207
Stereochemical mechanisms of tRNA methyltransferases. PMID:19944101
Cellular dynamics of tRNAs and their genes. PMID:19931532
The box H/ACA ribonucleoprotein complex: interplay of RNA and protein structures in post-transcriptional RNA modification. PMID:19917616
Structure-function analysis of Escherichia coli MnmG (GidA), a highly conserved tRNA-modifying enzyme. PMID:19801413
An analytical platform for mass spectrometry-based identification and chemical analysis of RNA in ribonucleoprotein complexes. PMID:19740761
Structural basis of AdoMet-dependent aminocarboxypropyl transfer reaction catalyzed by tRNA-wybutosine synthesizing enzyme, TYW2. PMID:19717466
Structural organization of box C/D RNA-guided RNA methyltransferase. PMID:19666563
Snapshots of dynamics in synthesizing N(6)-isopentenyladenosine at the tRNA anticodon. PMID:19435325
Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids. PMID:19411852
MODOMICS: a database of RNA modification pathways PubMed citations: 98.

98 articles citing: MODOMICS: a database of RNA modification pathways

A systematic dissection of determinants and consequences of snoRNA-guided pseudouridylation of human mRNA. PMID:35536311
Regulatory Role of N6-Methyladenosine in Longissimus Dorsi Development in Yak. PMID:35498742
"Superwobbling" and tRNA-34 Wobble and tRNA-37 Anticodon Loop Modifications in Evolution and Devolution of the Genetic Code. PMID:35207539
RNA modifications stabilize the tertiary structure of tRNAfMet by locally increasing conformational dynamics. PMID:35137185
SMC1A regulated by KIAA1429 in m6A-independent manner promotes EMT progress in breast cancer. PMID:34976433
Integrating m6A Regulators-Mediated Methylation Modification Models and Tumor Immune Microenvironment Characterization in Caucasian and Chinese Low-Grade Gliomas. PMID:34900988
Epitranscriptomics of cardiovascular diseases (Review). PMID:34791505
HNRNPA2B1, as a m6A Reader, Promotes Tumorigenesis and Metastasis of Oral Squamous Cell Carcinoma. PMID:34631545
Degradation of host translational machinery drives tRNA acquisition in viruses. PMID:34143976
In lysate RNA digestion provides insights into the angiogenin's specificity towards transfer RNAs. PMID:34085908
Significance of RNA N6-Methyladenosine Regulators in the Diagnosis and Subtype Classification of Childhood Asthma Using the Gene Expression Omnibus Database. PMID:33763115
Overview of host miRNA properties and their association with epigenetics, long non-coding RNAs, and Xeno-infectious factors. PMID:33632341
Isolation and initial structure-functional characterization of endogenous tRNA-derived stress-induced RNAs. PMID:32116132
High-resolution ion mobility spectrometry-mass spectrometry of isomeric/isobaric ribonucleotide variants. PMID:31697854
Structural and Energetic Effects of O2'-Ribose Methylation of Protonated Pyrimidine Nucleosides. PMID:31435890
Cicada Endosymbionts Have tRNAs That Are Correctly Processed Despite Having Genomes That Do Not Encode All of the tRNA Processing Machinery. PMID:31213566
Deciphering the Epitranscriptomic Signatures in Cell Fate Determination and Development. PMID:31123982
AtTrm5a catalyses 1-methylguanosine and 1-methylinosine formation on tRNAs and is important for vegetative and reproductive growth in Arabidopsis thaliana. PMID:30508117
The m6A‑methylase complex and mRNA export. PMID:30290229
PseUI: Pseudouridine sites identification based on RNA sequence information. PMID:30157750
Positive-sense RNA viruses reveal the complexity and dynamics of the cellular and viral epitranscriptomes during infection. PMID:29373715
Role of RNA modifications in brain and behavior. PMID:29244246
Refactoring the Genetic Code for Increased Evolvability. PMID:29138304
Quantification of Pseudouridine Levels in Cellular RNA Pools with a Modified HPLC-UV Assay. PMID:28872587
Gene regulation in the immune system by long noncoding RNAs. PMID:28829444
The Evolution of Substrate Specificity by tRNA Modification Enzymes. PMID:28601226
Lost in Translation: Defects in Transfer RNA Modifications and Neurological Disorders. PMID:28536502
Epitranscriptomics: Toward A Better Understanding of RNA Modifications. PMID:28533024
The 2'-O-methyladenosine nucleoside modification gene OsTRM13 positively regulates salt stress tolerance in rice. PMID:28369540
Structural landscape of base pairs containing post-transcriptional modifications in RNA. PMID:28341704
Random pseuoduridylation in vivo reveals critical region of Escherichia coli 23S rRNA for ribosome assembly. PMID:28334881
The modified base isopentenyladenosine and its derivatives in tRNA. PMID:28277934
Wobble uridine modifications-a reason to live, a reason to die?! PMID:28277930
A comprehensive collection of annotations to interpret sequence variation in human mitochondrial transfer RNAs. PMID:28185569
Modification of orthogonal tRNAs: unexpected consequences for sense codon reassignment. PMID:27915288
Determinants of tRNA Recognition by the Radical SAM Enzyme RlmN. PMID:27902775
tRNAmodpred: A computational method for predicting posttranscriptional modifications in tRNAs. PMID:27016142
Novel modes of RNA editing in mitochondria. PMID:27001515
Silent Polymorphisms: Can the tRNA Population Explain Changes in Protein Properties? PMID:26901226
Exploiting tRNAs to Boost Virulence. PMID:26797637
Bioengineering of noncoding RNAs for research agents and therapeutics. PMID:26763749
Global Epitranscriptomics Profiling of RNA Post-Transcriptional Modifications as an Effective Tool for Investigating the Epitranscriptomics of Stress Response. PMID:26733207
Chemical Modifications Mark Alternatively Spliced and Uncapped Messenger RNAs in Arabidopsis. PMID:26561561
Transcriptome-wide measurement of plant RNA secondary structure. PMID:26119389
Profiling ribonucleotide modifications at full-transcriptome level: a step toward MS-based epitranscriptomics. PMID:25995446
Highly Predictive Reprogramming of tRNA Modifications Is Linked to Selective Expression of Codon-Biased Genes. PMID:25772370
Distribution and frequencies of post-transcriptional modifications in tRNAs. PMID:25611331
tRNA modifications regulate translation during cellular stress. PMID:25304425
Molecular recognition and modification of the 30S ribosome by the aminoglycoside-resistance methyltransferase NpmA. PMID:24717845
2-Selenouridine triphosphate synthesis and Se-RNA transcription. PMID:23887148
The catalytic domain of topological knot tRNA methyltransferase (TrmH) discriminates between substrate tRNA and nonsubstrate tRNA via an induced-fit process. PMID:23867454
Bioinformatics and computational biology in Poland. PMID:23658507
The T. brucei TRM5 methyltransferase plays an essential role in mitochondrial protein synthesis and function. PMID:23520175
A rapid and sensitive non-radioactive method applicable for genome-wide analysis of Saccharomyces cerevisiae genes involved in small RNA biology. PMID:23417998
Transfer RNA modifications: nature's combinatorial chemistry playground. PMID:23139145
The tRNA recognition mechanism of folate/FAD-dependent tRNA methyltransferase (TrmFO). PMID:23095745
The methyltransferase adaptor protein Trm112 is involved in biogenesis of both ribosomal subunits. PMID:22956767
Altered tRNA characteristics and 3' maturation in bacterial symbionts with reduced genomes. PMID:22689638
Chemical approaches for structure and function of RNA in postgenomic era. PMID:22347623
Transfer RNA methytransferases and their corresponding modifications in budding yeast and humans: activities, predications, and potential roles in human health. PMID:22191691
MetalionRNA: computational predictor of metal-binding sites in RNA structures. PMID:22110243
Identification and modeling of a phosphatase-like domain in a tRNA 2'-O-ribosyl phosphate transferase Rit1p. PMID:22030622
Determinants of tRNA editing and modification: avoiding conundrums, affecting function. PMID:22024020
Loss of ribosomal RNA modification causes developmental defects in zebrafish. PMID:21908402
Comprehensive structural and substrate specificity classification of the Saccharomyces cerevisiae methyltransferome. PMID:21858014
DARS-RNP and QUASI-RNP: new statistical potentials for protein-RNA docking. PMID:21851628
Substrate tRNA recognition mechanism of a multisite-specific tRNA methyltransferase, Aquifex aeolicus Trm1, based on the X-ray crystal structure. PMID:21844194
tRNA structural and functional changes induced by oxidative stress. PMID:21833586
The yeast rapid tRNA decay pathway primarily monitors the structural integrity of the acceptor and T-stems of mature tRNA. PMID:21632824
Actin-binding protein ABP140 is a methyltransferase for 3-methylcytidine at position 32 of tRNAs in Saccharomyces cerevisiae. PMID:21518805
A domain of the actin binding protein Abp140 is the yeast methyltransferase responsible for 3-methylcytidine modification in the tRNA anti-codon loop. PMID:21518804
Pseudouridine at position 55 in tRNA controls the contents of other modified nucleotides for low-temperature adaptation in the extreme-thermophilic eubacterium Thermus thermophilus. PMID:21097467
REPAIRtoire--a database of DNA repair pathways. PMID:21051355
High-resolution structure of the nitrile reductase QueF combined with molecular simulations provide insight into enzyme mechanism. PMID:20875425
YibK is the 2'-O-methyltransferase TrmL that modifies the wobble nucleotide in Escherichia coli tRNA(Leu) isoacceptors. PMID:20855540
Flexible recognition of the tRNA G18 methylation target site by TrmH methyltransferase through first binding and induced fit processes. PMID:20053984
Crystal structure of Streptococcus pneumoniae Sp1610, a putative tRNA methyltransferase, in complex with S-adenosyl-L-methionine. PMID:20052680
N7-Methylguanine at position 46 (m7G46) in tRNA from Thermus thermophilus is required for cell viability at high temperatures through a tRNA modification network. PMID:19934251
The Sua5 protein is essential for normal translational regulation in yeast. PMID:19884342
Trm13p, the tRNA:Xm4 modification enzyme from Saccharomyces cerevisiae is a member of the Rossmann-fold MTase superfamily: prediction of structure and active site. PMID:19697067
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. PMID:19491098
A chemical screen for biological small molecule-RNA conjugates reveals CoA-linked RNA. PMID:19416889
The yfiC gene of E. coli encodes an adenine-N6 methyltransferase that specifically modifies A37 of tRNA1Val(cmo5UAC). PMID:19383770
tRNADB-CE: tRNA gene database curated manually by experts. PMID:18842632
The RNA acetyltransferase driven by ATP hydrolysis synthesizes N4-acetylcytidine of tRNA anticodon. PMID:18668122
The YqfN protein of Bacillus subtilis is the tRNA: m1A22 methyltransferase (TrmK). PMID:18420655
An embarrassment of riches: the enzymology of RNA modification. PMID:18294973
The 3D rRNA modification maps database: with interactive tools for ribosome analysis. PMID:17947322
Conserved amino acids in each subunit of the heteroligomeric tRNA m1A58 Mtase from Saccharomyces cerevisiae contribute to tRNA binding. PMID:17932071
C to U editing at position 32 of the anticodon loop precedes tRNA 5' leader removal in trypanosomatids. PMID:17916576
Cysteine of sequence motif VI is essential for nucleophilic catalysis by yeast tRNA m5C methyltransferase. PMID:17475914
Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases. PMID:17338813
New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA. PMID:17283215
The 2'-O-methyltransferase responsible for modification of yeast tRNA at position 4. PMID:17242307
The yfhQ gene of Escherichia coli encodes a tRNA:Cm32/Um32 methyltransferase. PMID:16848900
Differentiation of 2'-O- and 3'-O-methylated ribonucleosides by tandem mass spectrometry. PMID:16750383
THUMP from archaeal tRNA:m22G10 methyltransferase, a genuine autonomously folding domain. PMID:16687654
Molecular phylogenetics and comparative modeling of HEN1, a methyltransferase involved in plant microRNA biogenesis. PMID:16433904
MODOMICS: An Operational Guide to the Use of the RNA Modification Pathways Database PubMed citations: 10.

10 articles citing: MODOMICS: An Operational Guide to the Use of the RNA Modification Pathways Database

N6-Methyladenosine-Related Gene Signature Associated With Monocyte Infiltration Is Clinically Significant in Gestational Diabetes Mellitus. PMID:35370940
Chronic Hexavalent Chromium Exposure Upregulates the RNA Methyltransferase METTL3 Expression to Promote Cell Transformation, Cancer Stem Cell-Like Property, and Tumorigenesis. PMID:35201342
m6A Regulator-Mediated Methylation Modification Patterns and Tumor Microenvironment Cell-Infiltration Characterization in Head and Neck Cancer. PMID:35198565
Identification and mapping of post-transcriptional modifications on the HIV-1 antisense transcript Ast in human cells. PMID:35168996
m6A: An Emerging Role in Programmed Cell Death. PMID:35141221
S-adenosylmethionine-dependent methyltransferase inhibitor DZNep blocks transcription and translation of SARS-CoV-2 genome with a low tendency to select for drug-resistant viral variants. PMID:34968527
Human Mitochondrial Ribosomal RNA Modification-Based Classification Contributes to Discriminate the Prognosis and Immunotherapy Response of Glioma Patients. PMID:34566979
Computational methods for RNA modification detection from nanopore direct RNA sequencing data. PMID:34559589
NAT10-Mediated N4-Acetylcytidine of RNA Contributes to Post-transcriptional Regulation of Mouse Oocyte Maturation in vitro. PMID:34395433
RNA methyltransferase METTL16: Targets and function. PMID:34227247
http://dx.doi.org/10.1093/nar/gks1007

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rna modification
metasource: Fairsharing.org
version: FAIRsharing.org: MODOMICS; MODOMICS; DOI: https://doi.org/10.25504/FAIRsharing.3qh2tg; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

rna sequence
metasource: Fairsharing.org
version: FAIRsharing.org: MODOMICS; MODOMICS; DOI: https://doi.org/10.25504/FAIRsharing.3qh2tg; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

ribonucleic acid
metasource: Fairsharing.org
version: FAIRsharing.org: MODOMICS; MODOMICS; DOI: https://doi.org/10.25504/FAIRsharing.3qh2tg; Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

rna sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metabolic and signaling pathways
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metabolic pathways
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

functional, regulatory and non-coding rna
metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:52.339479

enzymes
metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:52.339479

gene transcripts
metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:52.339479

molecular interactions, pathways and networks
metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:52.339479

rna splicing
metasource: bio.tools
version: extracted_at: 2022-11-04T11:25:52.339479

rna modification rna sequence rna rna sequence metabolic and signaling pathways metabolic and signaling pathways functional, regulatory and non-coding rna enzyme gene transcripts molecular interactions, pathways and networks rna splicing

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RNA Modification Database

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RNArchitecture

REPAIRtoire

RNAcentral

RRMdb

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Comparative RNA Web

RNA FRABASE

ncRNAs database

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5S Ribosomal RNA Database