Exon architecture controls mRNA m 6 A suppression and gene expression

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

(2022) Lulu Hu et al.   NATURE BIOTECHNOLOGY

FTO mediates LINE1 m 6 A demethylation and chromatin regulation in mESCs and mouse development

(2022) Jiangbo Wei et al.   SCIENCE

m 6 A RNA methylation: from mechanisms to therapeutic potential

(2021) P Cody He et al.   EMBO JOURNAL

A neural m6A/Ythdf pathway is required for learning and memory in Drosophila

(2021) Lijuan Kan et al.   Nature Communications

Widespread Exon Junction Complex Footprints in the RNA Degradome Mark mRNA Degradation Before Steady-state Translation

(2020) Wen‐Chi Lee et al.   PLANT CELL

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

(2020) Jun Liu et al.   SCIENCE

A large-scale binding and functional map of human RNA-binding proteins

(2020) Eric L. Van Nostrand et al.   NATURE

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

(2020) Zijie Zhang et al.   NATURE GENETICS

Analysis of m6A RNA methylation in Caenorhabditis elegans

(2020) Erdem Sendinc et al.   Cell Discovery

Promoter-proximal pausing mediated by the exon junction complex regulates splicing

(2019) Junaid Akhtar et al.   Nature Communications

Histone H3 trimethylation at lysine 36 guides m6A RNA modification co-transcriptionally

(2019) Huilin Huang et al.   NATURE

Co-transcriptional Loading of RNA Export Factors Shapes the Human Transcriptome

(2019) Nicolas Viphakone et al.   MOLECULAR CELL

Nuclear TARBP2 Drives Oncogenic Dysregulation of RNA Splicing and Decay

(2019) Lisa Fish et al.   MOLECULAR CELL

Nascent RNA and the Coordination of Splicing with Transcription

(2019) Karla M. Neugebauer   Cold Spring Harbor Perspectives in Biology

Regulation of Co-transcriptional Pre-mRNA Splicing by m6A through the Low-Complexity Protein hnRNPG

(2019) Katherine I. Zhou et al.   MOLECULAR CELL

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

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

PolyASite 2.0: a consolidated atlas of polyadenylation sites from 3′ end sequencing

(2019) Christina J Herrmann et al.   NUCLEIC ACIDS RESEARCH

LINC00680 and TTN-AS1 Stabilized by EIF4A3 Promoted Malignant Biological Behaviors of Glioblastoma Cells

(2019) Wei Tang et al.   Molecular Therapy-Nucleic Acids

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

(2018) Rui Su et al.   CELL

Recognition of RNA N6-methyladenosine by IGF2BP proteins enhances mRNA stability and translation

(2018) Huilin Huang et al.   NATURE CELL BIOLOGY

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

(2018) Annita Louloupi et al.   Cell Reports

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

The SMAD2/3 interactome reveals that TGFβ controls m6A mRNA methylation in pluripotency

(2018) Alessandro Bertero et al.   NATURE

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

A dynamic N6-methyladenosine methylome regulates intrinsic and acquired resistance to tyrosine kinase inhibitors

(2018) Fei Yan et al.   CELL RESEARCH

Higher-Order Organization Principles of Pre-translational mRNPs

(2018) Mihir Metkar et al.   MOLECULAR CELL

Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing

(2018) Lorea Blazquez et al.   MOLECULAR CELL

Exon Junction Complexes Suppress Spurious Splice Sites to Safeguard Transcriptome Integrity

(2018) Volker Boehm et al.   MOLECULAR CELL

The Exon Junction Complex Undergoes a Compositional Switch that Alters mRNP Structure and Nonsense-Mediated mRNA Decay Activity

(2018) Justin W. Mabin et al.   Cell Reports

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

Promoter-bound METTL3 maintains myeloid leukaemia by m6A-dependent translation control

(2017) Isaia Barbieri et al.   NATURE

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

(2017) Marek Bartosovic et al.   NUCLEIC ACIDS RESEARCH

Y14 governs p53 expression and modulates DNA damage sensitivity

(2017) Chia-Chen Lu et al.   Scientific Reports

Nuclear m 6 A Reader YTHDC1 Regulates mRNA Splicing

(2016) Wen Xiao et al.   MOLECULAR CELL

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

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

Messenger RNA modifications: Form, distribution, and function

(2016) W. V. Gilbert et al.   SCIENCE

Exon Junction Complexes: Supervising the Gene Expression Assembly Line

(2016) Volker Boehm et al.   TRENDS IN GENETICS

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

(2016) Hao Du et al.   Nature Communications

Haploinsufficiency for Core Exon Junction Complex Components Disrupts Embryonic Neurogenesis and Causes p53-Mediated Microcephaly

(2016) Hanqian Mao et al.   PLoS Genetics

N6-methyladenosine Modulates Messenger RNA Translation Efficiency

(2015) Xiao Wang 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

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim 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

Predicting effective microRNA target sites in mammalian mRNAs

(2015) Vikram Agarwal et al.   eLife

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Levenshtein error-correcting barcodes for multiplexed DNA sequencing

(2013) Tilo Buschmann et al.   BMC BIOINFORMATICS

N6-methyladenosine-dependent regulation of messenger RNA stability

(2013) Xiao Wang et al.   NATURE

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

The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts

(2012) Alexander G. Baltz et al.   MOLECULAR 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

HEXEvent: a database of Human EXon splicing Events

(2012) Anke Busch et al.   NUCLEIC ACIDS RESEARCH

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst 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

The exon junction complex component Magoh controls brain size by regulating neural stem cell division

(2010) Debra L Silver et al.   NATURE NEUROSCIENCE

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY