N(6)-methyladenosine (m6A) is the most abundant modified base in eukaryotic mRNA and has been linked to diverse effects on mRNA fate. Current mapping approaches localize m6A residues to transcript regions 100-200 nt long but cannot identify precise m6A positions on a transcriptome-wide level. Here we developed m6A individual-nucleotide-resolution cross-linking and immunoprecipitation (miCLIP) and used it to demonstrate that antibodies to m6A can induce specific mutational signatures at m6A residues after ultraviolet light-induced antibody-RNA cross-linking and reverse transcription. We found that these antibodies similarly induced mutational signatures at N(6),2'-O-dimethyladenosine (m6Am), a modification found at the first nucleotide of certain mRNAs. Using these signatures, we mapped m6A and m6Am at single-nucleotide resolution in human and mouse mRNA and identified small nucleolar RNAs (snoRNAs) as a new class of m6A-containing non-coding RNAs (ncRNAs).
Comparison of methylated sequences in messenger RNA and heterogeneous nuclear RNA from mouse L cells
The 5'-termini of heterogeneous nuclear RNA: a comparison among molecules of different sizes and ages
Histone mRNAs contain blocked and methylated 5' terminal sequences but lack methylated nucleosides at internal positions
The methylated constituents of L cell messenger RNA: evidence for an unusual cluster at the 5' terminus
Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
Probing N6-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA
PAR-CLIP data indicate that Nrd1-Nab3-dependent transcription termination regulates expression of hundreds of protein coding genes in yeast
Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis
HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism
Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5' sites
Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins
High-resolution N(6) -methyladenosine (m(6) A) map using photo-crosslinking-assisted m(6) A sequencing
RMBase: a resource for decoding the landscape of RNA modifications from high-throughput sequencing data
N6-methyladenosine modification in mRNA: machinery, function and implications for health and diseases
Attomole quantification and global profile of RNA modifications: Epitranscriptome of human neural stem cells
N(6)-Methyladenosine: a conformational marker that regulates the substrate specificity of human demethylases FTO and ALKBH5
Translational regulation in blood stages of the malaria parasite Plasmodium spp.: systems-wide studies pave the way
N(6)-Methyladenosine Methyltransferases and Demethylases: New Regulators of Stem Cell Pluripotency and Differentiation
The RNA Epistructurome: Uncovering RNA Function by Studying Structure and Post-Transcriptional Modifications
The Role of The RNA Demethylase FTO (Fat Mass and Obesity-Associated) and mRNA Methylation in Hippocampal Memory Formation
Identifying N6 -methyladenosine sites using multi-interval nucleotide pair position specificity and support vector machine
The N6 -methyladenosine (m6 A)-forming enzyme METTL3 controls myeloid differentiation of normal hematopoietic and leukemia cells
Most m6A RNA modifications in protein-coding regions are evolutionarily unconserved and likely nonfunctional
Enzymatic or In Vivo Installation of Propargyl Groups in Combination with Click Chemistry for the Enrichment and Detection of Methyltransferase Target Sites in RNA
CLIP-seq analysis of multi-mapped reads discovers novel functional RNA regulatory sites in the human transcriptome
N6-methyladenosine demethylase FTO targets pre-mRNAs and regulates alternative splicing and 3'-end processing
Glycogen synthase kinase-3 (GSK-3) activity regulates mRNA methylation in mouse embryonic stem cells
RNA epitranscriptomics: Regulation of infection of RNA and DNA viruses by N6 -methyladenosine (m6 A)
Quantification of methylation efficiency at a specific N6 -methyladenosine position in rRNA by using BNA probes
The m6 A reader protein YTHDC2 interacts with the small ribosomal subunit and the 5'-3' exoribonuclease XRN1
An Elongation- and Ligation-Based qPCR Amplification Method for the Radiolabeling-Free Detection of Locus-Specific N6 -Methyladenosine Modification
N⁶-methyladenosine (m⁶A): Revisiting the Old with Focus on New, an Arabidopsis thaliana Centered Review
Global analysis of N6-methyladenosine functions and its disease association using deep learning and network-based methods
Mapping N6 -Methyladenosine (m6 A) in RNA: Established Methods, Remaining Challenges, and Emerging Approaches
Gene2vec: gene subsequence embedding for prediction of mammalian N6 -methyladenosine sites from mRNA
Molecular basis for the specific and multivariant recognitions of RNA substrates by human hnRNP A2/B1
Eukaryotic Translation Elongation is Modulated by Single Natural Nucleotide Derivatives in the Coding Sequences of mRNAs
The epitranscriptome in translation regulation: mRNA and tRNA modifications as the two sides of the same coin?
Region-specific RNA m6 A methylation represents a new layer of control in the gene regulatory network in the mouse brain
Human METTL16 is a N6-methyladenosine (m6A) methyltransferase that targets pre-mRNAs and various non-coding RNAs.
Transcriptome-wide analysis of N6-methyladenosine uncovers its regulatory role in gene expression in the lepidopteran Bombyx mori
Viral N6 -methyladenosine upregulates replication and pathogenesis of human respiratory syncytial virus
Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences
A molecular-level perspective on the frequency, distribution, and consequences of messenger RNA modifications
The role of N6-methyladenosine modification on diapause in silkworm (Bombyx mori) strains that exhibit different voltinism
CAP-MAP: cap analysis protocol with minimal analyte processing, a rapid and sensitive approach to analysing mRNA cap structures
Development and validation of monoclonal antibodies against N6-methyladenosine for the detection of RNA modifications
Deoxyribozyme-based method for absolute quantification of N 6-methyladenosine fractions at specific sites of RNA.
CRISPR Tools for Physiology and Cell State Changes: Potential of Transcriptional Engineering and Epigenome Editing.
Long non-coding RNA RHPN1-AS1 promotes tumorigenesis and metastasis of ovarian cancer by acting as a ceRNA against miR-596 and upregulating LETM1.
m6A-Atlas: a comprehensive knowledgebase for unraveling the N6-methyladenosine (m6A) epitranscriptome.
So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes.
RMDisease: a database of genetic variants that affect RNA modifications, with implications for epitranscriptome pathogenesis.
Understanding RNA modifications: the promises and technological bottlenecks of the 'epitranscriptome'
N6 -methyladenosine modification of hepatitis B virus RNA differentially regulates the viral life cycle
Single-nucleotide-resolution sequencing of human N6-methyldeoxyadenosine reveals strand-asymmetric clusters associated with SSBP1 on the mitochondrial genome
Nucleotide Modifications Decrease Innate Immune Response Induced by Synthetic Analogs of snRNAs and snoRNAs
Excessive miR-25-3p maturation via N6 -methyladenosine stimulated by cigarette smoke promotes pancreatic cancer progression
Long Non-coding RNA Expression Profile and Functional Analysis in Children With Acute Fulminant Myocarditis
HSP90 inhibitors stimulate DNAJB4 protein expression through a mechanism involving N6 -methyladenosine
Direct RNA sequencing enables m6A detection in endogenous transcript isoforms at base specific resolution
Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification.
Hypoxia Promotes Vascular Smooth Muscle Cell (VSMC) Differentiation of Adipose-Derived Stem Cell (ADSC) by Regulating Mettl3 and Paracrine Factors
Identification of pathology-specific regulators of m6 A RNA modification to optimize lung cancer management in the context of predictive, preventive, and personalized medicine
m6aViewer: software for the detection, analysis, and visualization of N6-methyladenosine peaks from m6A-seq/ME-RIP sequencing data
Viral and cellular N6 -methyladenosine and N6 ,2'-O-dimethyladenosine epitranscriptomes in the KSHV life cycle
Synaptic N6 -methyladenosine (m6 A) epitranscriptome reveals functional partitioning of localized transcripts
Mettl3 Regulates Osteogenic Differentiation and Alternative Splicing of Vegfa in Bone Marrow Mesenchymal Stem Cells
WHISTLE: a high-accuracy map of the human N6-methyladenosine (m6A) epitranscriptome predicted using a machine learning approach
RBM15 Modulates the Function of Chromatin Remodeling Factor BAF155 Through RNA Methylation in Developing Cortex
m6Acomet: large-scale functional prediction of individual m6 A RNA methylation sites from an RNA co-methylation network
WITMSG: Large-scale Prediction of Human Intronic m6 A RNA Methylation Sites from Sequence and Genomic Features
Direct RNA Sequencing for the Study of Synthesis, Processing, and Degradation of Modified Transcripts
New Insights on the Role of N6 -Methyladenosine RNA Methylation in the Physiology and Pathology of the Nervous System
The epitranscriptome in modulating spatiotemporal RNA translation in neuronal post-synaptic function
Finely tuned conformational dynamics regulate the protective function of the lncRNA MALAT1 triple helix
Transcriptome-wide dynamics of extensive m6 A mRNA methylation during Plasmodium falciparum blood-stage development
Electrochemical competitive immunodetection of messenger RNA modified with N6-methyladenosine by using DNA-modified mesoporous PtCo nanospheres
N6 -Methyladenosine Demethylase FTO Contributes to Neuropathic Pain by Stabilizing G9a Expression in Primary Sensory Neurons
How Do You Identify m6 A Methylation in Transcriptomes at High Resolution? A Comparison of Recent Datasets
Sex-Dependent RNA Editing and N6 -adenosine RNA Methylation Profiling in the Gonads of a Fish, the Olive Flounder (Paralichthys olivaceus )
N6-Methyladenosine in RNA and DNA: An Epitranscriptomic and Epigenetic Player Implicated in Determination of Stem Cell Fate
Methods for RNA Modification Mapping Using Deep Sequencing: Established and New Emerging Technologies
Discovery of a new predominant cytosine DNA modification that is linked to gene expression in malaria parasites
Synthesis of Triazole-Linked SAM-Adenosine Conjugates: Functionalization of Adenosine at N-1 or N-6 Position without Protecting Groups.
A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry.
m6 A Reader: Epitranscriptome Target Prediction and Functional Characterization of N6 -Methyladenosine (m6 A) Readers
A fluorescent methylation-switchable probe for highly sensitive analysis of FTO N6 -methyladenosine demethylase activity in cells
ALKBH5 regulates anti-PD-1 therapy response by modulating lactate and suppressive immune cell accumulation in tumor microenvironment.
Multifaceted Functions and Novel Insight Into the Regulatory Role of RNA N6 -Methyladenosine Modification in Musculoskeletal Disorders
Principles of mRNA control by human PUM proteins elucidated from multimodal experiments and integrative data analysis.
REW-ISA: unveiling local functional blocks in epi-transcriptome profiling data via an RNA expression-weighted iterative signature algorithm
LEAD-m6 A-seq for Locus-Specific Detection of N6 -Methyladenosine and Quantification of Differential Methylation.
Direct RNA sequencing reveals m6 A modifications on adenovirus RNA are necessary for efficient splicing
MetaTX: deciphering the distribution of mRNA-related features in the presence of isoform ambiguity, with applications in epitranscriptome analysis.
The N6-Methyladenosine Features of mRNA and Aberrant Expression of m6A Modified Genes in Gastric Cancer and Their Potential Impact on the Risk and Prognosis
R-2-hydroxyglutarate attenuates aerobic glycolysis in leukemia by targeting the FTO/m6A/PFKP/LDHB axis.
Small changes, big implications: The impact of m6 A RNA methylation on gene expression in pluripotency and development
Ythdf is a N6-methyladenosine reader that modulates Fmr1 target mRNA selection and restricts axonal growth in Drosophila.
Quantitative profiling of N6 -methyladenosine at single-base resolution in stem-differentiating xylem of Populus trichocarpa using Nanopore direct RNA sequencing
Structural Insights Into m6A-Erasers: A Step Toward Understanding Molecule Specificity and Potential Antiviral Targeting.
Regulatory Role of the RNA N6-Methyladenosine Modification in Immunoregulatory Cells and Immune-Related Bone Homeostasis Associated With Rheumatoid Arthritis.
Secondary Structural Model of MALAT1 Becomes Unstructured in Chronic Myeloid Leukemia and Undergoes Structural Rearrangement in Cervical Cancer.
m6AmPred: Identifying RNA N6, 2'-O-dimethyladenosine (m6Am) sites based on sequence-derived information.
Regulation of Gene Expression Associated With the N6-Methyladenosine (m6A) Enzyme System and Its Significance in Cancer.
PCB126 Exposure Revealed Alterations in m6A RNA Modifications in Transcripts Associated With AHR Activation.
Predicting sites of epitranscriptome modifications using unsupervised representation learning based on generative adversarial networks
Targeting SNHG3/miR-186-5p reverses the increased m6A level caused by platinum treatment through regulating METTL3 in esophageal cancer.
Integrating transcriptomes and somatic mutations to identify RNA methylation regulators as a prognostic marker in hepatocellular carcinoma.
Integrative analyses of transcriptome data reveal the mechanisms of post-transcriptional regulation.
Evolutionary conservation of the DRACH signatures of potential N6-methyladenosine (m6A) sites among influenza A viruses.
5' End Nicotinamide Adenine Dinucleotide Cap in Human Cells Promotes RNA Decay through DXO-Mediated deNADding
N6-methyladenosine RNA modification suppresses antiviral innate sensing pathways via reshaping double-stranded RNA.
Identification of m6A residues at single-nucleotide resolution using eCLIP and an accessible custom analysis pipeline.
The role of N6-methyladenosine modification in the life cycle and disease pathogenesis of hepatitis B and C viruses.
Ribosome 18S m6A Methyltransferase METTL5 Promotes Translation Initiation and Breast Cancer Cell Growth.
Deciphering Epitranscriptome: Modification of mRNA Bases Provides a New Perspective for Post-transcriptional Regulation of Gene Expression.
The crucial roles of N6-methyladenosine (m6A) modification in the carcinogenesis and progression of colorectal cancer.
Suppression of m6A mRNA modification by DNA hypermethylated ALKBH5 aggravates the oncological behavior of KRAS mutation/LKB1 loss lung cancer.
Relevance of N6-methyladenosine regulators for transcriptome: Implications for development and the cardiovascular system.
Rapidly Growing Protein-Centric Technologies to Extensively Identify Protein-RNA Interactions: Application to the Analysis of Co-Transcriptional RNA Processing.
Regulatory Mechanisms of the RNA Modification m6A and Significance in Brain Function in Health and Disease.
Emerging Role of m6 A Methylome in Brain Development: Implications for Neurological Disorders and Potential Treatment.
RNA m6A modification orchestrates a LINE-1-host interaction that facilitates retrotransposition and contributes to long gene vulnerability.
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