Chemical and structural effects of base modifications in messenger RNA

The existence of 5-hydroxymethylcytosine and 5-formylcytosine in both DNA and RNA in mammals

(2016) Hao-Ying Zhang et al.   CHEMICAL COMMUNICATIONS

RNA epigenetics — chemical messages for posttranscriptional gene regulation

(2016) Ian A Roundtree et al.   CURRENT OPINION IN CHEMICAL 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

Transcriptome-wide mapping reveals reversible and dynamic N1-methyladenosine methylome

(2016) Xiaoyu Li et al.   Nature Chemical Biology

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

mRNA capping: biological functions and applications

(2016) Anand Ramanathan et al.   NUCLEIC ACIDS RESEARCH

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

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

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

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

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

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

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

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

RNA editing by ADAR1 prevents MDA5 sensing of endogenous dsRNA as nonself

(2015) B. J. Liddicoat 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

Mammalian WTAP is a regulatory subunit of the RNA N6-methyladenosine methyltransferase

(2014) Xiao-Li Ping et al.   CELL RESEARCH

Structure of the YTH domain of human YTHDF2 in complex with an m6A mononucleotide reveals an aromatic cage for m6A recognition

(2014) Fudong Li 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

Tet-Mediated Formation of 5-Hydroxymethylcytosine in RNA

(2014) Lijuan Fu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

(2014) Thomas M. Carlile et al.   NATURE

Structural basis for selective binding of m6A RNA by the YTHDC1 YTH domain

(2014) Chao Xu et al.   Nature Chemical Biology

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

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

Genome-wide identification and functional analysis of Apobec-1-mediated C-to-U RNA editing in mouse small intestine and liver

(2014) Valerie Blanc et al.   GENOME BIOLOGY

High-Resolution Mapping Reveals a Conserved, Widespread, Dynamic mRNA Methylation Program in Yeast Meiosis

(2013) Schraga Schwartz et al.   CELL

A Decade of Riboswitches

(2013) Alexander Serganov et al.   CELL

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

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

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

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

Identification of direct targets and modified bases of RNA cytosine methyltransferases

(2013) Vahid Khoddami et al.   NATURE BIOTECHNOLOGY

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

(2013) Jianzhao Liu et al.   Nature Chemical Biology

Proteins that contain a functional Z-DNA-binding domain localize to cytoplasmic stress granules

(2013) Siew Kit Ng et al.   NUCLEIC ACIDS RESEARCH

The contribution of pseudouridine to stabilities and structure of RNAs

(2013) Elzbieta Kierzek 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

NSun2-Mediated Cytosine-5 Methylation of Vault Noncoding RNA Determines Its Processing into Regulatory Small RNAs

(2013) Shobbir Hussain et al.   Cell Reports

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

(2012) Kate D. Meyer et al.   CELL

Structural Basis for dsRNA Recognition, Filament Formation, and Antiviral Signal Activation by MDA5

(2012) Bin Wu 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

RNA SHAPE analysis in living cells

(2012) Robert C Spitale et al.   Nature Chemical Biology

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

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

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

(2012) P. B. Cattenoz et al.   RNA

Tudor-SN and ADAR1 are components of cytoplasmic stress granules

(2012) R. Weissbach et al.   RNA

Rationalization and prediction of selective decoding of pseudouridine-modified nonsense and sense codons

(2012) M. Parisien et al.   RNA

The tRNA methyltransferase NSun2 stabilizes p16INK4 mRNA by methylating the 3′-untranslated region of p16

(2012) Xiaotian Zhang et al.   Nature Communications

The DNA methyltranferase Dnmt2 participates in RNA processing during cellular stress

(2011) Devi Thiagarajan et al.   Epigenetics

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

Transcriptome-wide sequencing reveals numerous APOBEC1 mRNA-editing targets in transcript 3′ UTRs

(2011) Brad R Rosenberg et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine

(2011) S. Ito et al.   SCIENCE

tRNA Stabilization by Modified Nucleotides

(2010) Yuri Motorin et al.   BIOCHEMISTRY

A Flexible RNA Backbone within the Polypyrimidine Tract Is Required for U2AF65 Binding and Pre-mRNA Splicing In Vivo

(2010) C. Chen et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2010) Masayuki Sakurai et al.   Nature Chemical Biology

Effect of 1-methyladenine on thermodynamic stabilities of double-helical DNA structures

(2009) Hao Yang et al.   FEBS LETTERS

Altered Nuclear Retention of mRNAs Containing Inverted Repeats in Human Embryonic Stem Cells: Functional Role of a Nuclear Noncoding RNA

(2009) Ling-Ling Chen et al.   MOLECULAR CELL

Improving CMC-derivatization of pseudouridine in RNA for mass spectrometric detection

(2008) Anita Durairaj et al.   ANALYTICA CHIMICA ACTA

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

(2008) Katalin Karikó et al.   MOLECULAR THERAPY

The potential and challenges of nanopore sequencing

(2008) Daniel Branton et al.   NATURE BIOTECHNOLOGY

RNA cytosine methylation analysis by bisulfite sequencing

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