Detecting RNA modifications in the epitranscriptome: predict and validate

The ASA's Statement onp-Values: Context, Process, and Purpose

(2016) Ronald L. Wasserstein et al.   AMERICAN STATISTICIAN

Mass spectrometry of modified RNAs: recent developments

(2016) Collin Wetzel et al.   ANALYST

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

(2016) Wei Huang et al.   ANALYTICAL CHEMISTRY

RNA epigenetics — chemical messages for posttranscriptional gene regulation

(2016) Ian A Roundtree et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Pseudouridylation meets next-generation sequencing

(2016) Maryam Zaringhalam et al.   METHODS

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

(2016) Robert Ross et al.   METHODS

High-throughput sequencing for 1-methyladenosine (m1A) mapping in RNA

(2016) Lyudmil Tserovski et al.   METHODS

The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA

(2016) Dan Dominissini et al.   NATURE

Transcriptome-wide mapping reveals reversible and dynamic N1-methyladenosine methylome

(2016) Xiaoyu Li et al.   Nature Chemical Biology

RNA modifications: what have we learned and where are we headed?

(2016) Michaela Frye et al.   NATURE REVIEWS GENETICS

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

(2016) Joos Aschenbrenner et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Masato Taoka et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Virginie Marchand et al.   NUCLEIC ACIDS RESEARCH

tRNA base methylation identification and quantification via high-throughput sequencing

(2016) Wesley C. Clark et al.   RNA

Cracking the epitranscriptome

(2016) Schraga Schwartz   RNA

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

(2016) Ryan M. Nottingham et al.   RNA

Transcriptome-wide distribution and function of RNA hydroxymethylcytosine

(2016) B. Delatte et al.   SCIENCE

Deficient methylation and formylation of mt-tRNAMet wobble cytosine in a patient carrying mutations in NSUN3

(2016) Lindsey Van Haute et al.   Nature Communications

Going global: the new era of mapping modifications in RNA

(2016) Patrick A. Limbach et al.   Wiley Interdisciplinary Reviews-RNA

Enhanced Detection of Post-Transcriptional Modifications Using a Mass-Exclusion List Strategy for RNA Modification Mapping by LC-MS/MS

(2015) Xiaoyu Cao et al.   ANALYTICAL CHEMISTRY

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

(2015) Lijuan Fu et al.   ANALYTICAL CHEMISTRY

meRanTK: methylated RNA analysis ToolKit: Table 1.

(2015) Dietmar Rieder et al.   BIOINFORMATICS

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

(2015) Alice Louise Burgess et al.   BMC PLANT BIOLOGY

Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry

(2015) Erin E. Duffy et al.   MOLECULAR CELL

Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome

(2015) Xiaoyu Li et al.   Nature Chemical Biology

Efficient and quantitative high-throughput tRNA sequencing

(2015) Guanqun Zheng et al.   NATURE METHODS

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

(2015) Aaron E Cozen et al.   NATURE METHODS

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

(2015) Bastian Linder et al.   NATURE METHODS

Transcriptome-wide identification of adenosine-to-inosine editing using the ICE-seq method

(2015) Tsutomu Suzuki et al.   Nature Protocols

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

(2015) Martin Müller et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Maria Basanta-Sanchez et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Wen-Ju Sun et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Balasubrahmanym Addepalli et al.   RNA

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

(2015) Sara Haag et al.   RNA

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

(2015) Yidan Qin et al.   RNA

RNA epigenetics

(2015) Nian Liu et al.   Translational Research

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

(2015) Shahar Alon et al.   eLife

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

(2015) Gabrielle Bourgeois et al.   PLoS One

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

(2015) Eikan Mishima et al.   PLoS One

Pseudouridine: Still mysterious, but never a fake (uridine)!

(2015) Felix Spenkuch et al.   RNA Biology

High-ResolutionN6-Methyladenosine (m6A) Map Using Photo-Crosslinking-Assisted m6A Sequencing

(2014) Kai Chen et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

RNA editing, epitranscriptomics, and processing in cancer progression

(2014) Keren L Witkin et al.   CANCER BIOLOGY & THERAPY

Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA

(2014) Schraga Schwartz et al.   CELL

Profiling of RNA modifications by multiplexed stable isotope labelling

(2014) Stefanie Kellner et al.   CHEMICAL COMMUNICATIONS

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

(2014) M. Sakurai et al.   GENOME RESEARCH

Nanopores Discriminate among Five C5-Cytosine Variants in DNA

(2014) Zachary L. Wescoe et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A map of 5-methylcytosine residues in Trypanosoma brucei tRNA revealed by sodium bisulfite sequencing

(2014) Kevin T. Militello et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

(2014) Thomas M. Carlile et al.   NATURE

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

(2014) Hana Cahová et al.   NATURE

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

(2014) Michael J. Booth et al.   Nature Chemistry

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

(2014) Vahid Khoddami et al.   Nature Protocols

Absolute and relative quantification of RNA modifications via biosynthetic isotopomers

(2014) Stefanie Kellner et al.   NUCLEIC ACIDS RESEARCH

Partial Methylation at Am100 in 18S rRNA of Baker's Yeast Reveals Ribosome Heterogeneity on the Level of Eukaryotic rRNA Modification

(2014) Markus Buchhaupt et al.   PLoS One

Transcriptome-Wide Mapping of Pseudouridines: Pseudouridine Synthases Modify Specific mRNAs in S. cerevisiae

(2014) Alexander F. Lovejoy et al.   PLoS One

Mod-seq: high-throughput sequencing for chemical probing of RNA structure

(2014) J. Talkish et al.   RNA

NSUN4 Is a Dual Function Mitochondrial Protein Required for Both Methylation of 12S rRNA and Coordination of Mitoribosomal Assembly

(2014) Metodi Dimitrov Metodiev et al.   PLoS Genetics

The global identification of tRNA isoacceptors by targeted tandem mass spectrometry

(2013) Collin Wetzel et al.   ANALYST

High-Resolution Mapping Reveals a Conserved, Widespread, Dynamic mRNA Methylation Program in Yeast Meiosis

(2013) Schraga Schwartz et al.   CELL

Posttranscriptional RNA Modifications: Playing Metabolic Games in a Cell’s Chemical Legoland

(2013) Mark Helm et al.   CHEMISTRY & BIOLOGY

Recent developments and applications of capillary electrophoresis with laser-induced fluorescence detection in biological samples

(2013) Eunmi Ban et al.   JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES

Identification of direct targets and modified bases of RNA cytosine methyltransferases

(2013) Vahid Khoddami et al.   NATURE BIOTECHNOLOGY

Target recognition, RNA methylation activity and transcriptional regulation of the Dictyostelium discoideum Dnmt2-homologue (DnmA)

(2013) S. Muller et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Sunny Sharma et al.   NUCLEIC ACIDS RESEARCH

Structure-Function Relationship of Substituted Bromomethylcoumarins in Nucleoside Specificity of RNA Alkylation

(2013) Stefanie Kellner et al.   PLoS One

Long non-coding RNAs as targets for cytosine methylation

(2013) Thomas Amort et al.   RNA Biology

HAMR: high-throughput annotation of modified ribonucleotides

(2013) P. Ryvkin et al.   RNA

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

(2013) N. Liu et al.   RNA

NSun2-Mediated Cytosine-5 Methylation of Vault Noncoding RNA Determines Its Processing into Regulatory Small RNAs

(2013) Shobbir Hussain et al.   Cell Reports

Transcriptome-Wide Mapping of 5-methylcytidine RNA Modifications in Bacteria, Archaea, and Yeast Reveals m5C within Archaeal mRNAs

(2013) Sarit Edelheit et al.   PLoS Genetics

Characterizing 5-methylcytosine in the mammalian epitranscriptome

(2013) Shobbir Hussain et al.   GENOME BIOLOGY

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

(2013) Igor D Vilfan et al.   JOURNAL OF NANOBIOTECHNOLOGY

Label-Free MicroRNA Profiling Not Biased by 3′ End 2′-O-Methylation

(2012) Ye Shen et al.   ANALYTICAL CHEMISTRY

Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons

(2012) Kate D. Meyer et al.   CELL

Systematic identification of edited microRNAs in the human brain

(2012) S. Alon et al.   GENOME RESEARCH

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

(2012) Dan Dominissini et al.   NATURE

Mapping recently identified nucleotide variants in the genome and transcriptome

(2012) Chun-Xiao Song et al.   NATURE BIOTECHNOLOGY

DNA methylome analysis using short bisulfite sequencing data

(2012) Felix Krueger et al.   NATURE METHODS

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

(2012) Zhi-Wei Dong et al.   NUCLEIC ACIDS RESEARCH

Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA

(2012) Jeffrey E. Squires et al.   NUCLEIC ACIDS RESEARCH

MODOMICS: a database of RNA modification pathways—2013 update

(2012) Magdalena A. Machnicka et al.   NUCLEIC ACIDS RESEARCH

The birth of the Epitranscriptome: deciphering the function of RNA modifications

(2012) Yogesh Saletore et al.   GENOME BIOLOGY

Traces of post-transcriptional RNA modifications in deep sequencing data

(2011) Sven Findeiß et al.   BIOLOGICAL CHEMISTRY

Adenosine-to-inosine RNA editing meets cancer

(2011) D. Dominissini et al.   CARCINOGENESIS

N6-Methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO

(2011) Guifang Jia et al.   Nature Chemical Biology

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

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

(2011) Stefanie Kellner et al.   NUCLEIC ACIDS RESEARCH

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

(2011) C. A. Raabe et al.   RNA

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

(2011) M. Hafner et al.   RNA

RNA nucleotide methylation

(2011) Yuri Motorin et al.   Wiley Interdisciplinary Reviews-RNA

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

Advances in RNA structure analysis by chemical probing

(2010) Kevin M Weeks   CURRENT OPINION IN STRUCTURAL BIOLOGY

Inosine cyanoethylation identifies A-to-I RNA editing sites in the human transcriptome

(2010) Masayuki Sakurai et al.   Nature Chemical Biology

Spliceosomal snRNA modifications and their function

(2010) John Karijolich et al.   RNA Biology

Detection of RNA modifications

(2010) Stefanie Kellner et al.   RNA Biology

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

(2010) D. B. Munafo et al.   RNA

Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications

(2009) H. Alexander Ebhardt et al.   NUCLEIC ACIDS RESEARCH

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

(2009) Yuri Motorin et al.   NUCLEIC ACIDS RESEARCH

Adenosine-to-inosine RNA editing

(2009) Boris Zinshteyn et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

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

(2008) Anita Durairaj et al.   ANALYTICA CHIMICA ACTA

Methyl-DNA immunoprecipitation (MeDIP): Hunting down the DNA methylome

(2008) Filipe V. Jacinto et al.   BIOTECHNIQUES

RNA cytosine methylation analysis by bisulfite sequencing

(2008) M. Schaefer et al.   NUCLEIC ACIDS RESEARCH

tRNAdb 2009: compilation of tRNA sequences and tRNA genes

(2008) F. Juhling et al.   NUCLEIC ACIDS RESEARCH