Advances in the profiling of N6-methyladenosine (m6A) modifications

WITMSG: Large-scale prediction of human intronic m6A RNA methylation sites from sequence and genomic features

(2020) Lian Liu et al.   CURRENT GENOMICS

M6A2Target: a comprehensive database for targets of m6A writers, erasers and readers

(2020) Shuang Deng et al.   BRIEFINGS IN BIOINFORMATICS

A metabolic labeling method detects m6A transcriptome-wide at single base resolution

(2020) Xiao Shu et al.   Nature Chemical Biology

Targeted mRNA demethylation using an engineered dCas13b-ALKBH5 fusion protein

(2020) Jiexin Li et al.   NUCLEIC ACIDS RESEARCH

m6A Editing: New Tool to Improve Crop Quality?

(2020) Hong-xiang Zheng et al.   TRENDS IN PLANT SCIENCE

Genetic analyses support the contribution of mRNA N6-methyladenosine (m6A) modification to human disease heritability

(2020) Zijie Zhang et al.   NATURE GENETICS

Alteration of N6-methyladenosine epitranscriptome profile in unilateral ureteral obstructive nephropathy

(2020) Xueyan Li et al.   Epigenomics

RMVar: an updated database of functional variants involved in RNA modifications

(2020) Xiaotong Luo et al.   NUCLEIC ACIDS RESEARCH

WHISTLE: a high-accuracy map of the human N6-methyladenosine (m6A) epitranscriptome predicted using a machine learning approach

(2019) Kunqi Chen et al.   NUCLEIC ACIDS RESEARCH

Targeting the RNA m6A Reader YTHDF2 Selectively Compromises Cancer Stem Cells in Acute Myeloid Leukemia

(2019) Jasmin Paris et al.   Cell Stem Cell

Increasing the accuracy of nanopore DNA sequencing using a time-varying cross membrane voltage

(2019) Matthew T. Noakes et al.   NATURE BIOTECHNOLOGY

m6Acomet: large-scale functional prediction of individual m6A RNA methylation sites from an RNA co-methylation network

(2019) Xiangyu Wu et al.   BMC BIOINFORMATICS

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

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

FMRP Modulates Neural Differentiation through m6A-Dependent mRNA Nuclear Export

(2019) Brittany M. Edens et al.   Cell Reports

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

(2019) Zhang Zhang et al.   Science Advances

Dynamic methylome of internal mRNA N7-methylguanosine and its regulatory role in translation

(2019) Lionel Malbec et al.   CELL RESEARCH

Programmable RNA N6-methyladenosine editing by CRISPR-Cas9 conjugates

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

Site-specific m6A editing

(2019) Jiangbo Wei et al.   Nature Chemical Biology

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

(2019) Kate D. Meyer   NATURE METHODS

Recent advances in the detection of base modifications using the Nanopore sequencer

(2019) Liu Xu et al.   JOURNAL OF HUMAN GENETICS

Accurate detection of m6A RNA modifications in native RNA sequences

(2019) Huanle Liu et al.   Nature Communications

OUP accepted manuscript

(2018)   BIOINFORMATICS

Dynamic transcriptomic m6A decoration: writers, erasers, readers and functions in RNA metabolism

(2018) Ying Yang et al.   CELL RESEARCH

Precise Antibody-Independent m6A Identification via 4SedTTP-Involved and FTO-Assisted Strategy at Single-Nucleotide Resolution

(2018) Tingting Hong et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

(2018) Jing Wen et al.   MOLECULAR CELL

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

The m6A Reader ECT2 Controls Trichome Morphology by Affecting mRNA Stability in Arabidopsis

(2018) Lian-Huan Wei et al.   PLANT CELL

N6-methyl-adenosine level in Nicotiana tabacum is associated with tobacco mosaic virus

(2018) Zhurui Li et al.   Virology Journal

Identification of a selective DNA ligase for accurate recognition and ultrasensitive quantification of N6-methyladenosine in RNA at one-nucleotide resolution

(2018) Weiliang Liu et al.   Chemical Science

M6APred-EL: A sequence-based predictor for identifying N6-methyladenosine sites using ensemble learning

(2018) Leyi Wei et al.   Molecular Therapy-Nucleic Acids

BERMP: a cross-species classifier for predicting m6A sites by integrating a deep learning algorithm and a random forest approach

(2018) Yu Huang et al.   International Journal of Biological Sciences

N 6 -Methyladenosine-Sensitive RNA-Cleaving Deoxyribozymes

(2018) Maksim V. Sednev et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

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

N6-Methyladenosine Inhibits Local Ribonucleolytic Cleavage to Stabilize mRNAs in Arabidopsis

(2018) Stephen J. Anderson et al.   Cell Reports

N6-Allyladenosine: A New Small Molecule for RNA Labeling Identified by Mutation Assay

(2017) Xiao Shu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

m6A modulates haematopoietic stem and progenitor cell specification

(2017) Chunxia Zhang et al.   NATURE

Enhancing GTEx by bridging the gaps between genotype, gene expression, and disease

(2017) Barbara E Stranger et al.   NATURE GENETICS

The N6-methyladenosine (m6A)-forming enzyme METTL3 controls myeloid differentiation of normal hematopoietic and leukemia cells

(2017) Ly P Vu et al.   NATURE MEDICINE

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

(2017) Qing Dai et al.   NATURE METHODS

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

(2017) Marek Bartosovic et al.   NUCLEIC ACIDS RESEARCH

RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data

(2017) Jia-Jia Xuan et al.   NUCLEIC ACIDS RESEARCH

m6AVar: a database of functional variants involved in m6A modification

(2017) Yueyuan Zheng et al.   NUCLEIC ACIDS RESEARCH

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

The m6A pathway facilitates sex determination in Drosophila

(2017) Lijuan Kan et al.   Nature Communications

YTHDC1 mediates nuclear export of N6-methyladenosine methylated mRNAs

(2017) Ian A Roundtree et al.   eLife

Identifying N6-methyladenosine sites using multi-interval nucleotide pair position specificity and support vector machine

(2017) Pengwei Xing et al.   Scientific Reports

Development of a CRISPR-Cas9 Tool Kit for Comprehensive Engineering of Bacillus subtilis

(2016) Adam W. Westbrook et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Extending CRISPR-Cas9 Technology from Genome Editing to Transcriptional Engineering in the Genus Clostridium

(2016) Mark R. Bruder et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

N 6 -Methyladenosine RNA Modification Regulates Shoot Stem Cell Fate in Arabidopsis

(2016) Lisha Shen et al.   DEVELOPMENTAL CELL

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

SRAMP: prediction of mammalian N6-methyladenosine (m6A) sites based on sequence-derived features

(2016) Yuan Zhou 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

Transcriptome-wide distribution and function of RNA hydroxymethylcytosine

(2016) B. Delatte et al.   SCIENCE

N 6-Methyladenine hinders RNA- and DNA-directed DNA synthesis: application in human rRNA methylation analysis of clinical specimens

(2016) Shaoru Wang et al.   Chemical Science

Characterization of eukaryotic DNA N6-methyladenine by a highly sensitive restriction enzyme-assisted sequencing

(2016) Guan-Zheng Luo et al.   Nature Communications

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

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

(2015) Claudio R. Alarcón 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

N6-methyladenosine marks primary microRNAs for processing

(2015) Claudio R. Alarcón 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

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

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

(2015) Bastian Linder et al.   NATURE METHODS

RMBase: a resource for decoding the landscape of RNA modifications from high-throughput sequencing data

(2015) Wen-Ju Sun et al.   NUCLEIC ACIDS RESEARCH

Determination of Oxidation Products of 5-Methylcytosine in Plants by Chemical Derivatization Coupled with Liquid Chromatography/Tandem Mass Spectrometry Analysis

(2014) Yang Tang et al.   ANALYTICAL CHEMISTRY

High-ResolutionN6-Methyladenosine (m6A) Map Using Photo-Crosslinking-Assisted m6A Sequencing

(2014) Kai Chen et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package

(2014) Jia Meng et al.   METHODS

TAIL-seq: Genome-wide Determination of Poly(A) Tail Length and 3′ End Modifications

(2014) Hyeshik Chang et al.   MOLECULAR CELL

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

(2014) Thomas M. Carlile et al.   NATURE

N6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells

(2014) Yang Wang et al.   NATURE CELL BIOLOGY

Transcriptome-wide N6-methyladenosine profiling of rice callus and leaf reveals the presence of tissue-specific competitors involved in selective mRNA modification

(2014) Yuli Li et al.   RNA Biology

Unique features of the m6A methylome in Arabidopsis thaliana

(2014) Guan-Zheng Luo et al.   Nature Communications

HITS-CLIP and Integrative Modeling Define the Rbfox Splicing-Regulatory Network Linked to Brain Development and Autism

(2014) Sebastien M. Weyn-Vanhentenryck et al.   Cell Reports

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

(2013) Schraga Schwartz et al.   CELL

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

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

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

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

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

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

(2012) Kate D. Meyer et al.   CELL

Individual RNA Base Recognition in Immobilized Oligonucleotides Using a Protein Nanopore

(2012) Mariam Ayub et al.   NANO LETTERS

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

(2012) Dan Dominissini et al.   NATURE

Automated forward and reverse ratcheting of DNA in a nanopore at 5-Å precision

(2012) Gerald M Cherf et al.   NATURE BIOTECHNOLOGY

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

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

Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data

(2011) Chaolin Zhang et al.   NATURE BIOTECHNOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

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

(2010) Benjamin A Flusberg et al.   NATURE METHODS

MTA Is an Arabidopsis Messenger RNA Adenosine Methylase and Interacts with a Homolog of a Sex-Specific Splicing Factor

(2008) S. Zhong et al.   PLANT CELL