Detecting RNA modifications in the epitranscriptome: predict and validate (Q39143334)

9 September 2017

Detecting RNA modifications in the epitranscriptome: predict and validate (English)

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9 September 2017

Mark Helm

1

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author name string

Yuri Motorin

series ordinal

2

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9 September 2017

20 February 2017

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9 September 2017

Nature Reviews Genetics

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9 September 2017

18

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9 September 2017

275-291

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9 September 2017

5

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https://scigraph.springernature.com/pub.10.1038/nrg.2016.169

9 September 2017

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Four newly located pseudouridylate residues in Escherichia coli 23S ribosomal RNA are all at the peptidyltransferase center: analysis by the application of a new sequencing technique.

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Conservation of tRNA and rRNA 5-methylcytosine in the kingdom Plantae

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RNA 5-Methylcytosine Analysis by Bisulfite Sequencing

31 March 2020

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DNA methylome analysis using short bisulfite sequencing data

31 March 2020

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Quantitative sequencing of 5-formylcytosine in DNA at single-base resolution

31 March 2020

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Deficient methylation and formylation of mt-tRNA(Met) wobble cytosine in a patient carrying mutations in NSUN3

31 March 2020

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Use of specific chemical reagents for detection of modified nucleotides in RNA.

31 March 2020

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Efficient and quantitative high-throughput tRNA sequencing.

31 March 2020

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tRNA base methylation identification and quantification via high-throughput sequencing.

31 March 2020

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ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments

31 March 2020

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Pseudouridylation meets next-generation sequencing

31 March 2020

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Characterizing 5-methylcytosine in the mammalian epitranscriptome

31 March 2020

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Mechanism and biological role of Dnmt2 in Nucleic Acid Methylation.

31 March 2020

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Antisera specific for carcinogen-DNA adducts and carcinogen-modified DNA: applications for detection of xenobiotics in biological samples

31 March 2020

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Immunochemical Detection of Minor Bases in Nucleic Acids

31 March 2020

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31 March 2020

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Antibody-nucleic acid complexes. Antigenic domains within nucleosides as defined by solid-phase immunoassay

31 March 2020

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Mapping of N6-methyladenosine residues in bovine prolactin mRNA

31 March 2020

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Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

31 March 2020

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Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons

31 March 2020

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Immuno-Northern Blotting: Detection of RNA Modifications by Using Antibodies against Modified Nucleosides.

31 March 2020

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RNA biochemistry. Transcriptome-wide distribution and function of RNA hydroxymethylcytosine.

31 March 2020

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Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome

31 March 2020

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High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis

31 March 2020

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Methyl-DNA immunoprecipitation (MeDIP): hunting down the DNA methylome.

31 March 2020

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High-resolution N(6) -methyladenosine (m(6) A) map using photo-crosslinking-assisted m(6) A sequencing

31 March 2020

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31 March 2020

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31 March 2020

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5-methylcytosine in RNA: detection, enzymatic formation and biological functions

31 March 2020

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NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs

31 March 2020

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NSUN4 is a dual function mitochondrial protein required for both methylation of 12S rRNA and coordination of mitoribosomal assembly

31 March 2020

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Identification of direct targets and modified bases of RNA cytosine methyltransferases

31 March 2020

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Transcriptome-wide target profiling of RNA cytosine methyltransferases using the mechanism-based enrichment procedure Aza-IP

31 March 2020

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NSUN6 is a human RNA methyltransferase that catalyzes formation of m5C72 in specific tRNAs

31 March 2020

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Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP

31 March 2020

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The mechanism of pseudouridine synthase I as deduced from its interaction with 5-fluorouracil-tRNA.

31 March 2020

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Not all pseudouridine synthases are potently inhibited by RNA containing 5-fluorouridine

31 March 2020

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NAD captureSeq indicates NAD as a bacterial cap for a subset of regulatory RNAs

31 March 2020

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Counting absolute numbers of molecules using unique molecular identifiers

31 March 2020

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High-throughput sequencing of human plasma RNA by using thermostable group II intron reverse transcriptases.

31 March 2020

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RNA-seq of human reference RNA samples using a thermostable group II intron reverse transcriptase.

31 March 2020

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Detection of reverse transcriptase termination sites using cDNA ligation and massive parallel sequencing

31 March 2020

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Illumina-based RiboMethSeq approach for mapping of 2'-O-Me residues in RNA.

31 March 2020

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The complete chemical structure of Saccharomyces cerevisiae rRNA: partial pseudouridylation of U2345 in 25S rRNA by snoRNA snR9

31 March 2020

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RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries

31 March 2020

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Optimization of enzymatic reaction conditions for generating representative pools of cDNA from small RNA.

31 March 2020

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The rocks and shallows of deep RNA sequencing: Examples in the Vibrio cholerae RNome

31 March 2020

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Label-free microRNA profiling not biased by 3' end 2'-O-methylation.

31 March 2020

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32P-Postlabeling ofN-(Deoxyguanosin-8-yl)arylamine Adducts: A Comparative Study of Labeling Efficiencies

31 March 2020

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RMBase: a resource for decoding the landscape of RNA modifications from high-throughput sequencing data

31 March 2020

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Quantitative mass spectrometry in proteomics: a critical review

31 March 2020

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Detection of RNA nucleoside modifications with the uridine-specific ribonuclease MC1 from Momordica charantia

31 March 2020

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Enhanced detection of post-transcriptional modifications using a mass-exclusion list strategy for RNA modification mapping by LC-MS/MS

31 March 2020

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Mass spectrometry of modified RNAs: recent developments

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Sequence mapping of transfer RNA chemical modifications by liquid chromatography tandem mass spectrometry

31 March 2020

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The global identification of tRNA isoacceptors by targeted tandem mass spectrometry

31 March 2020

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Absolute and relative quantification of RNA modifications via biosynthetic isotopomers.

31 March 2020

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Nucleoside Analysis by Hydrophilic Interaction Liquid Chromatography Coupled with Mass Spectrometry.

31 March 2020

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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

31 March 2020

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A Platform for Discovery and Quantification of Modified Ribonucleosides in RNA: Application to Stress-Induced Reprogramming of tRNA Modifications

31 March 2020

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Attomole quantification and global profile of RNA modifications: Epitranscriptome of human neural stem cells

31 March 2020

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Determination of DNA and RNA Methylation in Circulating Tumor Cells by Mass Spectrometry.

31 March 2020

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Search for differences in post-transcriptional modification patterns of mitochondrial DNA-encoded wild-type and mutant human tRNALys and tRNALeu(UUR).

31 March 2020

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Chaplet column chromatography: isolation of a large set of individual RNAs in a single step

31 March 2020

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Identification of a novel methyltransferase, Bmt2, responsible for the N-1-methyl-adenosine base modification of 25S rRNA in Saccharomyces cerevisiae

31 March 2020

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Partial methylation at Am100 in 18S rRNA of baker's yeast reveals ribosome heterogeneity on the level of eukaryotic rRNA modification

31 March 2020

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Eukaryotic rRNA Modification by Yeast 5-Methylcytosine-Methyltransferases and Human Proliferation-Associated Antigen p120.

31 March 2020

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Detection of RNA modifications.

31 March 2020

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Detection of enzymatic activity of transfer RNA modification enzymes using radiolabeled tRNA substrates

31 March 2020

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Mobilities of modified ribonucleotides on two-dimensional cellulose thin-layer chromatography

31 March 2020

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A different approach to RNA sequencing

31 March 2020

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tRNAdb 2009: compilation of tRNA sequences and tRNA genes

31 March 2020

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Detection and quantitation of RNA base modifications

31 March 2020

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Use of DNAzymes for site-specific analysis of ribonucleotide modifications

31 March 2020

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[10] Using DNAzylnes to cut, process, and map RNA molecules for structural studies or modification

31 March 2020

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Probing N6-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA

31 March 2020

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Probing RNA Modification Status at Single-Nucleotide Resolution in Total RNA

31 March 2020

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Probing N⁶-methyladenosine (m⁶A) RNA Modification in Total RNA with SCARLET

31 March 2020

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A systematic, ligation-based approach to study RNA modifications

31 March 2020

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Identification of recognition residues for ligation-based detection and quantitation of pseudouridine and N6-methyladenosine

31 March 2020

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Detection and discovery of RNA modifications using microarrays

31 March 2020

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Classical and novel approaches to the detection and localization of the numerous modified nucleotides in eukaryotic ribosomal RNA.

31 March 2020

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Direct and site-specific quantification of RNA 2'-O-methylation by PCR with an engineered DNA polymerase

31 March 2020

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RTL-P: a sensitive approach for detecting sites of 2'-O-methylation in RNA molecules

31 March 2020

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Structure-function relationship of substituted bromomethylcoumarins in nucleoside specificity of RNA alkylation

31 March 2020

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A multifunctional bioconjugate module for versatile photoaffinity labeling and click chemistry of RNA.

31 March 2020

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A biochemical landscape of A-to-I RNA editing in the human brain transcriptome.

31 March 2020

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Dynamic modulation of Dnmt2-dependent tRNA methylation by the micronutrient queuine

31 March 2020

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Analysis of RNA base modification and structural rearrangement by single-molecule real-time detection of reverse transcription

31 March 2020

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Nanopores discriminate among five C5-cytosine variants in DNA

31 March 2020

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Profiling of RNA modifications by multiplexed stable isotope labelling.

31 March 2020

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The ASA's statement on p-values: context, process, and purpose

31 March 2020

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meRanTK: methylated RNA analysis ToolKit.

31 March 2020

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The majority of transcripts in the squid nervous system are extensively recoded by A-to-I RNA editing

31 March 2020

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CoverageAnalyzer (CAn): A Tool for Inspection of Modification Signatures in RNA Sequencing Profiles

31 March 2020

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Mass spectrometry of the fifth nucleoside: a review of the identification of pseudouridine in nucleic acids

31 March 2020

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Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry

31 March 2020

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Effects of dilute HCl on yeast tRNAPhe and E. coli tRNA1fMet

31 March 2020

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Replacement of wybutine by hydrazines and its effect on the active conformation of yeast tRNAPhe

31 March 2020

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Direct chemical method for sequencing RNA

31 March 2020

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Tertiary structure interactions of 7-methylguanosine in yeast tRNA Phe as studied by borohydride reduction

31 March 2020

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The specificities of four yeast dihydrouridine synthases for cytoplasmic tRNAs

31 March 2020

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Macromolecular arrangement in the aminoacyl-tRNA.elongation factor Tu.GTP ternary complex. A fluorescence energy transfer study

31 March 2020

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Affinity electrophoresis for monitoring terminal phosphorylation and the presence of queuosine in RNA. Application of polyacrylamide containing a covalently bound boronic acid.

31 March 2020

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Interaction of tRNAs and of phosphorothioate-substituted nucleic acids with an organomercurial. Probing the chemical environment of thiolated residues by affinity electrophoresis

31 March 2020

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Identification of the rrmA gene encoding the 23S rRNA m1G745 methyltransferase in Escherichia coli and characterization of an m1G745-deficient mutant

31 March 2020

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12 December 2020

5'-Terminal and internal methylated nucleosides in herpes simplex virus type 1 mRNA.

1 reference

12 December 2020

A new method for detecting sites of 2'-O-methylation in RNA molecules

1 reference

12 December 2020

Characterisation of a new, fully active fluorescent derivative of E. coli tRNA Phe.

1 reference

12 December 2020

Immunoassay of Carcinogen Modified DNA

1 reference

12 December 2020

The reverse transcription signature of N-1-methyladenosine in RNA-Seq is sequence dependent

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12 December 2020

Thiolation and 2-methylthio- modification of Bacillus subtilis transfer ribonucleic acids

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12 December 2020

Nucleotide Methylation Patterns in Eukaryotic mRNA

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Profiling of ribose methylations in RNA by high-throughput sequencing

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Identifiers

DOI

10.1038/NRG.2016.169

1 reference

PubMed ID

28216634

Dimensions Publication ID

9 September 2017

0 references

1 reference

PubMed ID

28216634