Methods for RNA Modification Mapping Using Deep Sequencing: Established and New Emerging Technologies

Precise Antibody-Independent m6A Identification via 4SedTTP-Involved and FTO-Assisted Strategy at Single-Nucleotide Resolution

(2018) Tingting Hong et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Mettl1/Wdr4-Mediated m 7 G tRNA Methylome Is Required for Normal mRNA Translation and Embryonic Stem Cell Self-Renewal and Differentiation

(2018) Shuibin Lin et al.   MOLECULAR CELL

Distinguishing RNA modifications from noise in epitranscriptome maps

(2018) Anya V Grozhik et al.   Nature Chemical Biology

Topological Characterization of Human and Mouse m5C Epitranscriptome Revealed by Bisulfite Sequencing

(2018) Zhen Wei et al.   International Journal of Genomics

A Chemical Signature for Cytidine Acetylation in RNA

(2018) Justin M. Thomas et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

M1A within cytoplasmic mRNAs at single nucleotide resolution: A reconciled transcriptome-wide map

(2018) Schraga Schwartz   RNA

Perspectives on topology of the human m1A methylome at single nucleotide resolution

(2018) Xushen Xiong et al.   RNA

AlkAniline-Seq: Profiling of m7 G and m3 C RNA Modifications at Single Nucleotide Resolution

(2018) Virginie Marchand et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Acetylation of Cytidine in mRNA Promotes Translation Efficiency

(2018) Daniel Arango et al.   CELL

Bisulfite-Free, Nanoscale Analysis of 5-Hydroxymethylcytosine at Single Base Resolution

(2018) Hu Zeng et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

TRUB1 is the predominant pseudouridine synthase acting on mammalian mRNA via a predictable and conserved code

(2017) Modi Safra et al.   GENOME RESEARCH

Statistically robust methylation calling for whole-transcriptome bisulfite sequencing reveals distinct methylation patterns for mouse RNAs

(2017) Carine Legrand et al.   GENOME RESEARCH

Base-Resolution Mapping Reveals Distinct m 1 A Methylome in Nuclear- and Mitochondrial-Encoded Transcripts

(2017) Xiaoyu Li et al.   MOLECULAR CELL

The m1A landscape on cytosolic and mitochondrial mRNA at single-base resolution

(2017) Modi Safra et al.   NATURE

Nm-seq maps 2′-O-methylation sites in human mRNA with base precision

(2017) Qing Dai et al.   NATURE METHODS

Thiol-linked alkylation of RNA to assess expression dynamics

(2017) Veronika A Herzog et al.   NATURE METHODS

Substoichiometric ribose methylations in spliceosomal snRNAs

(2017) Nicolai Krogh et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Transcriptome-Wide Mapping of RNA 5-Methylcytosine in Arabidopsis mRNAs and Noncoding RNAs

(2017) Rakesh David et al.   PLANT CELL

Evidence for rRNA 2′-O-methylation plasticity: Control of intrinsic translational capabilities of human ribosomes

(2017) Jenny Erales et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput and site-specific identification of 2′- O -methylation sites using ribose oxidation sequencing (RibOxi-seq)

(2017) Yinzhou Zhu et al.   RNA

mRNA pseudouridylation affects RNA metabolism in the parasite Toxoplasma gondii

(2017) Margaret A. Nakamoto et al.   RNA

Identification of sites of 2′-O-methylation vulnerability in human ribosomal RNAs by systematic mapping

(2017) Sunny Sharma et al.   Scientific Reports

Pseudouridylation meets next-generation sequencing

(2016) Maryam Zaringhalam 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

m6A-LAIC-seq reveals the census and complexity of the m6A epitranscriptome

(2016) Benoit Molinie et al.   NATURE METHODS

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

High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq

(2016) Rafal Gumienny et al.   NUCLEIC ACIDS RESEARCH

High-throughput single-base resolution mapping of RNA 2΄-O-methylated residues

(2016) Danny Incarnato 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

Profiling of 2′-O-Me in human rRNA reveals a subset of fractionally modified positions and provides evidence for ribosome heterogeneity

(2016) Nicolai Krogh et al.   NUCLEIC ACIDS RESEARCH

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

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

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

(2015) Ralf Hauenschild et al.   NUCLEIC ACIDS RESEARCH

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

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

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

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

(2014) Schraga Schwartz et al.   CELL

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

(2014) Thomas M. Carlile et al.   NATURE

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

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

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

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

Genome-wide Profiling of 5-Formylcytosine Reveals Its Roles in Epigenetic Priming

(2013) Chun-Xiao Song et al.   CELL

Transcriptome-wide mapping of N6-methyladenosine by m6A-seq based on immunocapturing and massively parallel sequencing

(2013) Dan Dominissini et al.   Nature Protocols

HAMR: high-throughput annotation of modified ribonucleotides

(2013) P. Ryvkin 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

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

(2012) Kate D. Meyer et al.   CELL

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

(2012) Dan Dominissini et al.   NATURE

RNA cytosine methylation by Dnmt2 and NSun2 promotes tRNA stability and protein synthesis

(2012) Francesca Tuorto et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

Quantification of oxidized levels of specific RNA species using an aldehyde reactive probe

(2011) Mikiei Tanaka et al.   ANALYTICAL BIOCHEMISTRY

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

(2010) Markus Hafner et al.   CELL

An assay for RNA oxidation induced abasic sites using the Aldehyde Reactive Probe

(2010) Mikiei Tanaka et al.   FREE RADICAL RESEARCH

RNA cytosine methylation analysis by bisulfite sequencing

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