Multiple links between 5-methylcytosine content of mRNA and translation

Methods for RNA Modification Mapping Using Deep Sequencing: Established and New Emerging Technologies

(2019) Yuri Motorin et al.   Genes

Eukaryotic 5-methylcytosine (m5C) RNA Methyltransferases: Mechanisms, Cellular Functions, and Links to Disease

(2019) Katherine Bohnsack et al.   Genes

Where, When, and How: Context-Dependent Functions of RNA Methylation Writers, Readers, and Erasers

(2019) Hailing Shi et al.   MOLECULAR CELL

Genome-wide identification of mRNA 5-methylcytosine in mammals

(2019) Tao Huang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

DNA repair enzymes ALKBH2, ALKBH3, and AlkB oxidize 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine in vitro

(2019) Ke Bian et al.   NUCLEIC ACIDS RESEARCH

Messenger RNA Modifications in Plants

(2019) Lisha Shen et al.   TRENDS IN PLANT SCIENCE

mRNA methylation in cell senescence

(2019) Gabriel Casella et al.   Wiley Interdisciplinary Reviews-RNA

The epitranscriptome in translation regulation: mRNA and tRNA modifications as the two sides of the same coin?

(2019) Namit Ranjan et al.   FEBS LETTERS

5-methylcytosine promotes pathogenesis of bladder cancer through stabilizing mRNAs

(2019) Xin Chen et al.   NATURE CELL BIOLOGY

Extensive Epitranscriptomic Methylation of A and C Residues on Murine Leukemia Virus Transcripts Enhances Viral Gene Expression

(2019) David G. Courtney et al.   mBio

Discovering and Mapping the Modified Nucleotides That Comprise the Epitranscriptome of mRNA

(2019) Bastian Linder et al.   Cold Spring Harbor Perspectives in Biology

Depletion of TRDMT1 affects 5-methylcytosine modification of mRNA and inhibits HEK293 cell proliferation and migration

(2019) Songlei Xue et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Epitranscriptomic Addition of m5C to HIV-1 Transcripts Regulates Viral Gene Expression

(2019) David G. Courtney et al.   Cell Host & Microbe

m5C Methylation Guides Systemic Transport of Messenger RNA over Graft Junctions in Plants

(2019) Lei Yang et al.   CURRENT BIOLOGY

RNA 5-Methylcytosine Facilitates the Maternal-to-Zygotic Transition by Preventing Maternal mRNA Decay

(2019) Ying Yang et al.   MOLECULAR CELL

Reading, writing and erasing mRNA methylation

(2019) Sara Zaccara et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

N 6 -Methyladenosines Modulate A-to-I RNA Editing

(2018) Jian-Feng Xiang et al.   MOLECULAR CELL

RNA cytosine methylation and methyltransferases mediate chromatin organization and 5-azacytidine response and resistance in leukaemia

(2018) Jason X. Cheng et al.   Nature Communications

Topological Characterization of Human and Mouse m5C Epitranscriptome Revealed by Bisulfite Sequencing

(2018) Zhen Wei et al.   International Journal of Genomics

Chemical Modifications in the Life of an mRNA Transcript

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

Acetylation of Cytidine in mRNA Promotes Translation Efficiency

(2018) Daniel Arango et al.   CELL

Effects of NSUN2 deficiency on the mRNA 5-methylcytosine modification and gene expression profile in HEK293 cells

(2018) Zhen Sun et al.   Epigenomics

The dynamic RNA modification 5‐methylcytosine and its emerging role as an epitranscriptomic mark

(2018) Lukas Trixl et al.   Wiley Interdisciplinary Reviews-RNA

Statistically robust methylation calling for whole-transcriptome bisulfite sequencing reveals distinct methylation patterns for mouse RNAs

(2017) Carine Legrand et al.   GENOME RESEARCH

The Dark Side of the Epitranscriptome: Chemical Modifications in Long Non-Coding RNAs

(2017) Roland Jacob et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Viral Epitranscriptomics

(2017) Edward M. Kennedy et al.   JOURNAL OF VIROLOGY

5-Methylcytosine RNA Methylation in Arabidopsis Thaliana

(2017) Xuean Cui et al.   Molecular Plant

MODOMICS: a database of RNA modification pathways. 2017 update

(2017) Pietro Boccaletto et al.   NUCLEIC ACIDS RESEARCH

Transcriptome-Wide Mapping of RNA 5-Methylcytosine in Arabidopsis mRNAs and Noncoding RNAs

(2017) Rakesh David et al.   PLANT CELL

Understanding RNA modifications: the promises and technological bottlenecks of the ‘epitranscriptome’

(2017) Matthias Schaefer et al.   Open Biology

The emerging epitranscriptomics of long noncoding RNAs

(2016) Andrew Shafik et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

5-hydroxymethylcytosine is detected in RNA from mouse brain tissues

(2016) Zhigang Miao et al.   BRAIN RESEARCH

The existence of 5-hydroxymethylcytosine and 5-formylcytosine in both DNA and RNA in mammals

(2016) Hao-Ying Zhang et al.   CHEMICAL COMMUNICATIONS

RNA epigenetics — chemical messages for posttranscriptional gene regulation

(2016) Ian A Roundtree et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Emerging roles of RNA modifications in bacteria

(2016) Carmelita Nora Marbaniang et al.   CURRENT OPINION IN MICROBIOLOGY

Deciphering the epitranscriptome: A green perspective

(2016) Alice Burgess et al.   Journal of Integrative Plant Biology

Identification of human RNA editing sites: A historical perspective

(2016) Gokul Ramaswami et al.   METHODS

Regulation of Poly(A) Tail and Translation during the Somatic Cell Cycle

(2016) Jong-Eun Park et al.   MOLECULAR CELL

Stem cell function and stress response are controlled by protein synthesis

(2016) Sandra Blanco et al.   NATURE

Tuning the ribosome: The influence of rRNA modification on eukaryotic ribosome biogenesis and function

(2016) Katherine E. Sloan et al.   RNA Biology

Transcriptome-wide distribution and function of RNA hydroxymethylcytosine

(2016) B. Delatte et al.   SCIENCE

Formation and determination of the oxidation products of 5-methylcytosine in RNA

(2016) Wei Huang et al.   Chemical Science

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

(2016) Hao Du et al.   Nature Communications

Deposition of 5-Methylcytosine on Enhancer RNAs Enables the Coactivator Function of PGC-1α

(2016) Francesca Aguilo et al.   Cell Reports

mRNA methylation by NSUN2 in cell proliferation

(2016) Wengong Wang   Wiley Interdisciplinary Reviews-RNA

meRanTK: methylated RNA analysis ToolKit: Table 1.

(2015) Dietmar Rieder et al.   BIOINFORMATICS

The Arabidopsis epitranscriptome

(2015) Rupert G Fray et al.   CURRENT OPINION IN PLANT BIOLOGY

GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes

(2015) Patricia P. Chan et al.   NUCLEIC ACIDS RESEARCH

RNA epigenetics

(2015) Nian Liu et al.   Translational Research

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Role of RNA methyltransferases in tissue renewal and pathology

(2014) Sandra Blanco et al.   CURRENT OPINION IN CELL BIOLOGY

Aberrant methylation of tRNAs links cellular stress to neuro-developmental disorders

(2014) S. Blanco et al.   EMBO JOURNAL

tRNA fragments in human health and disease

(2014) Paul Anderson et al.   FEBS LETTERS

Posttranscriptional RNA Modifications: Playing Metabolic Games in a Cell’s Chemical Legoland

(2013) Mark Helm et al.   CHEMISTRY & BIOLOGY

Expression of NOL1/NOP2/sun domain (Nsun) RNA methyltransferase family genes in early mouse embryogenesis

(2013) Lijun Chi et al.   GENE EXPRESSION PATTERNS

N6-methyladenosine-dependent regulation of messenger RNA stability

(2013) Xiao Wang et al.   NATURE

Identification of direct targets and modified bases of RNA cytosine methyltransferases

(2013) Vahid Khoddami et al.   NATURE BIOTECHNOLOGY

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

(2013) Jianzhao Liu et al.   Nature Chemical Biology

Yeast Nop2 and Rcm1 methylate C2870 and C2278 of the 25S rRNA, respectively

(2013) Sunny Sharma et al.   NUCLEIC ACIDS RESEARCH

NSun2-Mediated Cytosine-5 Methylation of Vault Noncoding RNA Determines Its Processing into Regulatory Small RNAs

(2013) Shobbir Hussain et al.   Cell Reports

Transcriptome-Wide Mapping of 5-methylcytidine RNA Modifications in Bacteria, Archaea, and Yeast Reveals m5C within Archaeal mRNAs

(2013) Sarit Edelheit et al.   PLoS Genetics

Mapping and significance of the mRNA methylome

(2013) Tennille Sibbritt et al.   Wiley Interdisciplinary Reviews-RNA

Characterizing 5-methylcytosine in the mammalian epitranscriptome

(2013) Shobbir Hussain et al.   GENOME BIOLOGY

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

(2012) Kate D. Meyer et al.   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

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

(2012) Jeffrey E. Squires 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

The birth of the Epitranscriptome: deciphering the function of RNA modifications

(2012) Yogesh Saletore et al.   GENOME BIOLOGY

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

(2012) Altuna Akalin et al.   GENOME BIOLOGY

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

RNA methylation by Dnmt2 protects transfer RNAs against stress-induced cleavage

(2010) M. Schaefer et al.   GENES & DEVELOPMENT

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Do all modifications benefit all tRNAs?

(2009) Eric M. Phizicky et al.   FEBS LETTERS