A molecular-level perspective on the frequency, distribution, and consequences of messenger RNA modifications

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

(2019) Yuri Motorin et al.   Genes

Eukaryotic Translation Elongation is Modulated by Single Natural Nucleotide Derivatives in the Coding Sequences of mRNAs

(2019) Thomas Philipp Hoernes et al.   Genes

Analysis of human acetylation stoichiometry defines mechanistic constraints on protein regulation

(2019) Bogi Karbech Hansen et al.   Nature Communications

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

Structural insights into FTO’s catalytic mechanism for the demethylation of multiple RNA substrates

(2019) Xiao Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Resolution Ribosome Profiling Defines Discrete Ribosome Elongation States and Translational Regulation during Cellular Stress

(2019) Colin Chih-Chien Wu et al.   MOLECULAR CELL

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

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

Where, When, and How: Context-Dependent Functions of RNA Methylation Writers, Readers, and Erasers

(2019) Hailing Shi et al.   MOLECULAR CELL

A Quantitative and Predictive Model for RNA Binding by Human Pumilio Proteins

(2019) Inga Jarmoskaite et al.   MOLECULAR CELL

Genome-wide identification of mRNA 5-methylcytosine in mammals

(2019) Tao Huang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mettl3-mediated mRNA m6A methylation promotes dendritic cell activation

(2019) Huamin Wang et al.   Nature Communications

Identification and Quantification of Modified Nucleosides in Saccharomyces cerevisiae mRNAs

(2019) Mehmet Tardu et al.   ACS Chemical Biology

AlkB Homologue 1 Demethylates N3-Methylcytidine in mRNA of Mammals

(2019) Cheng-Jie Ma et al.   ACS Chemical Biology

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

(2019) Radha Raman Pandey et al.   CELL

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

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

Transcriptome-wide analysis of pseudouridylation of mRNA and non-coding RNAs in Arabidopsis

(2019) Lirong Sun et al.   JOURNAL OF EXPERIMENTAL BOTANY

PCIF1 Catalyzes m6Am mRNA Methylation to Regulate Gene Expression

(2019) Erdem Sendinc et al.   MOLECULAR CELL

Analysis and Interpretation of Protein Post-Translational Modification Site Stoichiometry

(2019) Gabriela Prus et al.   TRENDS IN BIOCHEMICAL SCIENCES

mRNA structure determines modification by pseudouridine synthase 1

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

Reading, writing and erasing mRNA methylation

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

mRNA structure regulates protein expression through changes in functional half-life

(2019) David M. Mauger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Existence of Internal N7-Methylguanosine Modification in mRNA Determined by Differential Enzyme Treatment Coupled with Mass Spectrometry Analysis

(2018) Jie-Mei Chu et al.   ACS Chemical Biology

Identification of YTH Domain-Containing Proteins as the Readers for N1-Methyladenosine in RNA

(2018) Xiaoxia Dai et al.   ANALYTICAL CHEMISTRY

A-to-I RNA Editing Contributes to Proteomic Diversity in Cancer

(2018) Xinxin Peng et al.   CANCER CELL

Modifications and functional genomics of human transfer RNA

(2018) Tao Pan   CELL RESEARCH

Determining mRNA half-lives on a transcriptome-wide scale

(2018) Andrew Lugowski et al.   METHODS

Potential link between m 6 A modification and systemic lupus erythematosus

(2018) Lian-Ju Li et al.   MOLECULAR IMMUNOLOGY

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

(2018) Huilin Huang et al.   NATURE CELL BIOLOGY

Structural and evolutionary insights into ribosomal RNA methylation

(2018) Petr V Sergiev et al.   Nature Chemical Biology

Distinguishing RNA modifications from noise in epitranscriptome maps

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

A brave new world of RNA-binding proteins

(2018) Matthias W. Hentze et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

2′-O-methylation in mRNA disrupts tRNA decoding during translation elongation

(2018) Junhong Choi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Atomic mutagenesis of stop codon nucleotides reveals the chemical prerequisites for release factor-mediated peptide release

(2018) Thomas Philipp Hoernes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TwoCk1δtranscripts regulated by m6A methylation code for two antagonistic kinases in the control of the circadian clock

(2018) Jean-Michel Fustin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The m6A reader protein YTHDC2 interacts with the small ribosomal subunit and the 5′-3′ exoribonuclease XRN1

(2018) Jens Kretschmer et al.   RNA

Reading m 6 A in the Transcriptome: m 6 A-Binding Proteins

(2018) Deepak P. Patil et al.   TRENDS IN CELL BIOLOGY

A potentially abundant junctional RNA motif stabilized by m6A and Mg2+

(2018) Bei Liu et al.   Nature Communications

2′-O-methylation in mRNA disrupts tRNA decoding during translation elongation

(2018) Junhong Choi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2018) Jiangbo Wei et al.   MOLECULAR CELL

The role of RNA adenosine demethylases in the control of gene expression

(2018) Veronika Rajecka et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Acetylation of Cytidine in mRNA Promotes Translation Efficiency

(2018) Daniel Arango et al.   CELL

A novel m6A reader Prrc2a controls oligodendroglial specification and myelination

(2018) Rong Wu et al.   CELL RESEARCH

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

(2018) Hanxiao Sun et al.   CELL RESEARCH

Inosine induces context-dependent recoding and translational stalling

(2018) Konstantin Licht et al.   NUCLEIC ACIDS RESEARCH

Circadian Clock Regulation of Hepatic Lipid Metabolism by Modulation of m6A mRNA Methylation

(2018) Xiang Zhong et al.   Cell Reports

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

Three distinct 3-methylcytidine (m 3 C) methyltransferases modify tRNA and mRNA in mice and humans

(2017) Luang Xu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Thio-Modification of tRNA at the Wobble Position as Regulator of the Kinetics of Decoding and Translocation on the Ribosome

(2017) Namit Ranjan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Viral Epitranscriptomics

(2017) Edward M. Kennedy et al.   JOURNAL OF VIROLOGY

Heterogeneity of Stop Codon Readthrough in Single Bacterial Cells and Implications for Population Fitness

(2017) Yongqiang Fan et al.   MOLECULAR CELL

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

(2017) Xiaoyu Li et al.   MOLECULAR CELL

5-Methylcytosine RNA Methylation in Arabidopsis Thaliana

(2017) Xuean Cui et al.   Molecular Plant

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

Detecting RNA modifications in the epitranscriptome: predict and validate

(2017) Mark Helm et al.   NATURE REVIEWS GENETICS

RNA modifications and structures cooperate to guide RNA–protein interactions

(2017) Cole J.T. Lewis et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

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

Position-dependent effects of regioisomeric methylated adenine and guanine ribonucleosides on translation

(2017) Changjun You et al.   NUCLEIC ACIDS RESEARCH

ALKBH10B Is an RNAN6-Methyladenosine Demethylase Affecting Arabidopsis Floral Transition

(2017) Hong-Chao Duan et al.   PLANT CELL

LC-MS-MS quantitative analysis reveals the association between FTO and DNA methylation

(2017) Yuting Zhu et al.   PLoS One

Arabidopsism6A demethylase activity modulates viral infection of a plant virus and the m6A abundance in its genomic RNAs

(2017) Mireya Martínez-Pérez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A to I editing in disease is not fake news

(2017) Prajakta Bajad et al.   RNA Biology

mRNA pseudouridylation affects RNA metabolism in the parasite Toxoplasma gondii

(2017) Margaret A. Nakamoto et al.   RNA

Pseudouridine and N 6 -methyladenosine modifications weaken PUF protein/RNA interactions

(2017) Pavanapuresan P. Vaidyanathan et al.   RNA

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

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

m 6 A RNA Methylation Regulates the Self-Renewal and Tumorigenesis of Glioblastoma Stem Cells

(2017) Qi Cui et al.   Cell Reports

YTHDC1 mediates nuclear export of N6-methyladenosine methylated mRNAs

(2017) Ian A Roundtree et al.   eLife

ALKBH1-Mediated tRNA Demethylation Regulates Translation

(2016) Fange Liu et al.   CELL

The DEAD-Box Protein Dhh1p Couples mRNA Decay and Translation by Monitoring Codon Optimality

(2016) Aditya Radhakrishnan et al.   CELL

Pseudouridylation of 7SK snRNA promotes 7SK snRNP formation to suppress HIV‐1 transcription and escape from latency

(2016) Yang Zhao et al.   EMBO REPORTS

Structural Basis for Translation Termination on a Pseudouridylated Stop Codon

(2016) Egor Svidritskiy et al.   JOURNAL OF MOLECULAR BIOLOGY

Nuclear m 6 A Reader YTHDC1 Regulates mRNA Splicing

(2016) Wen Xiao et al.   MOLECULAR CELL

The m 6 A Methyltransferase METTL3 Promotes Translation in Human Cancer Cells

(2016) Shuibin Lin et al.   MOLECULAR CELL

m6A potentiates Sxl alternative pre-mRNA splicing for robust Drosophila sex determination

(2016) Irmgard U. Haussmann et al.   NATURE

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

m1A and m1G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs

(2016) Huiqing Zhou et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

N6-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics

(2016) Junhong Choi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Base pairing and structural insights into the 5-formylcytosine in RNA duplex

(2016) Rui Wang et al.   NUCLEIC ACIDS RESEARCH

Hypoxia induces the breast cancer stem cell phenotype by HIF-dependent and ALKBH5-mediated m6A-demethylation of NANOG mRNA

(2016) Chuanzhao Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

mRNA modifications: Dynamic regulators of gene expression?

(2016) Thomas Philipp Hoernes et al.   RNA Biology

The emerging biology of RNA post-transcriptional modifications

(2016) Sigrid Nachtergaele et al.   RNA Biology

Cracking the epitranscriptome

(2016) Schraga Schwartz   RNA

Transcriptome-wide distribution and function of RNA hydroxymethylcytosine

(2016) B. Delatte et al.   SCIENCE

Messenger RNA modifications: Form, distribution, and function

(2016) W. V. Gilbert et al.   SCIENCE

m1A and m1G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs

(2016) Huiqing Zhou et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

N6-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics

(2016) Junhong Choi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing

(2016) Pedro G. Ferreira et al.   Scientific Reports

Large-Scale Measurement of Absolute Protein Glycosylation Stoichiometry

(2015) Shisheng Sun et al.   ANALYTICAL CHEMISTRY

The Clothes Make the mRNA: Past and Present Trends in mRNP Fashion

(2015) Guramrit Singh et al.   Annual Review of Biochemistry

Codon Optimality Is a Major Determinant of mRNA Stability

(2015) Vladimir Presnyak et al.   CELL

N6-methyladenosine Modulates Messenger RNA Translation Efficiency

(2015) Xiao Wang et al.   CELL

Acetyl Coenzyme A: A Central Metabolite and Second Messenger

(2015) Federico Pietrocola et al.   Cell Metabolism

Formation and Abundance of 5-Hydroxymethylcytosine in RNA

(2015) Sabrina M. Huber et al.   CHEMBIOCHEM

Acetyl-CoA and the regulation of metabolism: mechanisms and consequences

(2015) Lei Shi et al.   CURRENT OPINION IN CELL BIOLOGY

Structure and Thermodynamics of N6-Methyladenosine in RNA: A Spring-Loaded Base Modification

(2015) Caroline Roost et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Acetylation dynamics and stoichiometry in Saccharomyces cerevisiae

(2015) B. T. Weinert et al.   Molecular Systems Biology

Structural imprints in vivo decode RNA regulatory mechanisms

(2015) Robert C. Spitale et al.   NATURE

Dynamic m6A mRNA methylation directs translational control of heat shock response

(2015) Jun Zhou et al.   NATURE

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

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

(2015) Kazuko Nishikura   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Protein mistranslation protects bacteria against oxidative stress

(2015) Yongqiang Fan et al.   NUCLEIC ACIDS RESEARCH

Widespread occurrence ofN6-methyladenosine in bacterial mRNA

(2015) Xin Deng et al.   NUCLEIC ACIDS RESEARCH

Nucleotide modifications within bacterial messenger RNAs regulate their translation and are able to rewire the genetic code

(2015) Thomas Philipp Hoernes et al.   NUCLEIC ACIDS RESEARCH

Temperature dependent mistranslation in a hyperthermophile adapts proteins to lower temperatures

(2015) Michael H. Schwartz et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Eric M. Phizicky et al.   RNA

O6-Methylguanosine leads to position-dependent effects on ribosome speed and fidelity

(2015) Benjamin H. Hudson et al.   RNA

Metabolic Enzymes Enjoying New Partnerships as RNA-Binding Proteins

(2015) Alfredo Castello et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Large-scale determination of absolute phosphorylation stoichiometries in human cells by motif-targeting quantitative proteomics

(2015) Chia-Feng Tsai et al.   Nature Communications

The majority of transcripts in the squid nervous system are extensively recoded by A-to-I RNA editing

(2015) Shahar Alon et al.   eLife

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

FTO-dependent demethylation of N6-methyladenosine regulates mRNA splicing and is required for adipogenesis

(2014) Xu Zhao et al.   CELL RESEARCH

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

(2014) M. Sakurai et al.   GENOME RESEARCH

Stoichiometry of Site-specific Lysine Acetylation in an Entire Proteome

(2014) Josue Baeza et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Absolute Proteome and Phosphoproteome Dynamics during the Cell Cycle ofSchizosaccharomyces pombe(Fission Yeast)

(2014) Alejandro Carpy et al.   MOLECULAR & CELLULAR PROTEOMICS

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

(2014) Thomas M. Carlile et al.   NATURE

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

Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments

(2014) Liana F Lareau et al.   eLife

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

(2013) Mark Helm et al.   CHEMISTRY & BIOLOGY

A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes

(2013) L. Bazak et al.   GENOME RESEARCH

Evaluating the reproducibility of quantifying modified nucleosides from ribonucleic acids by LC–UV–MS

(2013) Susan P. Russell et al.   JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES

Unusual base pairing during the decoding of a stop codon by the ribosome

(2013) Israel S. Fernández et al.   NATURE

N6-methyladenosine-dependent regulation of messenger RNA stability

(2013) Xiao Wang et al.   NATURE

Identifying RNA editing sites using RNA sequencing data alone

(2013) Gokul Ramaswami et al.   NATURE METHODS

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

(2013) N. Liu et al.   RNA

Mapping and significance of the mRNA methylome

(2013) Tennille Sibbritt et al.   Wiley Interdisciplinary Reviews-RNA

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

(2012) Kate D. Meyer et al.   CELL

S-adenosylmethionine (SAMe) therapy in liver disease: A review of current evidence and clinical utility

(2012) Quentin M. Anstee et al.   JOURNAL OF HEPATOLOGY

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

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

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

RNA Editing Underlies Temperature Adaptation in K+ Channels from Polar Octopuses

(2012) S. Garrett et al.   SCIENCE

The birth of the Epitranscriptome: deciphering the function of RNA modifications

(2012) Yogesh Saletore et al.   GENOME BIOLOGY

High levels of RNA-editing site conservation amongst 15 laboratory mouse strains

(2012) Petr Daneck et al.   GENOME BIOLOGY

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

A large-scale method to measure absolute protein phosphorylation stoichiometries

(2011) Ronghu Wu et al.   NATURE METHODS

Precision Mapping of an In Vivo N-Glycoproteome Reveals Rigid Topological and Sequence Constraints

(2010) Dorota F. Zielinska et al.   CELL

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

(2010) Masayuki Sakurai et al.   Nature Chemical Biology

Modification of 16S ribosomal RNA by the KsgA methyltransferase restructures the 30S subunit to optimize ribosome function

(2010) H. Demirci et al.   RNA

Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis

(2010) J. V. Olsen et al.   Science Signaling

A Quantitative Systems Approach Reveals Dynamic Control of tRNA Modifications during Cellular Stress

(2010) Clement T. Y. Chan et al.   PLoS Genetics

Nucleotide modifications in three functionally important regions of the Saccharomyces cerevisiae ribosome affect translation accuracy

(2009) Agnès Baudin-Baillieu et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Incorporation of Pseudouridine Into mRNA Yields Superior Nonimmunogenic Vector With Increased Translational Capacity and Biological Stability

(2008) Katalin Karikó et al.   MOLECULAR THERAPY