Integrative network analysis identifies cell-specific trans regulators of m6A

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

(2019) Huilin Huang et al.   NATURE

RNA modifications regulating cell fate in cancer

(2019) Sylvain Delaunay et al.   NATURE CELL BIOLOGY

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

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

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

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RNA N6-methyladenosine modification in cancers: current status and perspectives

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METTL14 Inhibits Hematopoietic Stem/Progenitor Differentiation and Promotes Leukemogenesis via mRNA m 6 A Modification

(2018) Hengyou Weng et al.   Cell Stem Cell

Novel insights on m6A RNA methylation in tumorigenesis: a double-edged sword

(2018) Shaoyun Wang et al.   Molecular Cancer

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

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

Chemical Modifications in the Life of an mRNA Transcript

(2018) Sigrid Nachtergaele et al.   Annual Review of Genetics

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

(2018) Alessandro Bertero et al.   NATURE

m6A mRNA methylation regulates AKT activity to promote the proliferation and tumorigenicity of endometrial cancer

(2018) Jun Liu et al.   NATURE CELL BIOLOGY

Refined RIP-seq protocol for epitranscriptome analysis with low input materials

(2018) Yong Zeng et al.   PLOS BIOLOGY

RNA m6 A modification enzymes shape innate responses to DNA by regulating interferon β

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The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

Circadian Clock Regulation of Hepatic Lipid Metabolism by Modulation of m6A mRNA Methylation

(2018) Xiang Zhong 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

RNA Chemical Proteomics Reveals the N6-Methyladenosine (m6A)-Regulated Protein–RNA Interactome

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RNA m6A methylation regulates the ultraviolet-induced DNA damage response

(2017) Yang Xiang et al.   NATURE

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

(2017) Isaia Barbieri et al.   NATURE

Chemical and structural effects of base modifications in messenger RNA

(2017) Emily M. Harcourt et al.   NATURE

RNA fate determination through cotranscriptional adenosine methylation and microprocessor binding

(2017) Philip Knuckles et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

N6-methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis

(2017) Raghu R Edupuganti et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The RNA modification landscape in human disease

(2017) Nicky Jonkhout et al.   RNA

RNA fate determination through cotranscriptional adenosine methylation and microprocessor binding

(2017) Philip Knuckles et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

N6-methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis

(2017) Raghu R Edupuganti et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2017) Qi Cui et al.   Cell Reports

Viral and cellular N6-methyladenosine and N6,2′-O-dimethyladenosine epitranscriptomes in the KSHV life cycle

(2017) Brandon Tan et al.   Nature Microbiology

A novel algorithm for calling mRNA m6A peaks by modeling biological variances in MeRIP-seq data

(2016) Xiaodong Cui et al.   BIOINFORMATICS

Resources for the Comprehensive Discovery of Functional RNA Elements

(2016) Balaji Sundararaman et al.   MOLECULAR CELL

The m 6 A Methyltransferase METTL3 Promotes Translation in Human Cancer Cells

(2016) Shuibin Lin et al.   MOLECULAR CELL

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

(2016) Gianluigi Lichinchi et al.   Nature Microbiology

Mechanisms and Regulation of Alternative Pre-mRNA Splicing

(2015) Yeon Lee et al.   Annual Review of Biochemistry

dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering

(2015) Tal Galili   BIOINFORMATICS

Panorama of ancient metazoan macromolecular complexes

(2015) Cuihong Wan 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

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

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m6A RNA Modification Controls Cell Fate Transition in Mammalian Embryonic Stem Cells

(2014) Pedro J. Batista et al.   Cell Stem Cell

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

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

(2014) Schraga Schwartz et al.   Cell Reports

Identification of Wilms' Tumor 1-associating Protein Complex and Its Role in Alternative Splicing and the Cell Cycle

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A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

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

(2013) Jianzhao Liu et al.   Nature Chemical Biology

starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data

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Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal

(2013) J. Gao et al.   Science Signaling

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

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

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Genome-Wide Determination of a Broad ESRP-Regulated Posttranscriptional Network by High-Throughput Sequencing

(2012) K. A. Dittmar et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2012) Dan Dominissini et al.   NATURE

The cardiotonic steroid digitoxin regulates alternative splicing through depletion of the splicing factors SRSF3 and TRA2B

(2012) E. S. Anderson et al.   RNA

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1.

(2012) Ethan Cerami et al.   Cancer Discovery

Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43

(2011) Magdalini Polymenidou et al.   NATURE NEUROSCIENCE

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

starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data

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Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

WGCNA: an R package for weighted correlation network analysis

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