Mapping the epigenetic modifications of DNA and RNA

N6-Deoxyadenosine Methylation in Mammalian Mitochondrial DNA

(2020) Ziyang Hao et al.   MOLECULAR 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 origin of genomic N6-methyl-deoxyadenosine in mammalian cells

(2020) Michael U. Musheev et al.   Nature Chemical Biology

No evidence for DNA N6-methyladenine in mammals

(2020) Karolos Douvlataniotis et al.   Science Advances

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

The RNA N6-methyladenosine modification landscape of human fetal tissues

(2019) Shan Xiao et al.   NATURE CELL BIOLOGY

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

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

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

Nuclear hnRNPA2B1 initiates and amplifies the innate immune response to DNA viruses

(2019) Lei Wang et al.   SCIENCE

Regulation of Gene Expression by N-methyladenosine in Cancer

(2019) Jun Liu et al.   TRENDS IN CELL BIOLOGY

Sources of artifact in measurements of 6mA and 4mC abundance in eukaryotic genomic DNA

(2019) Zach K. O’Brown et al.   BMC GENOMICS

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

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

(2019) Ying Yang et al.   MOLECULAR CELL

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

(2019) Aaron M. Wenger et al.   NATURE BIOTECHNOLOGY

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

The diverse roles of DNA methylation in mammalian development and disease

(2019) Maxim V. C. Greenberg et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

N6-methyladenosine RNA modification–mediated cellular metabolism rewiring inhibits viral replication

(2019) Yang Liu et al.   SCIENCE

Reading Chemical Modifications in the Transcriptome

(2019) Jinghui Song et al.   JOURNAL OF MOLECULAR BIOLOGY

Nanopore native RNA sequencing of a human poly(A) transcriptome

(2019) Rachael E. Workman et al.   NATURE METHODS

Accurate detection of m6A RNA modifications in native RNA sequences

(2019) Huanle Liu et al.   Nature Communications

Epigenetic Modifications of mRNA and DNA in Plants

(2019) Zhe Liang et al.   Molecular Plant

Differential roles of human PUS10 in miRNA processing and tRNA pseudouridylation

(2019) Jinghui Song et al.   Nature Chemical Biology

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

R-2HG Exhibits Anti-tumor Activity by Targeting FTO/m 6 A/MYC/CEBPA Signaling

(2018) Rui Su et al.   CELL

N6-methyladenosine-binding proteins suppress HIV-1 infectivity and viral production

(2018) Wuxun Lu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

N 6 -Methyladenosine Guides mRNA Alternative Translation during Integrated Stress Response

(2018) Jun Zhou et al.   MOLECULAR CELL

Zc3h13 Regulates Nuclear RNA m 6 A Methylation and Mouse Embryonic Stem Cell Self-Renewal

(2018) Jing Wen et al.   MOLECULAR CELL

Tet2 promotes pathogen infection-induced myelopoiesis through mRNA oxidation

(2018) Qicong Shen et al.   NATURE

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Highly parallel direct RNA sequencing on an array of nanopores

(2018) Daniel R Garalde et al.   NATURE METHODS

A reassessment of DNA-immunoprecipitation-based genomic profiling

(2018) Antonio Lentini et al.   NATURE METHODS

Author Correction: Analysis of DNA methylation in cancer: location revisited

(2018) Alexander Koch et al.   Nature Reviews Clinical Oncology

Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

(2018) Simon Ardui et al.   NUCLEIC ACIDS RESEARCH

Transient N-6-Methyladenosine Transcriptome Sequencing Reveals a Regulatory Role of m6A in Splicing Efficiency

(2018) Annita Louloupi et al.   Cell Reports

Addition of m6A to SV40 late mRNAs enhances viral structural gene expression and replication

(2018) Kevin Tsai et al.   PLoS Pathogens

VIRMA mediates preferential m6A mRNA methylation in 3′UTR and near stop codon and associates with alternative polyadenylation

(2018) Yanan Yue et al.   Cell Discovery

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

(2018) Jiangbo Wei et al.   MOLECULAR CELL

Perspectives on topology of the human m1A methylome at single nucleotide resolution

(2018) Xushen Xiong et al.   RNA

Single-Nucleotide Resolution Analysis of 5-Hydroxymethylcytosine in DNA by Enzyme-Mediated Deamination in Combination with Sequencing

(2018) Qiao-Ying Li et al.   ANALYTICAL CHEMISTRY

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

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

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

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

(2018) Emily K Schutsky et al.   NATURE BIOTECHNOLOGY

The role of DNA methylation in epigenetics of aging

(2018) Archana Unnikrishnan et al.   PHARMACOLOGY & THERAPEUTICS

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

(2018) Shinichiro Akichika et al.   SCIENCE

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

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

RNA m6A methylation regulates the ultraviolet-induced DNA damage response

(2017) Yang Xiang et al.   NATURE

The m1A landscape on cytosolic and mitochondrial mRNA at single-base resolution

(2017) Modi Safra et al.   NATURE

Epitranscriptome sequencing technologies: decoding RNA modifications

(2017) Xiaoyu Li et al.   NATURE METHODS

Detecting DNA cytosine methylation using nanopore sequencing

(2017) Jared T Simpson et al.   NATURE METHODS

Mapping DNA methylation with high-throughput nanopore sequencing

(2017) Arthur C Rand et al.   NATURE METHODS

Genome-wide base-resolution mapping of DNA methylation in single cells using single-cell bisulfite sequencing (scBS-seq)

(2017) Stephen J Clark et al.   Nature Protocols

Dynamic m6A modification regulates local translation of mRNA in axons

(2017) Jun Yu et al.   NUCLEIC ACIDS RESEARCH

N6-methyladenosine demethylase FTO targets pre-mRNAs and regulates alternative splicing and 3′-end processing

(2017) Marek Bartosovic et al.   NUCLEIC ACIDS RESEARCH

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

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

(2017) Qi Cui et al.   Cell Reports

Mapping and elucidating the function of modified bases in DNA

(2017) Eun-Ang Raiber et al.   Nature Reviews Chemistry

AlkB homolog 3-mediated tRNA demethylation promotes protein synthesis in cancer cells

(2017) Yuko Ueda et al.   Scientific Reports

tRNA modification profiles of the fast-proliferating cancer cells

(2016) Chao Dong et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

The emerging epitranscriptomics of long noncoding RNAs

(2016) Andrew Shafik et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

ALKBH1-Mediated tRNA Demethylation Regulates Translation

(2016) Fange Liu et al.   CELL

Dynamics of Human and Viral RNA Methylation during Zika Virus Infection

(2016) Gianluigi Lichinchi et al.   Cell Host & Microbe

N6 -Methyladenosine in Flaviviridae Viral RNA Genomes Regulates Infection

(2016) Nandan S. Gokhale et al.   Cell Host & Microbe

Posttranscriptional m 6 A Editing of HIV-1 mRNAs Enhances Viral Gene Expression

(2016) Edward M. Kennedy et al.   Cell Host & Microbe

Pseudouridylation meets next-generation sequencing

(2016) Maryam Zaringhalam et al.   METHODS

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

Base-resolution profiling of active DNA demethylation using MAB-seq and caMAB-seq

(2016) Hao Wu et al.   Nature Protocols

RNA modifications: what have we learned and where are we headed?

(2016) Michaela Frye et al.   NATURE REVIEWS GENETICS

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

Recent advances in dynamic m6A RNA modification

(2016) Guangchao Cao et al.   Open Biology

N6-methyladenosine of HIV-1 RNA regulates viral infection and HIV-1 Gag protein expression

(2016) Nagaraja Tirumuru et al.   eLife

Dynamics of the human and viral m6A RNA methylomes during HIV-1 infection of T cells

(2016) Gianluigi Lichinchi et al.   Nature Microbiology

DNA Methylation on N6-Adenine in C. elegans

(2015) Eric Lieberman Greer et al.   CELL

N6-Methyladenine DNA Modification in Drosophila

(2015) Guoqiang Zhang et al.   CELL

N6-Methyldeoxyadenosine Marks Active Transcription Start Sites in Chlamydomonas

(2015) Ye Fu et al.   CELL

HNRNPA2B1 Is a Mediator of m6A-Dependent Nuclear RNA Processing Events

(2015) Claudio R. Alarcón et al.   CELL

Base-resolution maps of 5-formylcytosine and 5-carboxylcytosine reveal genome-wide DNA demethylation dynamics

(2015) Xingyu Lu et al.   CELL RESEARCH

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

(2015) Shengdong Ke et al.   GENES & DEVELOPMENT

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

Bisulfite-free, base-resolution analysis of 5-formylcytosine at the genome scale

(2015) Bo Xia et al.   NATURE METHODS

Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome

(2015) Bastian Linder et al.   NATURE METHODS

Transcriptome-wide dynamics of RNA pseudouridylation

(2015) John Karijolich et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

m6A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation

(2015) Shay Geula et al.   SCIENCE

Single-Base Resolution Analysis of 5-Formyl and 5-Carboxyl Cytosine Reveals Promoter DNA Methylation Dynamics

(2015) Francesco Neri et al.   Cell Reports

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

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

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

Active and Passive Demethylation of Male and Female Pronuclear DNA in the Mammalian Zygote

(2014) Fan Guo et al.   Cell Stem Cell

Chemical Methods for Decoding Cytosine Modifications in DNA

(2014) Michael J. Booth et al.   CHEMICAL REVIEWS

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

Single-base resolution analysis of active DNA demethylation using methylase-assisted bisulfite sequencing

(2014) Hao Wu et al.   NATURE BIOTECHNOLOGY

N6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells

(2014) Yang Wang et al.   NATURE CELL BIOLOGY

Quantitative sequencing of 5-formylcytosine in DNA at single-base resolution

(2014) Michael J. Booth et al.   Nature Chemistry

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

(2014) Sébastien A Smallwood et al.   NATURE METHODS

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

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

DNA Methylation in Mammals

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

Perturbation of m6A Writers Reveals Two Distinct Classes of mRNA Methylation at Internal and 5′ Sites

(2014) Schraga Schwartz et al.   Cell Reports

Single-Molecule Detection of 5-Hydroxymethylcytosine in DNA through Chemical Modification and Nanopore Analysis

(2013) Wen-Wu Li et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Genome-wide Analysis Reveals TET- and TDG-Dependent 5-Methylcytosine Oxidation Dynamics

(2013) Li Shen et al.   CELL

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

(2013) Schraga Schwartz et al.   CELL

Genome-wide Profiling of 5-Formylcytosine Reveals Its Roles in Epigenetic Priming

(2013) Chun-Xiao Song et al.   CELL

High-resolution DNA methylome analysis of primordial germ cells identifies gender-specific reprogramming in mice

(2013) H. Kobayashi et al.   GENOME RESEARCH

Chemical Modification-Assisted Bisulfite Sequencing (CAB-Seq) for 5-Carboxylcytosine Detection in DNA

(2013) Xingyu Lu 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

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

(2013) Jianzhao Liu et al.   Nature Chemical Biology

Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine

(2013) Michael J Booth et al.   Nature Protocols

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

Mouse Oocyte Methylomes at Base Resolution Reveal Genome-Wide Accumulation of Non-CpG Methylation and Role of DNA Methyltransferases

(2013) Kenjiro Shirane et al.   PLoS Genetics

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

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

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

Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing

(2012) Andrew Adey et al.   GENOME RESEARCH

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

(2012) Guanqun Zheng et al.   MOLECULAR CELL

Tet1 controls meiosis by regulating meiotic gene expression

(2012) Shinpei Yamaguchi et al.   NATURE

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

(2012) Dan Dominissini et al.   NATURE

Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine

(2012) Miao Yu et al.   Nature Protocols

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

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

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

(2012) M. J. Booth et al.   SCIENCE

The Discovery of 5-Formylcytosine in Embryonic Stem Cell DNA

(2011) Toni Pfaffeneder et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation

(2011) Gabriella Ficz 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

Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine

(2011) Chun-Xiao Song et al.   NATURE METHODS

Nanopore sensors for nucleic acid analysis

(2011) Bala Murali Venkatesan et al.   Nature Nanotechnology

Tet-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA

(2011) Y.-F. He et al.   SCIENCE

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

(2011) S. Ito et al.   SCIENCE

5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells

(2011) Hume Stroud et al.   GENOME BIOLOGY

Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine

(2010) Chun-Xiao Song et al.   NATURE BIOTECHNOLOGY

Grand Challenge Commentary: RNA epigenetics?

(2010) Chuan He   Nature Chemical Biology

Direct detection of DNA methylation during single-molecule, real-time sequencing

(2010) Benjamin A Flusberg et al.   NATURE METHODS

Continuous base identification for single-molecule nanopore DNA sequencing

(2009) James Clarke et al.   Nature Nanotechnology

Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1

(2009) M. Tahiliani et al.   SCIENCE

The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain

(2009) S. Kriaucionis et al.   SCIENCE

RNA cytosine methylation analysis by bisulfite sequencing

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