Exclusion of m6A from splice-site proximal regions by the exon junction complex dictates m6A topologies and mRNA stability

scDART-seq reveals distinct m6A signatures and mRNA methylation heterogeneity in single cells

(2022) Matthew Tegowski et al.   MOLECULAR CELL

Dynamic control of chromatin-associated m6A methylation regulates nascent RNA synthesis

(2022) Wenqi Xu et al.   MOLECULAR CELL

m6A RNA modifications are measured at single-base resolution across the mammalian transcriptome

(2022) Lulu Hu et al.   NATURE BIOTECHNOLOGY

Absolute quantification of single-base m6A methylation in the mammalian transcriptome using GLORI

(2022) Cong Liu et al.   NATURE BIOTECHNOLOGY

m6A RNA methylation regulates the fate of endogenous retroviruses

(2021) Tomasz Chelmicki et al.   NATURE

METTL3 regulates heterochromatin in mouse embryonic stem cells

(2021) Wenqi Xu et al.   NATURE

The RNA m6A reader YTHDC1 silences retrotransposons and guards ES cell identity

(2021) Jiadong Liu et al.   NATURE

Small-molecule inhibition of METTL3 as a strategy against myeloid leukaemia

(2021) Eliza Yankova et al.   NATURE

Nuclear m6A reader YTHDC1 regulates the scaffold function of LINE1 RNA in mouse ESCs and early embryos

(2021) Chuan Chen et al.   Protein & Cell

Gene Architecture Facilitates Intron-Mediated Enhancement of Transcription

(2021) Katherine Dwyer et al.   Frontiers in Molecular Biosciences

Acute depletion of METTL3 implicates N6-methyladenosine in alternative intron/exon inclusion in the nascent transcriptome

(2021) Guifeng Wei et al.   GENOME RESEARCH

Multiplexed profiling facilitates robust m6A quantification at site, gene and sample resolution

(2021) David Dierks et al.   NATURE METHODS

Deep and accurate detection of m6A RNA modifications using miCLIP2 and m6Aboost machine learning

(2021) Nadine Körtel et al.   NUCLEIC ACIDS RESEARCH

The Dynamics of Cytoplasmic mRNA Metabolism

(2020) Timothy J. Eisen et al.   MOLECULAR CELL

N6-methyladenosine of chromosome-associated regulatory RNA regulates chromatin state and transcription

(2020) Jun Liu et al.   SCIENCE

Limits in the detection of m6A changes using MeRIP/m6A-seq

(2020) Alexa B. R. McIntyre et al.   Scientific Reports

Predicting mRNA Abundance Directly from Genomic Sequence Using Deep Convolutional Neural Networks

(2020) Vikram Agarwal et al.   Cell Reports

A Unified Model for the Function of YTHDF Proteins in Regulating m6A-Modified mRNA

(2020) Sara Zaccara et al.   CELL

Gene Architecture and Sequence Composition Underpin Selective Dependency of Nuclear Export of Long RNAs on NXF1 and the TREX Complex

(2020) Binyamin Zuckerman et al.   MOLECULAR CELL

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

Regulation of transposable elements by DNA modifications

(2019) Özgen Deniz et al.   NATURE REVIEWS GENETICS

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

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

m6A promotes R-loop formation to facilitate transcription termination

(2019) Xin Yang et al.   CELL RESEARCH

Landscape and Regulation of m6A and m6Am Methylome across Human and Mouse Tissues

(2019) Jun’e Liu et al.   MOLECULAR CELL

N6-methyladenosine regulates the stability of RNA:DNA hybrids in human cells

(2019) Abdulkadir Abakir et al.   NATURE GENETICS

The dTAG system for immediate and target-specific protein degradation

(2018) Behnam Nabet et al.   Nature Chemical Biology

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

(2018) Annita Louloupi et al.   Cell Reports

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

mRNP architecture in translating and stress conditions reveals an ordered pathway of mRNP compaction

(2018) Anthony Khong et al.   JOURNAL OF CELL BIOLOGY

Spatial Organization of Single mRNPs at Different Stages of the Gene Expression Pathway

(2018) Srivathsan Adivarahan et al.   MOLECULAR CELL

Higher-Order Organization Principles of Pre-translational mRNPs

(2018) Mihir Metkar et al.   MOLECULAR CELL

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

Nuclear m 6 A Reader YTHDC1 Regulates mRNA Splicing

(2016) Wen Xiao et al.   MOLECULAR CELL

m6A modulates neuronal functions and sex determination in Drosophila

(2016) Tina Lence et al.   NATURE

Reversible methylation of m6Am in the 5′ cap controls mRNA stability

(2016) Jan Mauer et al.   NATURE

YTHDF2 destabilizes m6A-containing RNA through direct recruitment of the CCR4–NOT deadenylase complex

(2016) Hao Du et al.   Nature Communications

The exon junction complex: a lifelong guardian of mRNA fate

(2016) Lauren A. Woodward et al.   Wiley Interdisciplinary Reviews-RNA

Tracing Dynamic Changes of DNA Methylation at Single-Cell Resolution

(2015) Yonatan Stelzer 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

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

(2015) Bastian Linder et al.   NATURE METHODS

Simultaneous generation of many RNA-seq libraries in a single reaction

(2015) Alexander A Shishkin et al.   NATURE METHODS

The exon junction complex as a node of post-transcriptional networks

(2015) Hervé Le Hir et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2014) Schraga Schwartz et al.   Cell Reports

Differential protein occupancy profiling of the mRNA transcriptome

(2014) Markus Schueler et al.   GENOME BIOLOGY

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

(2013) Schraga Schwartz et al.   CELL

3' UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts

(2013) N. Spies et al.   GENOME RESEARCH

N6-methyladenosine-dependent regulation of messenger RNA stability

(2013) Xiao Wang et al.   NATURE

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

(2013) N. Liu et al.   RNA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The Cellular EJC Interactome Reveals Higher-Order mRNP Structure and an EJC-SR Protein Nexus

(2012) Guramrit Singh et al.   CELL

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

(2012) Kate D. Meyer et al.   CELL

Genome-wide analysis of long noncoding RNA stability

(2012) M. B. Clark et al.   GENOME RESEARCH

Perispeckles are major assembly sites for the exon junction core complex

(2012) Elisabeth Daguenet et al.   MOLECULAR BIOLOGY OF THE CELL

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

(2012) Dan Dominissini et al.   NATURE

CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex

(2012) Jérôme Saulière et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells

(2009) Christine Mayr et al.   CELL

The Hierarchy of Exon-Junction Complex Assembly by the Spliceosome Explains Key Features of Mammalian Nonsense-Mediated mRNA Decay

(2009) Niels H. Gehring et al.   PLOS BIOLOGY

Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells

(2008) L. V. Sharova et al.   DNA RESEARCH

Proliferating Cells Express mRNAs with Shortened 3' Untranslated Regions and Fewer MicroRNA Target Sites

(2008) R. Sandberg et al.   SCIENCE