The RNA Modification Database (RNAMDB)
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The RNA Modification Database contains information pertaining to naturally occurring RNA modifications. The database employs an easy-to-use, searchable interface for obtaining detailed data on the 109 currently known RNA modifications. Each entry provides the chemical structure, common name and symbol, elemental composition and mass, CA registry numbers and index name, phylogenetic source, type of RNA species.
Description
More detailed information about this field from each metasource.
The RNA Modification Database contains information pertaining to naturally occurring RNA modifications. The database employs an easy-to-use, searchable interface for obtaining detailed data on the 109 currently known RNA modifications. Each entry provides the chemical structure, common name and symbol, elemental composition and mass, CA registry numbers and index name, phylogenetic source, type of RNA species.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:33:33.769977
Webpage:
http://mods.rna.albany.edu/Webpage
More detailed information about this field from each metasource.
Publications:
Publications
More detailed information about this field from each metasource.
The RNA Modification Database, RNAMDB: 2011 update
PMID: 21071406
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:33.769977
Publications
More detailed information about this field from each metasource.
The RNA Modification Database, RNAMDB: 2011 update
PMID: 21071406
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:33.769977
-
The RNA Modification Database, RNAMDB: 2011 update
PubMed citations: 368.
368 articles citing: The RNA Modification Database, RNAMDB: 2011 update
Biological roles of RNA m5C modification and its implications in Cancer immunotherapy. PMID:35365216
Application of m6A and TME in Predicting the Prognosis and Treatment of Clear Cell Renal Cell Carcinoma. PMID:35281520
Correlation analysis of m6A-modified regulators with immune microenvironment infiltrating cells in lung adenocarcinoma. PMID:35196365
Site-Specific Profiling of 4-Thiouridine Across Transfer RNA Genes in Escherichia coli. PMID:35155896
Human cancer cells compensate the genes unfavorable for translation by N 6-methyladenosine modification and enhance their translation efficiency. PMID:35116782
Construction of a risk prediction model using m6A RNA methylation regulators in prostate cancer: comprehensive bioinformatic analysis and histological validation. PMID:35045837
Profiling of N6-Methyladenosine (m6A) Modification Landscape in Response to Drought Stress in Apple (Malus prunifolia (Willd.) Borkh). PMID:35009106
Personal Perspectives on Plant Ribosomal RNA Genes Research: From Precursor-rRNA to Molecular Evolution. PMID:34992624
Transcriptome-wide N 6-Methyladenosine Methylome Profiling Reveals m6A Regulation of Skeletal Myoblast Differentiation in Cattle (Bos taurus). PMID:34938736
TCF4 and HuR mediated-METTL14 suppresses dissemination of colorectal cancer via N6-methyladenosine-dependent silencing of ARRDC4. PMID:34916487
Synthesis and structure elucidation of the human tRNA nucleoside mannosyl-queuosine. PMID:34880214
The Identification of RNA Modification Gene PUS7 as a Potential Biomarker of Ovarian Cancer. PMID:34827123
Epigenetic modifications in neuropathic pain. PMID:34823400
Methyltransferase-like 14 suppresses growth and metastasis of renal cell carcinoma by decreasing long noncoding RNA NEAT1. PMID:34813676
Epitranscriptomics of cardiovascular diseases (Review). PMID:34791505
Unique features of mRNA m6A methylomes during expansion of tomato (Solanum lycopersicum) fruits. PMID:34730815
Machine learning applications in RNA modification sites prediction. PMID:34712397
Target-Specific Profiling of RNA m5C Methylation Level Using Amplicon Sequencing. PMID:34694621
Single-Neuron RNA Modification Analysis by Mass Spectrometry: Characterizing RNA Modification Patterns and Dynamics with Single-Cell Resolution. PMID:34672536
YRDC Mediates the Resistance of Lenvatinib in Hepatocarcinoma Cells via Modulating the Translation of KRAS. PMID:34658879
METTL3 improves cardiomyocyte proliferation upon myocardial infarction via upregulating miR-17-3p in a DGCR8-dependent manner. PMID:34645805
The Role of m6A Ribonucleic Acid Modification in the Occurrence of Atherosclerosis. PMID:34603394
METTL14-Mediated miR-30c-1-3p Maturation Represses the Progression of Lung Cancer via Regulation of MARCKSL1 Expression. PMID:34586620
Optimizing Efficient RNAi-Mediated Control of Hemipteran Pests (Psyllids, Leafhoppers, Whitefly): Modified Pyrimidines in dsRNA Triggers. PMID:34579315
The Latest Research Progress of m6A Modification and Its Writers, Erasers, Readers in Infertility: A Review. PMID:34568313
The Importance of the Epi-Transcriptome in Translation Fidelity. PMID:34564313
Long Non-Coding RNAs as Potential Diagnostic and Prognostic Biomarkers in Breast Cancer: Progress and Prospects. PMID:34527584
ALKBH5-mediated m6A mRNA methylation governs human embryonic stem cell cardiac commitment. PMID:34513291
KIAA1429 and ALKBH5 Oppositely Influence Aortic Dissection Progression via Regulating the Maturation of Pri-miR-143-3p in an m6A-Dependent Manner. PMID:34490238
The m6A Methyltransferase METTL14-Mediated N6-Methyladenosine Modification of PTEN mRNA Inhibits Tumor Growth and Metastasis in Stomach Adenocarcinoma. PMID:34476213
N6-Methyladenosine Modification and Its Regulation of Respiratory Viruses. PMID:34368152
Gene Characteristics and Prognostic Values of m6A RNA Methylation Regulators in Nonsmall Cell Lung Cancer. PMID:34367534
Characterization of Neuronal RNA Modifications during Non-associative Learning in Aplysia Reveals Key Roles for tRNAs in Behavioral Sensitization. PMID:34345669
Sequoia: an interactive visual analytics platform for interpretation and feature extraction from nanopore sequencing datasets. PMID:34233619
M6A-BiNP: predicting N6-methyladenosine sites based on bidirectional position-specific propensities of polynucleotides and pointwise joint mutual information. PMID:34161188
RNA modifications in hematopoietic malignancies: a new research frontier. PMID:34157073
The Biological Function, Mechanism, and Clinical Significance of m6A RNA Modifications in Head and Neck Carcinoma: A Systematic Review. PMID:34136491
Recent advances in functional annotation and prediction of the epitranscriptome. PMID:34136099
Transcriptome-Wide N6-Methyladenosine (m6A) Profiling of Susceptible and Resistant Wheat Varieties Reveals the Involvement of Variety-Specific m6A Modification Involved in Virus-Host Interaction Pathways. PMID:34122371
In lysate RNA digestion provides insights into the angiogenin's specificity towards transfer RNAs. PMID:34085908
The structure of the mouse ADAT2/ADAT3 complex reveals the molecular basis for mammalian tRNA wobble adenosine-to-inosine deamination. PMID:34057470
Agnostic Framework for the Classification/Identification of Organisms Based on RNA Post-Transcriptional Modifications. PMID:34043326
Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity. PMID:34038115
Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome. PMID:34029205
The human tRNA-guanine transglycosylase displays promiscuous nucleobase preference but strict tRNA specificity. PMID:34009357
Bioinformatic analyses and experimental validation of the role of m6A RNA methylation regulators in progression and prognosis of adrenocortical carcinoma. PMID:33952721
The occurrence order and cross-talk of different tRNA modifications. PMID:33881742
RNA methylation in chloroplasts or mitochondria in plants. PMID:33779501
N6 -methyladenosine modification of lncRNA Pvt1 governs epidermal stemness. PMID:33729590
Coding potential of circRNAs: new discoveries and challenges. PMID:33552732
Deciphering RNA modifications at base resolution: from chemistry to biology. PMID:33454749
RNA Metabolism Guided by RNA Modifications: The Role of SMUG1 in rRNA Quality Control. PMID:33430019
Gene signatures of 6-methyladenine regulators in women with lung adenocarcinoma and development of a risk scoring system: a retrospective study using the cancer genome atlas database. PMID:33428597
Single enzyme RT-PCR of full-length ribosomal RNA. PMID:33409375
Broad-range RNA modification analysis of complex biological samples using rapid C18-UPLC-MS. PMID:33356826
Deaminase-Independent Mode of Antiretroviral Action in Human and Mouse APOBEC3 Proteins. PMID:33322756
Terpene Chain Length Affects the Base Pairing Discrimination of S-geranyl-2-thiouridine in RNA Duplex. PMID:33319183
Posttranscriptional modifications at the 37th position in the anticodon stem-loop of tRNA: structural insights from MD simulations. PMID:33214333
The epitranscriptome in stem cell biology and neural development. PMID:33065280
S-adenosylmethionine tRNA modification: unexpected/unsuspected implications of former/new players. PMID:33061813
m6A RNA Methylation in Marine Plants: First Insights and Relevance for Biological Rhythms. PMID:33053767
Comparative patterns of modified nucleotides in individual tRNA species from a mesophilic and two thermophilic archaea. PMID:32994183
N6-methyladenosine (m6A) RNA methylation signature as a predictor of stomach adenocarcinoma outcomes and its association with immune checkpoint molecules. PMID:32972288
Functional Characterization of a Putative RNA Demethylase ALKBH6 in Arabidopsis Growth and Abiotic Stress Responses. PMID:32933187
RNA Drugs and RNA Targets for Small Molecules: Principles, Progress, and Challenges. PMID:32929000
Modified nucleic acids: replication, evolution, and next-generation therapeutics. PMID:32878624
Transcriptome-Wide N6-Methyladenosine (m6A) Methylome Profiling of Heat Stress in Pak-choi (Brassica rapa ssp. chinensis). PMID:32842619
Different Oxidation Pathways of 2-Selenouracil and 2-Thiouracil, Natural Components of Transfer RNA. PMID:32825053
Novel Links between TORC1 and Traditional Non-Coding RNA, tRNA. PMID:32825021
Biphasic Liquid Microjunction Extraction for Profiling Neuronal RNA Modifications by Liquid Chromatography-Tandem Mass Spectrometry. PMID:32786436
Structural, biochemical and functional analyses of tRNA-monooxygenase enzyme MiaE from Pseudomonas putida provide insights into tRNA/MiaE interaction. PMID:32785618
2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications. PMID:32716367
H/ACA snoRNA levels are regulated during stem cell differentiation. PMID:32710630
Decoding the epitranscriptional landscape from native RNA sequences. PMID:32710622
Bioinformatics approaches for deciphering the epitranscriptome: Recent progress and emerging topics. PMID:32670500
A Census and Categorization Method of Epitranscriptomic Marks. PMID:32630140
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
Exploration of Potential Roles of m6A Regulators in Colorectal Cancer Prognosis. PMID:32500031
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
RNA modifications in brain tumorigenesis. PMID:32375856
RNA methyltransferase NSUN2 promotes gastric cancer cell proliferation by repressing p57Kip2 by an m5C-dependent manner. PMID:32332707
A Natural Variation in PLEIOTROPIC DEVELOPMENTAL DEFECTS Uncovers a Crucial Role for Chloroplast tRNA Modification in Translation and Plant Development. PMID:32327539
C5-Substituted 2-Selenouridines Ensure Efficient Base Pairing with Guanosine; Consequences for Reading the NNG-3' Synonymous mRNA Codons. PMID:32326096
5-Methylcytosine RNA Modifications Promote Retrovirus Replication in an ALYREF Reader Protein-Dependent Manner. PMID:32321818
Naturally occurring modified ribonucleosides. PMID:32301288
Long noncoding RNA pncRNA-D reduces cyclin D1 gene expression and arrests cell cycle through RNA m6A modification. PMID:32165496
Isolation and initial structure-functional characterization of endogenous tRNA-derived stress-induced RNAs. PMID:32116132
In vitro ribosome synthesis and evolution through ribosome display. PMID:32111839
Ribonucleic Acid Sequence Characterization by Negative Electron Transfer Dissociation Mass Spectrometry. PMID:32091202
Archaeosine Modification of Archaeal tRNA: Role in Structural Stabilization. PMID:32041795
A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine. PMID:31945376
The presence of the ACA box in archaeal H/ACA guide RNAs promotes atypical pseudouridylation. PMID:31919243
Epitranscriptomic profiling in human placenta: N6-methyladenosine modification at the 5'-untranslated region is related to fetal growth and preeclampsia. PMID:31914637
Is There Any Sequence Feature in the RNA Pseudouridine Modification Prediction Problem? PMID:31865116
METTL14 Suppresses CRC Progression via Regulating N6-Methyladenosine-Dependent Primary miR-375 Processing. PMID:31839484
YTHDF2 Binds to 5-Methylcytosine in RNA and Modulates the Maturation of Ribosomal RNA. PMID:31815440
Radiation Induced One-Electron Oxidation of 2-Thiouracil in Aqueous Solutions. PMID:31810289
Investigation of RNA Editing Sites within Bound Regions of RNA-Binding Proteins. PMID:31795425
Antibiotic Resistance and Epigenetics: More to It than Meets the Eye. PMID:31740560
Association of N6-methyladenosine with viruses and related diseases. PMID:31711514
A Linear Regression Predictor for Identifying N6-Methyladenosine Sites Using Frequent Gapped K-mer Pattern. PMID:31707204
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
In search of the mRNA modification landscape in plants. PMID:31610789
RNA editing in the forefront of epitranscriptomics and human health. PMID:31547885
Epitranscriptomic systems regulate the translation of reactive oxygen species detoxifying and disease linked selenoproteins. PMID:31476365
Converging Fate of the Oxidation and Reduction of 8-Thioguanosine. PMID:31470553
Structural and Energetic Effects of O2'-Ribose Methylation of Protonated Pyrimidine Nucleosides. PMID:31435890
The study of METTL3 and METTL14 expressions in childhood ETV6/RUNX1-positive acute lymphoblastic leukemia. PMID:31429529
HSP90 inhibitors stimulate DNAJB4 protein expression through a mechanism involving N6-methyladenosine. PMID:31399576
Dissecting the role of RNA modification regulatory proteins in melanoma. PMID:31217906
Significant epitranscriptomes in heterogeneous cancer. PMID:31187550
RNA Regulatory Networks as a Control of Stochasticity in Biological Systems. PMID:31134128
Clinical Significance of TRMT6 in Hepatocellular Carcinoma: A Bioinformatics-Based Study. PMID:31128068
Epitranscriptomic RNA Methylation in Plant Development and Abiotic Stress Responses. PMID:31110512
N6-methyladenosine regulatory machinery in plants: composition, function and evolution. PMID:31070865
DNAmod: the DNA modification database. PMID:31016417
DRUM: Inference of Disease-Associated m6A RNA Methylation Sites From a Multi-Layer Heterogeneous Network. PMID:31001320
WHISTLE: a high-accuracy map of the human N6-methyladenosine (m6A) epitranscriptome predicted using a machine learning approach. PMID:30993345
The Versatile Roles of the tRNA Epitranscriptome during Cellular Responses to Toxic Exposures and Environmental Stress. PMID:30934574
Errors in translational decoding: tRNA wobbling or misincorporation? PMID:30921315
Deletion of Gtpbp3 in zebrafish revealed the hypertrophic cardiomyopathy manifested by aberrant mitochondrial tRNA metabolism. PMID:30916346
Bisubstrate analogues as structural tools to investigate m6A methyltransferase active sites. PMID:30879411
Gene signatures and prognostic values of m6A regulators in clear cell renal cell carcinoma - a retrospective study using TCGA database. PMID:30877265
PUS7 mutations impair pseudouridylation in humans and cause intellectual disability and microcephaly. PMID:30778726
tRNA modification and cancer: potential for therapeutic prevention and intervention. PMID:30744422
Bisulfite-free and base-resolution analysis of 5-methylcytidine and 5-hydroxymethylcytidine in RNA with peroxotungstate. PMID:30723849
The RNA degradosome promotes tRNA quality control through clearance of hypomodified tRNA. PMID:30622183
Lifestyle modifications: coordinating the tRNA epitranscriptome with codon bias to adapt translation during stress responses. PMID:30587213
Guide snoRNAs: Drivers or Passengers in Human Disease? PMID:30577491
Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis. PMID:30559359
RNA therapy: Are we using the right molecules? PMID:30521885
Viral RNA structure-based strategies to manipulate translation. PMID:30514982
Recent Advances in Our Understanding of the Biosynthesis of Sulfur Modifications in tRNAs. PMID:30450093
N6-methyladenine RNA modification and cancers. PMID:30416848
Unveiling the structural features that determine the dual methyltransferase activities of Streptococcus pneumoniae RlmCD. PMID:30388185
Visualizing the Role of 2'-OH rRNA Methylations in the Human Ribosome Structure. PMID:30366442
Active Site Breathing of Human Alkbh5 Revealed by Solution NMR and Accelerated Molecular Dynamics. PMID:30352661
tRNA epitranscriptomics and biased codon are linked to proteome expression in Plasmodium falciparum. PMID:30287681
PseUI: Pseudouridine sites identification based on RNA sequence information. PMID:30157750
Epitranscriptomic Code and Its Alterations in Human Disease. PMID:30120023
TYW1: A Radical SAM Enzyme Involved in the Biosynthesis of Wybutosine Bases. PMID:30097090
Biocompatible, Purified VEGF-A mRNA Improves Cardiac Function after Intracardiac Injection 1 Week Post-myocardial Infarction in Swine. PMID:30038937
Above the Epitranscriptome: RNA Modifications and Stem Cell Identity. PMID:29958477
Epitranscriptomics of cancer. PMID:29900123
Structural insight into the human mitochondrial tRNA purine N1-methyltransferase and ribonuclease P complexes. PMID:29880640
Structural and biochemical analysis of the dual-specificity Trm10 enzyme from Thermococcus kodakaraensis prompts reconsideration of its catalytic mechanism. PMID:29848639
Biochemical and Structural Characterization of a Schiff Base in the Radical-Mediated Biosynthesis of 4-Demethylwyosine by TYW1. PMID:29792696
Identification of YTH Domain-Containing Proteins as the Readers for N1-Methyladenosine in RNA. PMID:29791134
Base modifications affecting RNA polymerase and reverse transcriptase fidelity. PMID:29750267
The Emerging Field of Epitranscriptomics in Neurodevelopmental and Neuronal Disorders. PMID:29707539
Hijacking DNA methyltransferase transition state analogues to produce chemical scaffolds for PRMT inhibitors. PMID:29685976
m6A deposition: a boost from TGFβ. PMID:29679051
MicroRNA MultiTool: A Software for Identifying Modified and Unmodified Human microRNA Using Mass Spectrometry. PMID:29657285
Multiple functions of m6A RNA methylation in cancer. PMID:29587823
Modifications and functional genomics of human transfer RNA. PMID:29463900
Positive-sense RNA viruses reveal the complexity and dynamics of the cellular and viral epitranscriptomes during infection. PMID:29373715
Drugging tRNA aminoacylation. PMID:29345185
ALKBH5-dependent m6A demethylation controls splicing and stability of long 3'-UTR mRNAs in male germ cells. PMID:29279410
Identification of tRNA nucleoside modification genes critical for stress response and development in rice and Arabidopsis. PMID:29268705
Most m6A RNA Modifications in Protein-Coding Regions Are Evolutionarily Unconserved and Likely Nonfunctional. PMID:29228327
The fungal snoRNAome. PMID:29196413
Visualization of chemical modifications in the human 80S ribosome structure. PMID:29143818
High-throughput m6A-seq reveals RNA m6A methylation patterns in the chloroplast and mitochondria transcriptomes of Arabidopsis thaliana. PMID:29131848
The Dark Side of the Epitranscriptome: Chemical Modifications in Long Non-Coding RNAs. PMID:29125541
Fingerprints of Modified RNA Bases from Deep Sequencing Profiles. PMID:29111692
MODOMICS: a database of RNA modification pathways. 2017 update. PMID:29106616
Stress-induced Pseudouridylation Alters the Structural Equilibrium of Yeast U2 snRNA Stem II. PMID:29079482
Confronting the catalytic dark matter encoded by sequenced genomes. PMID:29059321
Reciprocal amplification of caspase-3 activity by nuclear export of a putative human RNA-modifying protein, PUS10 during TRAIL-induced apoptosis. PMID:28981101
Editing the Genome Without Double-Stranded DNA Breaks. PMID:28957631
Structural insights into substrate selectivity of ribosomal RNA methyltransferase RlmCD. PMID:28949991
The emerging complexity of the tRNA world: mammalian tRNAs beyond protein synthesis. PMID:28875994
The RNA modification landscape in human disease. PMID:28855326
Reverse Transcription Past Products of Guanine Oxidation in RNA Leads to Insertion of A and C opposite 8-Oxo-7,8-dihydroguanine and A and G opposite 5-Guanidinohydantoin and Spiroiminodihydantoin Diastereomers. PMID:28845978
Celebrating wobble decoding: Half a century and still much is new. PMID:28812932
TRMT1-Catalyzed tRNA Modifications Are Required for Redox Homeostasis To Ensure Proper Cellular Proliferation and Oxidative Stress Survival. PMID:28784718
The N6-Methyladenosine RNA modification in pluripotency and reprogramming. PMID:28683341
Control of box C/D snoRNP assembly by N6-methylation of adenine. PMID:28623187
The Evolution of Substrate Specificity by tRNA Modification Enzymes. PMID:28601226
The Importance of Being Modified: The Role of RNA Modifications in Translational Fidelity. PMID:28601219
Position-dependent effects of regioisomeric methylated adenine and guanine ribonucleosides on translation. PMID:28591780
Identification of an optimized 2'-O-methylated trinucleotide RNA motif inhibiting Toll-like receptors 7 and 8. PMID:28576825
A-to-I editing in human miRNAs is enriched in seed sequence, influenced by sequence contexts and significantly hypoedited in glioblastoma multiforme. PMID:28550310
Label-free, direct localization and relative quantitation of the RNA nucleobase methylations m6A, m5C, m3U, and m5U by top-down mass spectrometry. PMID:28549193
Structural basis for substrate binding and catalytic mechanism of a human RNA:m5C methyltransferase NSun6. PMID:28531330
The Profile and Dynamics of RNA Modifications in Animals. PMID:28449301
Identifying N6-methyladenosine sites using multi-interval nucleotide pair position specificity and support vector machine. PMID:28440291
QueF-Like, a Non-Homologous Archaeosine Synthase from the Crenarchaeota. PMID:28383498
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
Structural landscape of base pairs containing post-transcriptional modifications in RNA. PMID:28341704
International Standards for Genomes, Transcriptomes, and Metagenomes. PMID:28337071
N1-methyl-pseudouridine in mRNA enhances translation through eIF2α-dependent and independent mechanisms by increasing ribosome density. PMID:28334758
Diverse Mechanisms of Sulfur Decoration in Bacterial tRNA and Their Cellular Functions. PMID:28327539
Chemical and Conformational Diversity of Modified Nucleosides Affects tRNA Structure and Function. PMID:28300792
Antibodies specific for nucleic acid modifications. PMID:28277931
Mapping Post-Transcriptional Modifications onto Transfer Ribonucleic Acid Sequences by Liquid Chromatography Tandem Mass Spectrometry. PMID:28241457
AlkB homolog 3-mediated tRNA demethylation promotes protein synthesis in cancer cells. PMID:28205560
Metabolic influences on RNA biology and translation. PMID:28152618
RNA modifications and structures cooperate to guide RNA-protein interactions. PMID:28144031
Pseudouridine and N6-methyladenosine modifications weaken PUF protein/RNA interactions. PMID:28138061
Trm112, a Protein Activator of Methyltransferases Modifying Actors of the Eukaryotic Translational Apparatus. PMID:28134793
2'-O-Methyl-5-hydroxymethylcytidine: A Second Oxidative Derivative of 5-Methylcytidine in RNA. PMID:28107630
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
Intersections of post-transcriptional gene regulatory mechanisms with intermediary metabolism. PMID:28088440
Detecting N6-methyladenosine sites from RNA transcriptomes using ensemble Support Vector Machines. PMID:28079126
Activation mode of the eukaryotic m2G10 tRNA methyltransferase Trm11 by its partner protein Trm112. PMID:27986851
Genome recoding by tRNA modifications. PMID:27974624
Tuning the ribosome: The influence of rRNA modification on eukaryotic ribosome biogenesis and function. PMID:27911188
Interactions between the HIV-1 Unspliced mRNA and Host mRNA Decay Machineries. PMID:27886048
From profiles to function in epigenomics. PMID:27867193
Genome-wide screen identifies host colonization determinants in a bacterial gut symbiont. PMID:27849596
Post-transcriptional gene regulation by mRNA modifications. PMID:27808276
Update: Mechanisms Underlying N6-Methyladenosine Modification of Eukaryotic mRNA. PMID:27793360
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
Molecular basis of cobalamin-dependent RNA modification. PMID:27638883
tRNA base methylation identification and quantification via high-throughput sequencing. PMID:27613580
SMEpred workbench: A web server for predicting efficacy of chemicallymodified siRNAs. PMID:27603513
Identifying N 6-methyladenosine sites in the Arabidopsis thaliana transcriptome. PMID:27590733
S-Geranyl-2-thiouridine wobble nucleosides of bacterial tRNAs; chemical and enzymatic synthesis of S-geranylated-RNAs and their physicochemical characterization. PMID:27566149
YTHDF2 destabilizes m(6)A-containing RNA through direct recruitment of the CCR4-NOT deadenylase complex. PMID:27558897
Structure-function relationships of archaeal Cbf5 during in vivo RNA-guided pseudouridylation. PMID:27539785
Cytosine methylation of tRNA-Asp by DNMT2 has a role in translation of proteins containing poly-Asp sequences. PMID:27462411
An integrated, structure- and energy-based view of the genetic code. PMID:27448410
Who Watches the Watchmen: Roles of RNA Modifications in the RNA Interference Pathway. PMID:27441695
Dendrimer-RNA nanoparticles generate protective immunity against lethal Ebola, H1N1 influenza, and Toxoplasma gondii challenges with a single dose. PMID:27382155
Structural effects of modified ribonucleotides and magnesium in transfer RNAs. PMID:27364608
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
iPhos-PseEn: identifying phosphorylation sites in proteins by fusing different pseudo components into an ensemble classifier. PMID:27323404
Synthesis, base pairing and structure studies of geranylated RNA. PMID:27307604
An updated human snoRNAome. PMID:27174936
iCar-PseCp: identify carbonylation sites in proteins by Monte Carlo sampling and incorporating sequence coupled effects into general PseAAC. PMID:27153555
Nearest-neighbor parameters for 7-deaza-adenosine·uridine base pairs in RNA duplexes. PMID:27099368
Nucleoside modifications in the regulation of gene expression: focus on tRNA. PMID:27094388
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
Direct and site-specific quantification of RNA 2'-O-methylation by PCR with an engineered DNA polymerase. PMID:27016740
Nucleic Acid Modifications in Regulation of Gene Expression. PMID:26933737
Additive CHARMM force field for naturally occurring modified ribonucleotides. PMID:26841080
siRNAmod: A database of experimentally validated chemically modified siRNAs. PMID:26818131
Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code. PMID:26791911
Modifying the maker: Oxygenases target ribosome biology. PMID:26779412
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
NIPBL Controls RNA Biogenesis to Prevent Activation of the Stress Kinase PKR. PMID:26725122
Milk: an epigenetic amplifier of FTO-mediated transcription? Implications for Western diseases. PMID:26691922
Identification of methylated deoxyadenosines in vertebrates reveals diversity in DNA modifications. PMID:26689968
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
Mass spectrometry of modified RNAs: recent developments. PMID:26501195
Bidirectional Direct Sequencing of Noncanonical RNA by Two-Dimensional Analysis of Mass Chromatograms. PMID:26495937
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
Insights into molecular plasticity in protein complexes from Trm9-Trm112 tRNA modifying enzyme crystal structure. PMID:26438534
Transcriptome-Wide Identification of Pseudouridine Modifications Using Pseudo-seq. PMID:26423590
Identification and analysis of the N(6)-methyladenosine in the Saccharomyces cerevisiae transcriptome. PMID:26343792
Exometabolom analysis of breast cancer cell lines: Metabolic signature. PMID:26293811
Pseudo-Seq: Genome-Wide Detection of Pseudouridine Modifications in RNA. PMID:26253973
A Platform for Discovery and Quantification of Modified Ribonucleosides in RNA: Application to Stress-Induced Reprogramming of tRNA Modifications. PMID:26253965
Thermodynamic insights into 2-thiouridine-enhanced RNA hybridization. PMID:26240387
tRNA recognition by a bacterial tRNA Xm32 modification enzyme from the SPOUT methyltransferase superfamily. PMID:26202969
RNA N6-methyladenosine methylation in post-transcriptional gene expression regulation. PMID:26159994
From bacterial to human dihydrouridine synthase: automated structure determination. PMID:26143927
Modified mRNA as an alternative to plasmid DNA (pDNA) for transcript replacement and vaccination therapy. PMID:26125492
An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies. PMID:26117545
Functional Diversity of Haloacid Dehalogenase Superfamily Phosphatases from Saccharomyces cerevisiae: BIOCHEMICAL, STRUCTURAL, AND EVOLUTIONARY INSIGHTS. PMID:26071590
NMR-based Structural Analysis of Threonylcarbamoyl-AMP Synthase and Its Substrate Interactions. PMID:26060251
Mechanistic Studies of the Radical S-Adenosyl-L-methionine Enzyme 4-Demethylwyosine Synthase Reveal the Site of Hydrogen Atom Abstraction. PMID:26052987
MINT: software to identify motifs and short-range interactions in trajectories of nucleic acids. PMID:26024667
Draft Genome Sequence of Aneurinibacillus tyrosinisolvens LL-002T, Which Possesses Some Pseudouridine Synthases. PMID:26021921
Profiling ribonucleotide modifications at full-transcriptome level: a step toward MS-based epitranscriptomics. PMID:25995446
Chimeric MicroRNA-1291 Biosynthesized Efficiently in Escherichia coli Is Effective to Reduce Target Gene Expression in Human Carcinoma Cells and Improve Chemosensitivity. PMID:25934574
MTO1 worked as a modifier in the aminoglycosides sensitivity of yeast carrying a mitochondrial 15S rRNA C1477G mutation. PMID:25898254
Codon-biased translation can be regulated by wobble-base tRNA modification systems during cellular stress responses. PMID:25892531
Protein degradation and dynamic tRNA thiolation fine-tune translation at elevated temperatures. PMID:25870413
Abbreviated Pathway for Biosynthesis of 2-Thiouridine in Bacillus subtilis. PMID:25825430
RoboOligo: software for mass spectrometry data to support manual and de novo sequencing of post-transcriptionally modified ribonucleic acids. PMID:25820423
tRNA biology in mitochondria. PMID:25734984
N6-adenosine methylation in MiRNAs. PMID:25723394
2-Thiouracil deprived of thiocarbonyl function preferentially base pairs with guanine rather than adenine in RNA and DNA duplexes. PMID:25690900
Yeast Kre33 and human NAT10 are conserved 18S rRNA cytosine acetyltransferases that modify tRNAs assisted by the adaptor Tan1/THUMPD1. PMID:25653167
The identification and characterization of non-coding and coding RNAs and their modified nucleosides by mass spectrometry. PMID:25616408
Structure and function of dioxygenases in histone demethylation and DNA/RNA demethylation. PMID:25485134
Gold nanoparticle interference study during the isolation, quantification, purity and integrity analysis of RNA. PMID:25470814
Novel RNA modifications in the nervous system: form and function. PMID:25392485
Regulation of lncRNA expression. PMID:25311814
Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells. PMID:25192136
Influence of Sequence and Covalent Modifications on Yeast tRNA Dynamics. PMID:25136272
Absolute and relative quantification of RNA modifications via biosynthetic isotopomers. PMID:25129236
Tet-mediated formation of 5-hydroxymethylcytosine in RNA. PMID:25073028
A modified dinucleotide motif specifies tRNA recognition by TLR7. PMID:25051971
Protozoan ALKBH8 oxygenases display both DNA repair and tRNA modification activities. PMID:24914785
Structures of human ALKBH5 demethylase reveal a unique binding mode for specific single-stranded N6-methyladenosine RNA demethylation. PMID:24778178
The rise of regulatory RNA. PMID:24776770
Biosynthesis and functions of sulfur modifications in tRNA. PMID:24765101
Metabolic de-isotoping for improved LC-MS characterization of modified RNAs. PMID:24760295
Genome-wide mapping of cellular protein-RNA interactions enabled by chemical crosslinking. PMID:24747191
A highly conserved family of domains related to the DNA-glycosylase fold helps predict multiple novel pathways for RNA modifications. PMID:24646681
SAXS analysis of the tRNA-modifying enzyme complex MnmE/MnmG reveals a novel interaction mode and GTP-induced oligomerization. PMID:24634441
Crystal structures of the human RNA demethylase Alkbh5 reveal basis for substrate recognition. PMID:24616105
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
Methyltransferases modulate RNA stability in embryonic stem cells. PMID:24481042
High-performance liquid chromatography purification of chemically modified RNA aptamers. PMID:24373999
Structure modulation of helix 69 from Escherichia coli 23S ribosomal RNA by pseudouridylations. PMID:24371282
Regulatory RNAs: charming gene management styles for synthetic biology applications. PMID:24356572
Biochemical and structural studies of conserved Maf proteins revealed nucleotide pyrophosphatases with a preference for modified nucleotides. PMID:24210219
Modified RNA kick-starts cardiac repair. PMID:24104754
Crystal structure of tRNA m1G9 methyltransferase Trm10: insight into the catalytic mechanism and recognition of tRNA substrate. PMID:24081582
Computational approaches to predicting the impact of novel bases on RNA structure and stability. PMID:24063428
Endonuclease V cleaves at inosines in RNA. PMID:23912683
Role of forefinger and thumb loops in production of Ψ54 and Ψ55 in tRNAs by archaeal Pus10. PMID:23898217
Radical mediated ring formation in the biosynthesis of the hypermodified tRNA base wybutosine. PMID:23856057
The tRNA recognition mechanism of the minimalist SPOUT methyltransferase, TrmL. PMID:23804755
Expanded use of sense codons is regulated by modified cytidines in tRNA. PMID:23781103
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
Direct infusion analysis of nucleotide mixtures of very similar or identical elemental composition. PMID:23722961
S-Adenosyl-S-carboxymethyl-L-homocysteine: a novel cofactor found in the putative tRNA-modifying enzyme CmoA. PMID:23695253
Recognition of RNA duplexes by chemically modified triplex-forming oligonucleotides. PMID:23658228
Reconstitution and characterization of eukaryotic N6-threonylcarbamoylation of tRNA using a minimal enzyme system. PMID:23620299
Sprouts of RNA epigenetics: the discovery of mammalian RNA demethylases. PMID:23619745
The pre-mRNA retention and splicing complex controls tRNA maturation by promoting TAN1 expression. PMID:23605039
Long non-coding RNAs as targets for cytosine methylation. PMID:23595112
Exome-based analysis for RNA epigenome sequencing data. PMID:23589649
Evaluating the reproducibility of quantifying modified nucleosides from ribonucleic acids by LC-UV-MS. PMID:23500350
Structure and function of long noncoding RNAs in epigenetic regulation. PMID:23463315
N6-methyl-adenosine (m6A) in RNA: an old modification with a novel epigenetic function. PMID:23453015
Novel RNA regulatory mechanisms revealed in the epitranscriptome. PMID:23434792
RNA pseudouridylation: new insights into an old modification. PMID:23391857
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
Systemic delivery of modified mRNA encoding herpes simplex virus 1 thymidine kinase for targeted cancer gene therapy. PMID:23229091
Reversible RNA adenosine methylation in biological regulation. PMID:23218460
ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. PMID:23177736
MODOMICS: a database of RNA modification pathways--2013 update. PMID:23118484
Protein and nucleic acid methylating enzymes: mechanisms and regulation. PMID:23085277
A subcomplex of human mitochondrial RNase P is a bifunctional methyltransferase--extensive moonlighting in mitochondrial tRNA biogenesis. PMID:23042678
Characterization of modified RNA by top-down mass spectrometry. PMID:23042528
The human tRNA m (5) C methyltransferase Misu is multisite-specific. PMID:22995836
Discovery and biological characterization of geranylated RNA in bacteria. PMID:22983156
Dual RNA-seq of pathogen and host. PMID:22890146
Expression Profiling of a Heterogeneous Population of ncRNAs Employing a Mixed DNA/LNA Microarray. PMID:22778910
Identification and characterization of the Thermus thermophilus 5-methylcytidine (m5C) methyltransferase modifying 23 S ribosomal RNA (rRNA) base C1942. PMID:22711535
Hydrogen bond formation between the naturally modified nucleobase and phosphate backbone. PMID:22641848
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
Biosynthesis of pyrrolopyrimidines. PMID:22382038
Crystal structures of the tRNA:m2G6 methyltransferase Trm14/TrmN from two domains of life. PMID:22362751
Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA. PMID:22362734
Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA. PMID:22344696
Identification of modifications in microbial, native tRNA that suppress immunostimulatory activity. PMID:22312113
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
Human tRNA(Lys3)(UUU) is pre-structured by natural modifications for cognate and wobble codon binding through keto-enol tautomerism. PMID:22227389
Novel modifications in RNA. PMID:22148740
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
A single methyltransferase YefA (RlmCD) catalyses both m5U747 and m5U1939 modifications in Bacillus subtilis 23S rRNA. PMID:21824914
Conformation effects of base modification on the anticodon stem-loop of Bacillus subtilis tRNA(Tyr). PMID:21782828
Functional recognition of the modified human tRNALys3(UUU) anticodon domain by HIV's nucleocapsid protein and a peptide mimic. PMID:21762809
Pseudouridine formation in archaeal RNAs: The case of Haloferax volcanii. PMID:21628430
Actin-binding protein ABP140 is a methyltransferase for 3-methylcytidine at position 32 of tRNAs in Saccharomyces cerevisiae. PMID:21518805
The 2011 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. PMID:21177655
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rna
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:33.769977
functional, regulatory and non-coding rna
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:33.769977
nucleic acid structure analysis
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:33.769977
structure prediction
metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:33.769977
Tags
More detailed information about this field from each metasource.
rna
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:33:33.769977
functional, regulatory and non-coding rna
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:33:33.769977
nucleic acid structure analysis
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:33:33.769977
structure prediction
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:33:33.769977
rna functional, regulatory and non-coding rna nucleic acid structure analysis structure prediction
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