The epitranscriptome toolbox

scDART-seq reveals distinct m6A signatures and mRNA methylation heterogeneity in single cells

(2022) Matthew Tegowski et al.   MOLECULAR CELL

N6-methyladenosine RNA modification suppresses antiviral innate sensing pathways via reshaping double-stranded RNA

(2021) Weinan Qiu et al.   Nature Communications

The Regulation of RNA Modification Systems: The Next Frontier in Epitranscriptomics?

(2021) Matthias R. Schaefer   Genes

SHAPE Directed Discovery of New Functions in Large RNAs

(2021) Kevin M. Weeks   ACCOUNTS OF CHEMICAL RESEARCH

Modifications in an Emergency: The Role of N1-Methylpseudouridine in COVID-19 Vaccines

(2021) Kellie D. Nance et al.   ACS Central Science

How RNA modifications regulate the antiviral response*

(2021) Matthew G. Thompson et al.   IMMUNOLOGICAL REVIEWS

Mapping single-nucleotide m6A by m6A-REF-seq

(2021) Hong-Xuan Chen et al.   METHODS

Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation

(2021) Joo-Hyung Lee et al.   MOLECULAR CELL

Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore

(2021) Ploy N. Pratanwanich et al.   NATURE BIOTECHNOLOGY

A call for direct sequencing of full-length RNAs to identify all modifications

(2021) Juan D. Alfonzo et al.   NATURE GENETICS

Deep and accurate detection of m6A RNA modifications using miCLIP2 and m6Aboost machine learning

(2021) Nadine Körtel et al.   NUCLEIC ACIDS RESEARCH

m6Am-seq reveals the dynamic m6Am methylation in the human transcriptome

(2021) Hanxiao Sun et al.   Nature Communications

Nanopore sequencing technology, bioinformatics and applications

(2021) Yunhao Wang et al.   NATURE BIOTECHNOLOGY

Systematic calibration of epitranscriptomic maps using a synthetic modification-free RNA library

(2021) Zhang Zhang et al.   NATURE METHODS

Keth-seq for transcriptome-wide RNA structure mapping

(2020) Xiaocheng Weng et al.   Nature Chemical Biology

N6-methyladenosine of chromosome-associated regulatory RNA regulates chromatin state and transcription

(2020) Jun Liu et al.   SCIENCE

CAP-MAP: cap analysis protocol with minimal analyte processing, a rapid and sensitive approach to analysing mRNA cap structures

(2020) Alison Galloway et al.   Open Biology

Writers, readers and erasers of RNA modifications in cancer

(2020) Rosaura Esteve-Puig et al.   CANCER LETTERS

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

irCLASH reveals RNA substrates recognized by human ADARs

(2020) Yulong Song et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2020) Luca Cozzuto et al.   Frontiers in Genetics

The Contribution of Epigenetics to Cancer Immunotherapy

(2020) Lorea Villanueva et al.   TRENDS IN IMMUNOLOGY

TonEBP recognizes R-loops and initiates m6A RNA methylation for R-loop resolution

(2020) Hyun Je Kang et al.   NUCLEIC ACIDS RESEARCH

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

Transcriptome-wide Mapping of Internal N7-Methylguanosine Methylome in Mammalian mRNA

(2019) Li-Sheng Zhang et al.   MOLECULAR CELL

Deciphering the “m6A Code” via Antibody-Independent Quantitative Profiling

(2019) Miguel Angel Garcia-Campos et al.   CELL

The human 18S rRNA m6A methyltransferase METTL5 is stabilized by TRMT112

(2019) Nhan van Tran et al.   NUCLEIC ACIDS RESEARCH

Epigenetic loss of RNA-methyltransferase NSUN5 in glioma targets ribosomes to drive a stress adaptive translational program

(2019) Maxime Janin et al.   ACTA NEUROPATHOLOGICA

Programmable RNA N6-methyladenosine editing by CRISPR-Cas9 conjugates

(2019) Xiao-Min Liu et al.   Nature Chemical Biology

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

Reading, writing and erasing mRNA methylation

(2019) Sara Zaccara et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA

(2019) Jin Wang et al.   NUCLEIC ACIDS RESEARCH

m6A promotes R-loop formation to facilitate transcription termination

(2019) Xin Yang et al.   CELL RESEARCH

Probing RNA structure in vivo

(2019) David Mitchell et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing

(2018) Anthony M. Mustoe et al.   CELL

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

(2018) Qing Dai et al.   NATURE METHODS

Nano LC-MS using capillary columns enables accurate quantification of modified ribonucleosides at low femtomol levels

(2018) L Peter Sarin et al.   RNA

Nuclear m6A reader YTHDC1 regulates alternative polyadenylation and splicing during mouse oocyte development

(2018) Seth D. Kasowitz et al.   PLoS Genetics

Improving RNA modification mapping sequence coverage by LC-MS through a nonspecific RNase U2-E49A mutant

(2018) Beulah Solivio et al.   ANALYTICA CHIMICA ACTA

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

Cap-specific, terminal N6-methylation by a mammalian m6Am methyltransferase

(2018) Hanxiao Sun et al.   CELL RESEARCH

Single base resolution mapping of 2′-O-methylation sites in human mRNA and in 3′ terminal ends of small RNAs

(2018) Phillip J. Hsu et al.   METHODS

N6-Methyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation

(2018) Honghui Ma et al.   Nature Chemical Biology

Cap-specific terminal N6-methylation of RNA by an RNA polymerase II–associated methyltransferase

(2018) Shinichiro Akichika et al.   SCIENCE

RNA Chemical Proteomics Reveals the N6-Methyladenosine (m6A)-Regulated Protein–RNA Interactome

(2017) A. Emilia Arguello et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Stable Isotope Labeling for Improved Comparative Analysis of RNA Digests by Mass Spectrometry

(2017) Mellie June Paulines et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

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

(2017) Xiaoyu Li et al.   MOLECULAR CELL

Loud and Clear Epitranscriptomic m 1 A Signals: Now in Single-Base Resolution

(2017) Dan Dominissini 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

N6-methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis

(2017) Raghu R Edupuganti et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

N 6-methyladenosine alters RNA structure to regulate binding of a low-complexity protein

(2017) Nian Liu et al.   NUCLEIC ACIDS RESEARCH

MODOMICS: a database of RNA modification pathways. 2017 update

(2017) Pietro Boccaletto et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Yinzhou Zhu et al.   RNA

N6-methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis

(2017) Raghu R Edupuganti et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

YTHDC1 mediates nuclear export of N6-methyladenosine methylated mRNAs

(2017) Ian A Roundtree et al.   eLife

Mapping of Complete Set of Ribose and Base Modifications of Yeast rRNA by RP-HPLC and Mung Bean Nuclease Assay

(2017) Jun Yang et al.   PLoS One

Mass spectrometry of modified RNAs: recent developments

(2016) Collin Wetzel et al.   ANALYST

Decoding the RNA structurome

(2016) Zhipeng Lu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Nuclear m 6 A Reader YTHDC1 Regulates mRNA Splicing

(2016) Wen Xiao et al.   MOLECULAR CELL

The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA

(2016) Dan Dominissini et al.   NATURE

Reversible methylation of m6Am in the 5′ cap controls mRNA stability

(2016) Jan Mauer et al.   NATURE

m6A RNA methylation promotes XIST-mediated transcriptional repression

(2016) Deepak P. Patil 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

DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo

(2016) Meghan Zubradt et al.   NATURE METHODS

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

YTHDF2 destabilizes m6A-containing RNA through direct recruitment of the CCR4–NOT deadenylase complex

(2016) Hao Du et al.   Nature Communications

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

N 1 -methylpseudouridine-incorporated mRNA outperforms pseudouridine-incorporated mRNA by providing enhanced protein expression and reduced immunogenicity in mammalian cell lines and mice

(2015) Oliwia Andries et al.   JOURNAL OF CONTROLLED RELEASE

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

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

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

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

m6A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation

(2015) Shay Geula et al.   SCIENCE

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

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

(2014) Dan Su 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

Molecular basis for the recognition of methylated adenines in RNA by the eukaryotic YTH domain

(2014) S. Luo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

N6-methyladenosine-dependent regulation of messenger RNA stability

(2013) Xiao Wang et al.   NATURE

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

(2013) Dan Dominissini et al.   Nature Protocols

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

(2013) N. Liu et al.   RNA

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

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

(2012) Dan Dominissini et al.   NATURE

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

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

Genome-Wide Identification of Human RNA Editing Sites by Parallel DNA Capturing and Sequencing

(2009) J. B. Li et al.   SCIENCE