Going global: the new era of mapping modifications in RNA

Mass spectrometry of modified RNAs: recent developments

(2016) Collin Wetzel et al.   ANALYST

RDDpred: a condition-specific RNA-editing prediction model from RNA-seq data

(2016) Min-su Kim et al.   BMC GENOMICS

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

Transcriptome-wide distribution and function of RNA hydroxymethylcytosine

(2016) B. Delatte et al.   SCIENCE

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

N6-methyladenosine Modulates Messenger RNA Translation Efficiency

(2015) Xiao Wang et al.   CELL

A majority of m6A residues are in the last exons, allowing the potential for 3′ UTR regulation

(2015) Shengdong Ke et al.   GENES & DEVELOPMENT

Bidirectional Direct Sequencing of Noncanonical RNA by Two-Dimensional Analysis of Mass Chromatograms

(2015) Anders Björkbom et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

Inosine modifications in human tRNAs are incorporated at the precursor tRNA level

(2015) Adrian Gabriel Torres et al.   NUCLEIC ACIDS RESEARCH

A mass spectrometry-based method for comprehensive quantitative determination of post-transcriptional RNA modifications: the complete chemical structure ofSchizosaccharomyces pomberibosomal RNAs

(2015) Masato Taoka et al.   NUCLEIC ACIDS RESEARCH

RoboOligo: software for mass spectrometry data to support manual and de novo sequencing of post-transcriptionally modified ribonucleic acids

(2015) Paul J. Sample et al.   NUCLEIC ACIDS RESEARCH

Role of Oxidative RNA Damage in Chronic-Degenerative Diseases

(2015) Carmela Fimognari   Oxidative Medicine and Cellular Longevity

tRNA processing, modification, and subcellular dynamics: past, present, and future

(2015) Eric M. Phizicky et al.   RNA

The epitranscriptome in modulating spatiotemporal RNA translation in neuronal post-synaptic function

(2015) Shobbir Hussain et al.   Frontiers in Cellular Neuroscience

The identification and characterization of non-coding and coding RNAs and their modified nucleosides by mass spectrometry

(2015) Kirk W Gaston et al.   RNA Biology

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

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

The Pivotal Regulatory Landscape of RNA Modifications

(2014) Sheng Li et al.   Annual Review of Genomics and Human Genetics

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

(2014) Schraga Schwartz et al.   CELL

Quantitative Analysis of rRNA Modifications Using Stable Isotope Labeling and Mass Spectrometry

(2014) Anna M. Popova et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Systematic identification of tRNAome and its dynamics inLactococcus lactis

(2014) Pranav Puri et al.   MOLECULAR MICROBIOLOGY

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 analysis of ribonucleoside modifications in tRNA by HPLC-coupled mass spectrometry

(2014) Dan Su et al.   Nature Protocols

Gene expression regulation mediated through reversible m6A RNA methylation

(2014) Ye Fu et al.   NATURE REVIEWS GENETICS

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

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

Mass spectrometry sequencing of transfer ribonucleic acids by the comparative analysis of RNA digests (CARD) approach

(2013) Siwei Li et al.   ANALYST

The global identification of tRNA isoacceptors by targeted tandem mass spectrometry

(2013) Collin Wetzel et al.   ANALYST

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

(2013) Mark Helm et al.   CHEMISTRY & BIOLOGY

Nanopore-Based Identification of Individual Nucleotides for Direct RNA Sequencing

(2013) Mariam Ayub et al.   NANO LETTERS

N6-methyladenosine-dependent regulation of messenger RNA stability

(2013) Xiao Wang et al.   NATURE

Identification of direct targets and modified bases of RNA cytosine methyltransferases

(2013) Vahid Khoddami et al.   NATURE BIOTECHNOLOGY

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

(2013) Shobbir Hussain et al.   Cell Reports

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

Method for Comparative Analysis of Ribonucleic Acids Using Isotope Labeling and Mass Spectrometry

(2012) Siwei Li 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

Tet2 Facilitates the Derepression of Myeloid Target Genes during CEBPα-Induced Transdifferentiation of Pre-B Cells

(2012) Eric M. Kallin et al.   MOLECULAR CELL

Oxidative Damage to RNA in Aging and Neurodegenerative Disorders

(2012) Akihiko Nunomura et al.   NEUROTOXICITY RESEARCH

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

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

MODOMICS: a database of RNA modification pathways—2013 update

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

A Novel Computational Strategy to Identify A-to-I RNA Editing Sites by RNA-Seq Data: De Novo Detection in Human Spinal Cord Tissue

(2012) Ernesto Picardi et al.   PLoS One

Transcriptome-wide identification of A > I RNA editing sites by inosine specific cleavage

(2012) P. B. Cattenoz et al.   RNA

Transfer RNA modifications: nature's combinatorial chemistry playground

(2012) Jane E. Jackman et al.   Wiley Interdisciplinary Reviews-RNA

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

Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells

(2011) H. Wu et al.   GENES & DEVELOPMENT

Informatics for mass spectrometry-based RNA analysis

(2011) Hiroshi Nakayama et al.   MASS SPECTROMETRY REVIEWS

tRNA biology charges to the front

(2010) E. M. Phizicky et al.   GENES & DEVELOPMENT

Detection of RNA modifications

(2010) Stefanie Kellner et al.   RNA Biology

Bioinformatics analysis suggests base modifications of tRNAs and miRNAs in Arabidopsis thaliana

(2009) Kei Iida et al.   BMC GENOMICS

Do all modifications benefit all tRNAs?

(2009) Eric M. Phizicky et al.   FEBS LETTERS

RNA processing and its regulation: global insights into biological networks

(2009) Donny D. Licatalosi et al.   NATURE REVIEWS GENETICS

Ariadne: a database search engine for identification and chemical analysis of RNA using tandem mass spectrometry data

(2009) Hiroshi Nakayama et al.   NUCLEIC ACIDS RESEARCH

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

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS