Recent technical advances in the study of nucleic acid modifications

Protein-based molecular recognition tools for detecting and profiling RNA modifications

(2021) Steve D Knutson et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Selective Enrichment of A-to-I Edited Transcripts from Cellular RNA Using Endonuclease V

(2020) Steve D. Knutson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

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

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

Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping

(2020) Aldema Sas-Chen et al.   NATURE

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

(2020) Virginie Marchand et al.   NUCLEIC ACIDS RESEARCH

TET2 chemically modifies tRNAs and regulates tRNA fragment levels

(2020) Chongsheng He et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Sequence- and structure-specific cytosine-5 mRNA methylation by NSUN6

(2020) Tommaso Selmi et al.   NUCLEIC ACIDS RESEARCH

Eukaryotic 5-methylcytosine (m5C) RNA Methyltransferases: Mechanisms, Cellular Functions, and Links to Disease

(2019) Katherine Bohnsack 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

FTO controls reversible m6Am RNA methylation during snRNA biogenesis

(2019) Jan Mauer et al.   Nature Chemical Biology

Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution

(2019) Yibin Liu et al.   NATURE BIOTECHNOLOGY

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

(2019) Miguel Angel Garcia-Campos 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

5-methylcytosine promotes pathogenesis of bladder cancer through stabilizing mRNAs

(2019) Xin Chen et al.   NATURE CELL BIOLOGY

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

(2019) Nhan van Tran 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

Single-base mapping of m6A by an antibody-independent method

(2019) Zhang Zhang et al.   Science Advances

RNA 5-Methylcytosine Facilitates the Maternal-to-Zygotic Transition by Preventing Maternal mRNA Decay

(2019) Ying Yang et al.   MOLECULAR CELL

Programmable RNA N6-methyladenosine editing by CRISPR-Cas9 conjugates

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

mRNA structure determines modification by pseudouridine synthase 1

(2019) Thomas M. Carlile et al.   Nature Chemical Biology

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

(2019) Kate D. Meyer   NATURE METHODS

Pseudouridinylation of mRNA coding sequences alters translation

(2019) Daniel E. Eyler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accurate detection of m6A RNA modifications in native RNA sequences

(2019) Huanle Liu et al.   Nature Communications

Recognition of RNA N6-methyladenosine by IGF2BP proteins enhances mRNA stability and translation

(2018) Huilin Huang et al.   NATURE CELL BIOLOGY

Highly parallel direct RNA sequencing on an array of nanopores

(2018) Daniel R Garalde et al.   NATURE METHODS

Epitranscriptomic m 6 A Regulation of Axon Regeneration in the Adult Mammalian Nervous System

(2018) Yi-Lan Weng et al.   NEURON

ketu mutant mice uncover an essential meiotic function for the ancient RNA helicase YTHDC2

(2018) Devanshi Jain et al.   eLife

Targeted m6A Reader Proteins To Study Epitranscriptomic Regulation of Single RNAs

(2018) Simone Rauch et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A Chemical Signature for Cytidine Acetylation in RNA

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

Differential m6A, m6Am, and m1A Demethylation Mediated by FTO in the Cell Nucleus and Cytoplasm

(2018) Jiangbo Wei et al.   MOLECULAR CELL

Refined RIP-seq protocol for epitranscriptome analysis with low input materials

(2018) Yong Zeng et al.   PLOS BIOLOGY

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

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

(2018) Hanxiao Sun et al.   CELL RESEARCH

Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase

(2018) Emily K Schutsky et al.   NATURE BIOTECHNOLOGY

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

(2018) Shinichiro Akichika et al.   SCIENCE

The dynamic RNA modification 5‐methylcytosine and its emerging role as an epitranscriptomic mark

(2018) Lukas Trixl et al.   Wiley Interdisciplinary Reviews-RNA

m 6 A mRNA modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover

(2017) Shengdong Ke et al.   GENES & DEVELOPMENT

Epitranscriptome sequencing technologies: decoding RNA modifications

(2017) Xiaoyu Li 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

ALKBH1 is an RNA dioxygenase responsible for cytoplasmic and mitochondrial tRNA modifications

(2017) Layla Kawarada et al.   NUCLEIC ACIDS RESEARCH

MODOMICS: a database of RNA modification pathways. 2017 update

(2017) Pietro Boccaletto et al.   NUCLEIC ACIDS RESEARCH

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

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

Specialized box C/D snoRNPs act as antisense guides to target RNA base acetylation

(2017) Sunny Sharma et al.   PLoS Genetics

The conserved RNA helicase YTHDC2 regulates the transition from proliferation to differentiation in the germline

(2017) Alexis S Bailey et al.   eLife

YTHDC1 mediates nuclear export of N6-methyladenosine methylated mRNAs

(2017) Ian A Roundtree et al.   eLife

Role of TET enzymes in DNA methylation, development, and cancer

(2016) Kasper Dindler Rasmussen et al.   GENES & DEVELOPMENT

Nuclear m 6 A Reader YTHDC1 Regulates mRNA Splicing

(2016) Wen Xiao et al.   MOLECULAR CELL

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

(2016) Jan Mauer et al.   NATURE

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

(2016) Benoit Molinie et al.   NATURE METHODS

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

(2016) Hao Du et al.   Nature Communications

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

(2016) Lindsey Van Haute et al.   Nature Communications

5′ UTR m6A Promotes Cap-Independent Translation

(2015) Kate D. Meyer et al.   CELL

N6-methyladenosine Modulates Messenger RNA Translation Efficiency

(2015) Xiao Wang et al.   CELL

Formation and Abundance of 5-Hydroxymethylcytosine in RNA

(2015) Sabrina M. Huber et al.   CHEMBIOCHEM

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

(2015) Shengdong Ke et al.   GENES & DEVELOPMENT

Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome

(2015) Xiaoyu Li et al.   Nature Chemical Biology

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

A-to-I editing of coding and non-coding RNAs by ADARs

(2015) Kazuko Nishikura   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Yeast Kre33 and human NAT10 are conserved 18S rRNA cytosine acetyltransferases that modify tRNAs assisted by the adaptor Tan1/THUMPD1

(2015) Sunny Sharma et al.   NUCLEIC ACIDS RESEARCH

Methylation of ribosomal RNA by NSUN5 is a conserved mechanism modulating organismal lifespan

(2015) Markus Schosserer et al.   Nature Communications

Cytosine methylation of tRNA-Asp by DNMT2 has a role in translation of proteins containing poly-Asp sequences

(2015) Raghuvaran Shanmugam et al.   Cell Discovery

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

(2015) Gabrielle Bourgeois et al.   PLoS One

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

(2014) Schraga Schwartz et al.   CELL

A-to-I editing on tRNAs: Biochemical, biological and evolutionary implications

(2014) Adrian Gabriel Torres et al.   FEBS LETTERS

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

(2014) M. Sakurai et al.   GENOME RESEARCH

A Single Acetylation of 18 S rRNA Is Essential for Biogenesis of the Small Ribosomal Subunit inSaccharomyces cerevisiae

(2014) Satoshi Ito et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Human NAT10 Is an ATP-dependent RNA Acetyltransferase Responsible forN4-Acetylcytidine Formation in 18 S Ribosomal RNA (rRNA)

(2014) Satoshi Ito et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

(2014) Thomas M. Carlile et al.   NATURE

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

A cluster of methylations in the domain IV of 25S rRNA is required for ribosome stability

(2014) Andriana Gigova et al.   RNA

DNA Methylation in Mammals

(2014) E. Li et al.   Cold Spring Harbor Perspectives in Biology

Conformational Preferences of Modified Nucleoside N(4)-Acetylcytidine, ac4C Occur at “Wobble” 34th Position in the Anticodon Loop of tRNA

(2013) Bajarang V. Kumbhar et al.   CELL BIOCHEMISTRY AND BIOPHYSICS

TET enzymes, TDG and the dynamics of DNA demethylation

(2013) Rahul M. Kohli et al.   NATURE

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

Lack of evidence for existence of noncanonical RNA editing

(2013) Robert Piskol et al.   NATURE BIOTECHNOLOGY

A METTL3–METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation

(2013) Jianzhao Liu et al.   Nature Chemical Biology

DNA methylation: roles in mammalian development

(2013) Zachary D. Smith et al.   NATURE REVIEWS GENETICS

The mechanism of pseudouridine synthases from a covalent complex with RNA, and alternate specificity for U2605 versus U2604 between close homologs

(2013) Nadine Czudnochowski et al.   NUCLEIC ACIDS RESEARCH

Yeast Nop2 and Rcm1 methylate C2870 and C2278 of the 25S rRNA, respectively

(2013) Sunny Sharma et al.   NUCLEIC ACIDS RESEARCH

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

(2013) N. Liu et al.   RNA

FTO-mediated formation of N6-hydroxymethyladenosine and N6-formyladenosine in mammalian RNA

(2013) Ye Fu et al.   Nature Communications

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

Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome

(2012) Miao Yu et al.   CELL

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

(2012) Kate D. Meyer et al.   CELL

ALKBH5 Is a Mammalian RNA Demethylase that Impacts RNA Metabolism and Mouse Fertility

(2012) Guanqun Zheng et al.   MOLECULAR CELL

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

(2012) Dan Dominissini et al.   NATURE

Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome

(2012) Zhiyu Peng et al.   NATURE BIOTECHNOLOGY

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

(2012) P. B. Cattenoz et al.   RNA

Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution

(2012) M. J. Booth et al.   SCIENCE

Comment on "Widespread RNA and DNA Sequence Differences in the Human Transcriptome"

(2012) J. K. Pickrell et al.   SCIENCE

Comment on "Widespread RNA and DNA Sequence Differences in the Human Transcriptome"

(2012) W. Lin et al.   SCIENCE

Comment on "Widespread RNA and DNA Sequence Differences in the Human Transcriptome"

(2012) C. L. Kleinman et al.   SCIENCE

Accurate identification of A-to-I RNA editing in human by transcriptome sequencing

(2011) J. H. Bahn et al.   GENOME RESEARCH

Converting nonsense codons into sense codons by targeted pseudouridylation

(2011) John Karijolich et al.   NATURE

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

(2011) Guifang Jia et al.   Nature Chemical Biology

Widespread RNA and DNA Sequence Differences in the Human Transcriptome

(2011) M. Li et al.   SCIENCE

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

(2010) Markus Hafner et al.   CELL

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

(2010) Masayuki Sakurai et al.   Nature Chemical Biology

The Behaviour of 5-Hydroxymethylcytosine in Bisulfite Sequencing

(2010) Yun Huang et al.   PLoS One

The nucleolar RNA methyltransferase Misu (NSun2) is required for mitotic spindle stability

(2009) Shobbir Hussain et al.   JOURNAL OF CELL BIOLOGY

Unconventional decoding of the AUA codon as methionine by mitochondrial tRNA Met with the anticodon f 5 CAU as revealed with a mitochondrial in vitro translation system

(2009) Chie Takemoto et al.   NUCLEIC ACIDS RESEARCH

Adenosine-to-inosine RNA editing

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