Analysis of RNA Modifications by Second- and Third-Generation Deep Sequencing: 2020 Update

tRNA 2′-O-methylation by a duo of TRM7/FTSJ1 proteins modulates small RNA silencing in Drosophila

(2020) Margarita T Angelova et al.   NUCLEIC ACIDS RESEARCH

The Architecture of SARS-CoV-2 Transcriptome

(2020) Dongwan Kim et al.   CELL

A metabolic labeling method detects m6A transcriptome-wide at single base resolution

(2020) Xiao Shu et al.   Nature Chemical Biology

Antibody-free enzyme-assisted chemical approach for detection of N6-methyladenosine

(2020) Ye Wang et al.   Nature Chemical Biology

The large repertoire of 2’-O-methylation guided by C/D snoRNAs on Trypanosoma brucei rRNA

(2020) K. Shanmugha Rajan et al.   RNA Biology

Limits in the detection of m6A changes using MeRIP/m6A-seq

(2020) Alexa B. R. McIntyre et al.   Scientific Reports

Mapping the epigenetic modifications of DNA and RNA

(2020) Lin-Yong Zhao et al.   Protein & Cell

MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets

(2020) Luca Cozzuto et al.   Frontiers in Genetics

Gaussian Mixture Model-Based Unsupervised Nucleotide Modification Number Detection Using Nanopore Sequencing Readouts

(2020) Hongxu Ding et al.   BIOINFORMATICS

No Evidence for N7-Methylation of Guanosine (m7G) in Human let-7e

(2020) Jeppe Vinther   MOLECULAR CELL

Further Evidence Supporting N7-Methylation of Guanosine (m7G) in Human MicroRNAs

(2020) Tony Kouzarides et al.   MOLECULAR CELL

Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping

(2020) Aldema Sas-Chen et al.   NATURE

Decoding the epitranscriptional landscape from native RNA sequences

(2020) Piroon Jenjaroenpun et al.   NUCLEIC ACIDS RESEARCH

Accurate characterization of Escherichia coli tRNA modifications with a simple method of deep-sequencing library preparation

(2020) Ji Wang et al.   RNA Biology

LEAD‐m6A‐seq for Locus‐specific Detection of N6‐methyladenosine and Quantification of Differential Methylation

(2020) Chuan He et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

HydraPsiSeq: a method for systematic and quantitative mapping of pseudouridines in RNA

(2020) Virginie Marchand et al.   NUCLEIC ACIDS RESEARCH

The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2’-O-Me sites

(2020) Sowmya Ramachandran et al.   RNA

Manganese Ions Individually Alter the Reverse Transcription Signature of Modified Ribonucleosides

(2020) Marco Kristen et al.   Genes

Nucleotide resolution profiling of m3C RNA modification by HAC-seq

(2020) Jia Cui et al.   NUCLEIC ACIDS RESEARCH

NOseq: amplicon sequencing evaluation method for RNA m6A sites after chemical deamination

(2020) Stephan Werner et al.   NUCLEIC ACIDS RESEARCH

FTSJ3 is an RNA 2′-O-methyltransferase recruited by HIV to avoid innate immune sensing

(2019) Mathieu Ringeard et al.   NATURE

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

(2019) Yuri Motorin et al.   Genes

Transcriptome-wide profiling of multiple RNA modifications simultaneously at single-base resolution

(2019) Vahid Khoddami et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

METTL1 Promotes let-7 MicroRNA Processing via m7G Methylation

(2019) Luca Pandolfini et al.   MOLECULAR CELL

2'-O-methylation within prokaryotic and eukaryotic tRNA inhibits innate immune activation by endosomal Toll-like receptors but does not affect recognition of whole organisms

(2019) Isabel Freund et al.   RNA

Counting the Cuts: MAZTER-Seq Quantifies m6A Levels Using a Methylation-Sensitive Ribonuclease

(2019) Radha Raman Pandey et al.   CELL

Identification of the m6Am Methyltransferase PCIF1 Reveals the Location and Functions of m6Am in the Transcriptome

(2019) Konstantinos Boulias et al.   MOLECULAR CELL

PCIF1 Catalyzes m6Am mRNA Methylation to Regulate Gene Expression

(2019) Erdem Sendinc et al.   MOLECULAR CELL

Pseudouridines on Trypanosoma brucei spliceosomal small nuclear RNAs and their implication for RNA and protein interactions

(2019) K Shanmugha Rajan et al.   NUCLEIC ACIDS RESEARCH

FICC-Seq: a method for enzyme-specified profiling of methyl-5-uridine in cellular RNA

(2019) Jean-Michel Carter et al.   NUCLEIC ACIDS RESEARCH

Reading canonical and modified nucleobases in 16S ribosomal RNA using nanopore native RNA sequencing

(2019) Andrew M. Smith et al.   PLoS One

Discovering and Mapping the Modified Nucleotides That Comprise the Epitranscriptome of mRNA

(2019) Bastian Linder et al.   Cold Spring Harbor Perspectives in Biology

Dynamic methylome of internal mRNA N7-methylguanosine and its regulatory role in translation

(2019) Lionel Malbec et al.   CELL RESEARCH

Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis

(2019) Adrian Viehweger et al.   GENOME RESEARCH

DART-seq: an antibody-free method for global m6A detection

(2019) Kate D. Meyer   NATURE METHODS

Evolution of a reverse transcriptase to map N1-methyladenosine in human messenger RNA

(2019) Huiqing Zhou et al.   NATURE METHODS

Detection of internal N7-methylguanosine (m7G) RNA modifications by mutational profiling sequencing

(2019) Christel Enroth et al.   NUCLEIC ACIDS RESEARCH

Developmental changes of rRNA ribose methylations in the mouse

(2019) Jade Hebras et al.   RNA Biology

Chemo‐enzymatic treatment of RNA to facilitate analyses

(2019) Nils Muthmann et al.   Wiley Interdisciplinary Reviews-RNA

Recent advances in the detection of base modifications using the Nanopore sequencer

(2019) Liu Xu et al.   JOURNAL OF HUMAN GENETICS

Nucleotide resolution profiling of m7G tRNA modification by TRAC-Seq

(2019) Shuibin Lin et al.   Nature Protocols

Development and validation of monoclonal antibodies against N6-methyladenosine for the detection of RNA modifications

(2019) Shun Matsuzawa et al.   PLoS One

Direct RNA sequencing enables m6A detection in endogenous transcript isoforms at base-specific resolution

(2019) Daniel A. Lorenz et al.   RNA

Accurate detection of m6A RNA modifications in native RNA sequences

(2019) Huanle Liu et al.   Nature Communications

Antibody cross-reactivity accounts for widespread appearance of m1A in 5’UTRs

(2019) Anya V. Grozhik et al.   Nature Communications

Limited antibody specificity compromises epitranscriptomic analyses

(2019) Mark Helm et al.   Nature Communications

Enzymatic or In Vivo Installation of Propargyl Groups in Combination with Click Chemistry for the Enrichment and Detection of Methyltransferase Target Sites in RNA

(2018) Katja Hartstock et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

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

miCLIP-MaPseq, a Substrate Identification Approach for Radical SAM RNA Methylating Enzymes

(2018) Vanja Stojković 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

Pseudouridines have context-dependent mutation and stop rates in high-throughput sequencing

(2018) Katherine I. Zhou et al.   RNA Biology

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

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

Chemical Labeling and Affinity Capture of Inosine-Containing RNAs Using Acrylamidofluorescein

(2018) Steve D. Knutson et al.   BIOCONJUGATE CHEMISTRY

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

The landscape of the A-to-I RNA editome from 462 human genomes

(2018) Zhangyi Ouyang et al.   Scientific Reports

Emerging approaches for detection of methylation sites in RNA

(2018) Anna Ovcharenko et al.   Open Biology

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

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

An Elongation- and Ligation-Based qPCR Amplification Method for the Radiolabeling-Free Detection of Locus-Specific N 6 -Methyladenosine Modification

(2018) Yu Xiao et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Acetylation of Cytidine in mRNA Promotes Translation Efficiency

(2018) Daniel Arango et al.   CELL

Mapping N 6 -Methyladenosine (m6 A) in RNA: Established Methods, Remaining Challenges, and Emerging Approaches

(2018) Katja Hartstock et al.   CHEMISTRY-A EUROPEAN JOURNAL

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

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

Determination of enrichment factors for modified RNA in MeRIP experiments

(2018) Kaouthar Slama et al.   METHODS

Misincorporation signatures for detecting modifications in mRNA: Not as simple as it sounds

(2018) Aldema Sas-Chen et al.   METHODS

BisAMP: A web-based pipeline for targeted RNA cytosine-5 methylation analysis

(2018) Felix Bormann et al.   METHODS

Catalytic crosslinking-based methods for enzyme-specified profiling of RNA ribonucleotide modifications

(2018) Shobbir Hussain   METHODS

Sequencing-based methods for detection and quantitation of ribose methylations in RNA

(2018) Nicolai Krogh et al.   METHODS

Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis

(2018) Michael H. Schwartz et al.   Nature Communications

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

Fingerprints of Modified RNA Bases from Deep Sequencing Profiles

(2017) Anna M. Kietrys et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Epitranscriptomics: Shrinking maps of RNA modifications

(2017) Anya V. Grozhik et al.   NATURE

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

Detecting RNA modifications in the epitranscriptome: predict and validate

(2017) Mark Helm et al.   NATURE REVIEWS GENETICS

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

Antibodies specific for nucleic acid modifications

(2017) Regina Feederle et al.   RNA Biology

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

Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2

(2017) Steven Busan et al.   RNA

Pseudouridylation meets next-generation sequencing

(2016) Maryam Zaringhalam et al.   METHODS

Current covalent modification methods for detecting RNA in fixed and living cells

(2016) Josephin M. Holstein 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

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

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

N6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions

(2015) Nian Liu et al.   NATURE

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

Profiling of Ribose Methylations in RNA by High-Throughput Sequencing

(2014) Ulf Birkedal et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Trm4 and Nsun2 RNA:m5C Methyltransferases Form Metabolite-Dependent, Covalent Adducts with Previously Methylated RNA

(2014) Haley J. Moon et al.   BIOCHEMISTRY

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

(2014) Vahid Khoddami et al.   Nature Protocols

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

Identification of a Selective Polymerase Enables Detection of N6-Methyladenosine in RNA

(2013) Emily M. Harcourt et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Identification of direct targets and modified bases of RNA cytosine methyltransferases

(2013) Vahid Khoddami et al.   NATURE BIOTECHNOLOGY

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

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

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

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

(2010) Markus Hafner et al.   CELL

Expanding the chemical scope of RNA:methyltransferases to site-specific alkynylation of RNA for click labeling

(2010) Y. Motorin et al.   NUCLEIC ACIDS RESEARCH

RNA cytosine methylation analysis by bisulfite sequencing

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