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

TRUB1 is the predominant pseudouridine synthase acting on mammalian mRNA via a predictable and conserved code

(2017) Modi Safra et al.   GENOME RESEARCH

Function and Clinical Implications of Long Non-Coding RNAs in Melanoma

(2017) Georg Richtig et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

To Wnt or Lose: The Missing Non-Coding Linc in Colorectal Cancer

(2017) Peng Shen et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The Pseudouridine Synthase RPUSD4 Is an Essential Component of Mitochondrial RNA Granules

(2017) Sofia Zaganelli et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Knockdown of long non-coding RNA MALAT1 inhibits growth and motility of human hepatoma cells via modulation of miR-195

(2017) Dingli Liu et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

Oncogenic long noncoding RNA landscape in breast cancer

(2017) Shouping Xu et al.   Molecular Cancer

RNA m6A methylation regulates the ultraviolet-induced DNA damage response

(2017) Yang Xiang et al.   NATURE

Epitranscriptome sequencing technologies: decoding RNA modifications

(2017) Xiaoyu Li et al.   NATURE METHODS

Detecting RNA modifications in the epitranscriptome: predict and validate

(2017) Mark Helm et al.   NATURE REVIEWS GENETICS

Novel players in X inactivation: insights into Xist-mediated gene silencing and chromosome conformation

(2017) Simão T da Rocha et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Label-free, direct localization and relative quantitation of the RNA nucleobase methylations m6A, m5C, m3U, and m5U by top-down mass spectrometry

(2017) Heidelinde Glasner et al.   NUCLEIC ACIDS RESEARCH

Long Noncoding RNA MALAT1 Functions as a Sponge of MiR-200c in Ovarian Cancer

(2017) Meili Pa et al.   ONCOLOGY RESEARCH

The RNA modification landscape in human disease

(2017) Nicky Jonkhout et al.   RNA

Identification of Circulating Long Noncoding RNA HOTAIR as a Novel Biomarker for Diagnosis and Monitoring of Non–Small Cell Lung Cancer

(2017) Nandi Li et al.   TECHNOLOGY IN CANCER RESEARCH & TREATMENT

Long noncoding RNA XIST expedites metastasis and modulates epithelial–mesenchymal transition in colorectal cancer

(2017) Dong-liang Chen et al.   Cell Death & Disease

Role of the long non-coding RNA HOTAIR in hepatocellular carcinoma

(2017) Liming Wu et al.   Oncology Letters

Novel players in X inactivation: insights into Xist-mediated gene silencing and chromosome conformation

(2017) Simão T da Rocha 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

The emerging epitranscriptomics of long noncoding RNAs

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

RNA helicase YTHDC2 promotes cancer metastasis via the enhancement of the efficiency by which HIF-1α mRNA is translated

(2016) Atsushi Tanabe et al.   CANCER LETTERS

Steroid receptor RNA activator: Biologic function and role in disease

(2016) Chan Liu et al.   CLINICA CHIMICA ACTA

Genome-Wide miRNA Analysis Identifies miR-188-3p as a Novel Prognostic Marker and Molecular Factor Involved in Colorectal Carcinogenesis

(2016) Martin Pichler et al.   CLINICAL CANCER RESEARCH

Pseudouridine: the fifth RNA nucleotide with renewed interests

(2016) Xiaoyu Li et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

NSUN3 and ABH1 modify the wobble position of mt‐tRNAMetto expand codon recognition in mitochondrial translation

(2016) Sara Haag et al.   EMBO JOURNAL

The dark matter of the cancer genome: aberrations in regulatory elements, untranslated regions, splice sites, non‐coding RNA and synonymous mutations

(2016) Sven Diederichs et al.   EMBO Molecular Medicine

A pseudouridine synthase module is essential for mitochondrial protein synthesis and cell viability

(2016) Hana Antonicka et al.   EMBO REPORTS

A homozygous truncating mutation in PUS3 expands the role of tRNA modification in normal cognition

(2016) Ranad Shaheen et al.   HUMAN GENETICS

From junk to master regulators of invasion: lncRNA functions in migration, EMT and metastasis

(2016) Sonam Dhamija et al.   INTERNATIONAL JOURNAL OF CANCER

N 6 -Methyladenosine Modification in a Long Noncoding RNA Hairpin Predisposes Its Conformation to Protein Binding

(2016) Katherine I. Zhou et al.   JOURNAL OF MOLECULAR BIOLOGY

Nuclear m 6 A Reader YTHDC1 Regulates mRNA Splicing

(2016) Wen Xiao et al.   MOLECULAR CELL

Structural Basis for Cooperative Function of Mettl3 and Mettl14 Methyltransferases

(2016) Ping Wang et al.   MOLECULAR CELL

Structural basis of N6-adenosine methylation by the METTL3–METTL14 complex

(2016) Xiang Wang et al.   NATURE

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

(2016) Jan Mauer et al.   NATURE

m6A RNA methylation promotes XIST-mediated transcriptional repression

(2016) Deepak P. Patil et al.   NATURE

m6A-LAIC-seq reveals the census and complexity of the m6A epitranscriptome

(2016) Benoit Molinie et al.   NATURE METHODS

RNA modifications: what have we learned and where are we headed?

(2016) Michaela Frye et al.   NATURE REVIEWS GENETICS

COSMIC: somatic cancer genetics at high-resolution

(2016) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Methyltransferase-like protein 16 binds the 3′-terminal triple helix of MALAT1 long noncoding RNA

(2016) Jessica A. Brown et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hypoxia induces the breast cancer stem cell phenotype by HIF-dependent and ALKBH5-mediated m6A-demethylation of NANOG mRNA

(2016) Chuanzhao Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The RNA methyltransferase Dnmt2 methylates DNA in the structural context of a tRNA

(2016) Steffen Kaiser et al.   RNA Biology

Mechanism and biological role of Dnmt2 in Nucleic Acid Methylation

(2016) Albert Jeltsch et al.   RNA Biology

Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells

(2016) Joana Carlevaro-Fita et al.   RNA

Long noncoding RNAMALAT1-derived mascRNA is involved in cardiovascular innate immunity

(2016) Martina Gast et al.   Journal of Molecular Cell Biology

Overexpression of NSUN2 by DNA hypomethylation is associated with metastatic progression in human breast cancer

(2016) Jie Yi et al.   Oncotarget

Structural insights into the molecular mechanism of the m6A writer complex

(2016) Paweł Śledź et al.   eLife

Somatic cancer mutations in the DNMT2 tRNA methyltransferase alter its catalytic properties

(2015) Winfried Elhardt et al.   BIOCHIMIE

A Micropeptide Encoded by a Putative Long Noncoding RNA Regulates Muscle Performance

(2015) Douglas M. Anderson et al.   CELL

5′ UTR m6A Promotes Cap-Independent Translation

(2015) Kate D. Meyer et al.   CELL

Systematic Discovery of Xist RNA Binding Proteins

(2015) Ci Chu et al.   CELL

HNRNPA2B1 Is a Mediator of m6A-Dependent Nuclear RNA Processing Events

(2015) Claudio R. Alarcón et al.   CELL

N6-methyladenosine Modulates Messenger RNA Translation Efficiency

(2015) Xiao Wang et al.   CELL

Long Non-Coding RNAs in Cancer and Development: Where Do We Go from Here?

(2015) Monika Haemmerle et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Structure and Thermodynamics of N6-Methyladenosine in RNA: A Spring-Loaded Base Modification

(2015) Caroline Roost et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3

(2015) Colleen A. McHugh et al.   NATURE

Dynamic m6A mRNA methylation directs translational control of heat shock response

(2015) Jun Zhou et al.   NATURE

N6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions

(2015) Nian Liu et al.   NATURE

Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome

(2015) Xiaoyu Li et al.   Nature Chemical Biology

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

Detecting actively translated open reading frames in ribosome profiling data

(2015) Lorenzo Calviello et al.   NATURE METHODS

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

(2015) Bastian Linder et al.   NATURE METHODS

Noncoding RNAs in eukaryotic ribosome biogenesis and function

(2015) Denis L J Lafontaine   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A mass spectrometry-based method for direct determination of pseudouridine in RNA

(2015) Yoshio Yamauchi et al.   NUCLEIC ACIDS RESEARCH

Profiling ribonucleotide modifications at full-transcriptome level: a step toward MS-based epitranscriptomics

(2015) Rebecca E. Rose et al.   RNA

NSUN6 is a human RNA methyltransferase that catalyzes formation of m5C72 in specific tRNAs

(2015) Sara Haag et al.   RNA

A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation

(2015) A. Minajigi et al.   SCIENCE

Methylation of ribosomal RNA by NSUN5 is a conserved mechanism modulating organismal lifespan

(2015) Markus Schosserer et al.   Nature Communications

Noncoding RNAs in eukaryotic ribosome biogenesis and function

(2015) Denis L J Lafontaine   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Pseudouridine: Still mysterious, but never a fake (uridine)!

(2015) Felix Spenkuch et al.   RNA Biology

High-ResolutionN6-Methyladenosine (m6A) Map Using Photo-Crosslinking-Assisted m6A Sequencing

(2014) Kai Chen et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA

(2014) Schraga Schwartz et al.   CELL

The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones

(2014) Thomas R. Cech et al.   CELL

Mammalian WTAP is a regulatory subunit of the RNA N6-methyladenosine methyltransferase

(2014) Xiao-Li Ping et al.   CELL RESEARCH

Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation

(2014) A. A. Bazzini et al.   EMBO JOURNAL

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

(2014) Thomas M. Carlile et al.   NATURE

N6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells

(2014) Yang Wang et al.   NATURE CELL BIOLOGY

Structural basis for selective binding of m6A RNA by the YTHDC1 YTH domain

(2014) Chao Xu et al.   Nature Chemical Biology

Transcriptome-wide target profiling of RNA cytosine methyltransferases using the mechanism-based enrichment procedure Aza-IP

(2014) Vahid Khoddami et al.   Nature Protocols

Emerging roles of tRNA in adaptive translation, signalling dynamics and disease

(2014) Sebastian Kirchner et al.   NATURE REVIEWS GENETICS

lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs

(2014) Xiu Cheng Quek et al.   NUCLEIC ACIDS RESEARCH

Transcriptome-Wide Mapping of Pseudouridines: Pseudouridine Synthases Modify Specific mRNAs in S. cerevisiae

(2014) Alexander F. Lovejoy et al.   PLoS One

Role of tRNA modifications in human diseases

(2014) Adrian Gabriel Torres et al.   TRENDS IN MOLECULAR MEDICINE

Overexpression of long non-coding RNA MALAT1 is correlated with clinical progression and unfavorable prognosis in pancreatic cancer

(2014) Er-Jun Pang et al.   TUMOR BIOLOGY

Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes

(2014) Nicholas T. Ingolia et al.   Cell Reports

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

(2014) Schraga Schwartz et al.   Cell Reports

NSUN4 Is a Dual Function Mitochondrial Protein Required for Both Methylation of 12S rRNA and Coordination of Mitoribosomal Assembly

(2014) Metodi Dimitrov Metodiev et al.   PLoS Genetics

Xist RNA Is a Potent Suppressor of Hematologic Cancer in Mice

(2013) Eda Yildirim et al.   CELL

RNA-Methylation-Dependent RNA Processing Controls the Speed of the Circadian Clock

(2013) Jean-Michel Fustin et al.   CELL

Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins

(2013) Mitchell Guttman et al.   CELL

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

(2013) Mark Helm et al.   CHEMISTRY & BIOLOGY

The IGF2 intronic miR-483 selectively enhances transcription from IGF2 fetal promoters and enhances tumorigenesis

(2013) M. Liu et al.   GENES & DEVELOPMENT

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

(2013) Keiko Horiuchi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

MALAT1 — a paradigm for long noncoding RNA function in cancer

(2013) Tony Gutschner et al.   JOURNAL OF MOLECULAR MEDICINE-JMM

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

Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis

(2013) P. Juntawong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long non-coding RNAs as targets for cytosine methylation

(2013) Thomas Amort et al.   RNA Biology

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

(2013) N. Liu et al.   RNA

RNA pseudouridylation: new insights into an old modification

(2013) Junhui Ge et al.   TRENDS IN BIOCHEMICAL SCIENCES

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

Mutation in NSUN2, which Encodes an RNA Methyltransferase, Causes Autosomal-Recessive Intellectual Disability

(2012) Muzammil Ahmad Khan et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Mutations in NSUN2 Cause Autosomal- Recessive Intellectual Disability

(2012) Lia Abbasi-Moheb et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Noncoding RNA MALAT1 Is a Critical Regulator of the Metastasis Phenotype of Lung Cancer Cells

(2012) T. Gutschner et al.   CANCER RESEARCH

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

(2012) Kate D. Meyer et al.   CELL

Whole exome sequencing identifies a splicing mutation inNSUN2as a cause of a Dubowitz-like syndrome

(2012) Fernando Jose Martinez et al.   JOURNAL OF MEDICAL GENETICS

ALKBH5 Is a Mammalian RNA Demethylase that Impacts RNA Metabolism and Mouse Fertility

(2012) Guanqun Zheng et al.   MOLECULAR CELL

RNA discrimination

(2012) Monika S. Kowalczyk et al.   NATURE

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

(2012) Dan Dominissini et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

(2012) Jeffrey E. Squires et al.   NUCLEIC ACIDS RESEARCH

MODOMICS: a database of RNA modification pathways—2013 update

(2012) Magdalena A. Machnicka et al.   NUCLEIC ACIDS RESEARCH

The hallmarks of cancer

(2012) Tony Gutschner et al.   RNA Biology

Loss of the abundant nuclear non-coding RNAMALAT1is compatible with life and development

(2012) Moritz Eißmann et al.   RNA Biology

Malat1 is not an essential component of nuclear speckles in mice

(2012) S. Nakagawa et al.   RNA

Post-translational modification: nature's escape from genetic imprisonment and the basis for dynamic information encoding

(2012) Sudhakaran Prabakaran et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

The lncRNA Malat1 Is Dispensable for Mouse Development but Its Transcription Plays a cis-Regulatory Role in the Adult

(2012) Bin Zhang et al.   Cell Reports

Non-coding RNA and antisense RNA. Nature’s trash or treasure?

(2011) Stuart Knowling et al.   BIOCHIMIE

Tumor Suppressive MicroRNAs miR-34a/c Control Cancer Cell Expression of ULBP2, a Stress-Induced Ligand of the Natural Killer Cell Receptor NKG2D

(2011) A. Heinemann et al.   CANCER RESEARCH

Long Noncoding RNA HOTAIR Regulates Polycomb-Dependent Chromatin Modification and Is Associated with Poor Prognosis in Colorectal Cancers

(2011) R. Kogo et al.   CANCER RESEARCH

Invasion front-specific expression and prognostic significance of microRNA in colorectal liver metastases

(2011) Christoph Kahlert et al.   CANCER SCIENCE

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

Frequent Increased Gene Copy Number and High Protein Expression of tRNA (Cytosine-5-)-Methyltransferase (NSUN2) in Human Cancers

(2011) Mayumi Okamoto et al.   DNA AND CELL BIOLOGY

Noncoding RNA gene silencing through genomic integration of RNA destabilizing elements using zinc finger nucleases

(2011) T. Gutschner et al.   GENOME RESEARCH

Molecular Mechanisms of Long Noncoding RNAs

(2011) Kevin C. Wang et al.   MOLECULAR CELL

Converting nonsense codons into sense codons by targeted pseudouridylation

(2011) John Karijolich 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

Gene silencing in X-chromosome inactivation: advances in understanding facultative heterochromatin formation

(2011) Anton Wutz   NATURE REVIEWS GENETICS

Small nucleolar RNA 42 acts as an oncogene in lung tumorigenesis

(2011) Y-P Mei et al.   ONCOGENE

MacroRNA underdogs in a microRNA world: Evolutionary, regulatory, and biomedical significance of mammalian long non-protein-coding RNA

(2010) Leonard Lipovich et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response

(2010) Maite Huarte et al.   CELL

The Matrix Protein hnRNP U Is Required for Chromosomal Localization of Xist RNA

(2010) Yuko Hasegawa et al.   DEVELOPMENTAL CELL

A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression

(2010) Delphine Bernard et al.   EMBO JOURNAL

The idic(X)(q13) in myeloid malignancies: breakpoint clustering in segmental duplications and association with TET2 mutations

(2010) K. Paulsson et al.   HUMAN MOLECULAR GENETICS

The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation

(2010) Vidisha Tripathi et al.   MOLECULAR CELL

Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis

(2010) Rajnish A. Gupta et al.   NATURE

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution

(2010) Julian König et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Effect of pseudouridylation on the structure and activity of the catalytically essential P6.1 hairpin in human telomerase RNA

(2010) Nak-Kyoon Kim et al.   NUCLEIC ACIDS RESEARCH

The RNA modification database, RNAMDB: 2011 update

(2010) W. A. Cantara et al.   NUCLEIC ACIDS RESEARCH

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

Long noncoding RNAs in mammalian cells: what, where, and why?

(2010) Ling-Ling Chen et al.   Wiley Interdisciplinary Reviews-RNA

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

An operational definition of epigenetics

(2009) S. L. Berger et al.   GENES & DEVELOPMENT

Diagnostic criteria to distinguish hypocellular acute myeloid leukemia from hypocellular myelodysplastic syndromes and aplastic anemia: recommendations for a standardized approach

(2009) J. M. Bennett et al.   HAEMATOLOGICA

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

Many roads to maturity: microRNA biogenesis pathways and their regulation

(2009) Julia Winter et al.   NATURE CELL BIOLOGY

Mass spectrometry of the fifth nucleoside: A review of the identification of pseudouridine in nucleic acids

(2008) Anita Durairaj et al.   ANALYTICA CHIMICA ACTA

3′ End Processing of a Long Nuclear-Retained Noncoding RNA Yields a tRNA-like Cytoplasmic RNA

(2008) Jeremy E. Wilusz et al.   CELL

RNA cytosine methylation analysis by bisulfite sequencing

(2008) M. Schaefer et al.   NUCLEIC ACIDS RESEARCH

MTA Is an Arabidopsis Messenger RNA Adenosine Methylase and Interacts with a Homolog of a Sex-Specific Splicing Factor

(2008) S. Zhong et al.   PLANT CELL

Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities

(2008) Marcel E. Dinger et al.   PLoS Computational Biology