RNA Metabolism Guided by RNA Modifications: The Role of SMUG1 in rRNA Quality Control

The 18S ribosomal RNA m 6 A methyltransferase Mettl5 is required for normal walking behavior in Drosophila

(2020) Jessica Leismann et al.   EMBO REPORTS

HydraPsiSeq: a method for systematic and quantitative mapping of pseudouridines in RNA

(2020) Virginie Marchand et al.   NUCLEIC ACIDS RESEARCH

The chromatin landscape of the ribosomal RNA genes in mouse and human

(2019) Tom Moss et al.   CHROMOSOME RESEARCH

Interactions and activities of factors involved in the late stages of human 18S rRNA maturation

(2019) Katherine Elizabeth Sloan et al.   RNA Biology

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

(2019) Katherine Bohnsack et al.   Genes

Transcriptome-wide profiling of multiple RNA modifications simultaneously at single-base resolution

(2019) Vahid Khoddami et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The chemical diversity of RNA modifications

(2019) R. Jordan Ontiveros et al.   BIOCHEMICAL JOURNAL

Exonuclease requirements for mammalian ribosomal RNA biogenesis and surveillance

(2019) Mehdi Pirouz et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The human 18S rRNA m6A methyltransferase METTL5 is stabilized by TRMT112

(2019) Nhan van Tran et al.   NUCLEIC ACIDS RESEARCH

SMUG1 Promotes Telomere Maintenance through Telomerase RNA Processing

(2019) Penelope Kroustallaki et al.   Cell Reports

Mutations in the anticodon stem of tRNA cause accumulation and Met22-dependent decay of pre-tRNA in yeast

(2019) Matthew J. Payea et al.   RNA

Accurate detection of m6A RNA modifications in native RNA sequences

(2019) Huanle Liu et al.   Nature Communications

Adenosine methylation as a molecular imprint defining the fate of RNA

(2018) Philip Knuckles et al.   FEBS LETTERS

Cryo-EM structure of substrate-bound human telomerase holoenzyme

(2018) Thi Hoang Duong Nguyen et al.   NATURE

Structural and evolutionary insights into ribosomal RNA methylation

(2018) Petr V Sergiev et al.   Nature Chemical Biology

Oxidative stress damages rRNA inside the ribosome and differentially affects the catalytic center

(2018) Jessica Willi et al.   NUCLEIC ACIDS RESEARCH

RNA Framework: an all-in-one toolkit for the analysis of RNA structures and post-transcriptional modifications

(2018) Danny Incarnato et al.   NUCLEIC ACIDS RESEARCH

Pseudouridines have context-dependent mutation and stop rates in high-throughput sequencing

(2018) Katherine I. Zhou et al.   RNA Biology

Detecting RNA base methylations in single cells by in situ hybridization

(2018) Rohan T. Ranasinghe et al.   Nature Communications

Epitranscriptomics: A New Regulatory Mechanism of Brain Development and Function

(2018) Florian Noack et al.   Frontiers in Neuroscience

Reversible RNA Modification N 1 -methyladenosine (m 1 A) in mRNA and tRNA

(2018) Chi Zhang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Landscape of the complete RNA chemical modifications in the human 80S ribosome

(2018) Masato Taoka et al.   NUCLEIC ACIDS RESEARCH

A single N1-methyladenosine on the large ribosomal subunit rRNA impacts locally its structure and the translation of key metabolic enzymes

(2018) Sunny Sharma et al.   Scientific Reports

Ribosomal flavours: an acquired taste for specific mRNAs?

(2018) Christian Bates et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

RNA ribose methylation (2′-O-methylation): Occurrence, biosynthesis and biological functions

(2018) Lilia Ayadi et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Unraveling 3′-end RNA uridylation at nucleotide resolution

(2018) Mehdi Pirouz et al.   METHODS

Sequencing-based methods for detection and quantitation of ribose methylations in RNA

(2018) Nicolai Krogh et al.   METHODS

N6-Methyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation

(2018) Honghui Ma et al.   Nature Chemical Biology

Excision of uracil from DNA by hSMUG1 includes strand incision and processing

(2018) Marina Alexeeva et al.   NUCLEIC ACIDS RESEARCH

Detection and Analysis of RNA Ribose 2′-O-Methylations: Challenges and Solutions

(2018) Yuri Motorin et al.   Genes

Comparison of preribosomal RNA processing pathways in yeast, plant and human cells - focus on coordinated action of endo- and exoribonucleases

(2017) Rafal Tomecki et al.   FEBS LETTERS

Visualization of chemical modifications in the human 80S ribosome structure

(2017) S. Kundhavai Natchiar et al.   NATURE

Chemical and structural effects of base modifications in messenger RNA

(2017) Emily M. Harcourt et al.   NATURE

Detecting RNA modifications in the epitranscriptome: predict and validate

(2017) Mark Helm et al.   NATURE REVIEWS GENETICS

MeT-DB V2.0: elucidating context-specific functions of N6-methyl-adenosine methyltranscriptome

(2017) Hui Liu et al.   NUCLEIC ACIDS RESEARCH

MODOMICS: a database of RNA modification pathways. 2017 update

(2017) Pietro Boccaletto et al.   NUCLEIC ACIDS RESEARCH

High-throughput and site-specific identification of 2′- O -methylation sites using ribose oxidation sequencing (RibOxi-seq)

(2017) Yinzhou Zhu et al.   RNA

ASC1 and RPS3 : new actors in 18S nonfunctional rRNA decay

(2017) Kelly A. Limoncelli et al.   RNA

The RNA modification landscape in human disease

(2017) Nicky Jonkhout et al.   RNA

Widespread temperature sensitivity and tRNA decay due to mutations in a yeast tRNA

(2017) Matthew J. Payea et al.   RNA

Identification of sites of 2′-O-methylation vulnerability in human ribosomal RNAs by systematic mapping

(2017) Sunny Sharma et al.   Scientific Reports

Quality control of chemically damaged RNA

(2016) Carrie L. Simms et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

RNA epigenetics — chemical messages for posttranscriptional gene regulation

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

TUT‐DIS3L2 is a mammalian surveillance pathway for aberrant structured non‐coding RNAs

(2016) Dmytro Ustianenko et al.   EMBO JOURNAL

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

(2016) Ranad Shaheen et al.   HUMAN GENETICS

N6-Methylated Adenosine in RNA: From Bacteria to Humans

(2016) Petr V. Sergiev et al.   JOURNAL OF MOLECULAR BIOLOGY

Pseudouridylation meets next-generation sequencing

(2016) Maryam Zaringhalam et al.   METHODS

The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA

(2016) Dan Dominissini et al.   NATURE

Transcriptome-wide mapping reveals reversible and dynamic N1-methyladenosine methylome

(2016) Xiaoyu Li et al.   Nature Chemical Biology

Post-transcriptional gene regulation by mRNA modifications

(2016) Boxuan Simen Zhao et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Unusual C′/D′ motifs enable box C/D snoRNPs to modify multiple sites in the same rRNA target region

(2016) Robert Willem van Nues et al.   NUCLEIC ACIDS RESEARCH

Profiling of 2′-O-Me in human rRNA reveals a subset of fractionally modified positions and provides evidence for ribosome heterogeneity

(2016) Nicolai Krogh et al.   NUCLEIC ACIDS RESEARCH

Perlman syndrome nuclease DIS3L2 controls cytoplasmic non-coding RNAs and provides surveillance pathway for maturing snRNAs

(2016) Anna Łabno et al.   NUCLEIC ACIDS RESEARCH

Mechanism and regulation of the nonsense-mediated decay pathway

(2016) Nele Hug et al.   NUCLEIC ACIDS RESEARCH

Box C/D guide RNAs recognize a maximum of 10 nt of substrates

(2016) Zuxiao Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

RNA modification in Cajal bodies

(2016) U. Thomas Meier   RNA Biology

Transcriptome-wide distribution and function of RNA hydroxymethylcytosine

(2016) B. Delatte et al.   SCIENCE

Messenger RNA modifications: Form, distribution, and function

(2016) W. V. Gilbert et al.   SCIENCE

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

(2016) Wei Huang et al.   Chemical Science

Dis3l2-Mediated Decay Is a Quality Control Pathway for Noncoding RNAs

(2016) Mehdi Pirouz et al.   Cell Reports

On-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme

(2015) Claus-D. Kuhn et al.   CELL

Human telomerase: biogenesis, trafficking, recruitment, and activation

(2015) Jens C. Schmidt et al.   GENES & DEVELOPMENT

Surveillance and Cleavage of Eukaryotic tRNAs

(2015) Cyrille Megel et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Quality Control Pathways for Nucleus-Encoded Eukaryotic tRNA Biosynthesis and Subcellular Trafficking

(2015) Anita K. Hopper et al.   MOLECULAR AND CELLULAR BIOLOGY

The human 18S rRNA base methyltransferases DIMT1L and WBSCR22-TRMT112 but not rRNA modification are required for ribosome biogenesis

(2015) Christiane Zorbas et al.   MOLECULAR BIOLOGY OF THE CELL

ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments

(2015) Aaron E Cozen et al.   NATURE METHODS

A-to-I editing of coding and non-coding RNAs by ADARs

(2015) Kazuko Nishikura   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Nonsense-mediated mRNA decay: an intricate machinery that shapes transcriptomes

(2015) Søren Lykke-Andersen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2015) Markus Schosserer et al.   Nature Communications

A Single Let-7 MicroRNA Bypasses LIN28-Mediated Repression

(2015) Robinson Triboulet et al.   Cell Reports

Eukaryotic rRNA Modification by Yeast 5-Methylcytosine-Methyltransferases and Human Proliferation-Associated Antigen p120

(2015) Gabrielle Bourgeois et al.   PLoS One

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

(2015) Felix Spenkuch et al.   RNA Biology

Human dyskerin: beyond telomeres

(2014) Alberto Angrisani et al.   BIOLOGICAL CHEMISTRY

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

(2014) Schraga Schwartz et al.   CELL

Regulatory mechanisms of RNA function: emerging roles of DNA repair enzymes

(2014) Laure Jobert et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

mTOR regulates the nucleoplasmic diffusion of Xrn2 under conditions of heat stress

(2014) Kazunori Watanabe et al.   FEBS LETTERS

Identification of the determinants of tRNA function and susceptibility to rapid tRNA decay by high-throughput in vivo analysis

(2014) Michael P. Guy et al.   GENES & DEVELOPMENT

Protecting the proteome: Eukaryotic cotranslational quality control pathways

(2014) Jens Lykke-Andersen et al.   JOURNAL OF CELL BIOLOGY

Nanopores Discriminate among Five C5-Cytosine Variants in DNA

(2014) Zachary L. Wescoe et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

(2014) Thomas M. Carlile et al.   NATURE

The association of late-acting snoRNPs with human pre-ribosomal complexes requires the RNA helicase DDX21

(2014) Katherine E. Sloan et al.   NUCLEIC ACIDS RESEARCH

Uracil-DNA glycosylases-Structural and functional perspectives on an essential family of DNA repair enzymes

(2014) N. Schormann et al.   PROTEIN SCIENCE

An overview of pre-ribosomal RNA processing in eukaryotes

(2014) Anthony K. Henras et al.   Wiley Interdisciplinary Reviews-RNA

Epigenetic Function of Activation-Induced Cytidine Deaminase and Its Link to Lymphomagenesis

(2014) Pilar M. Dominguez et al.   Frontiers in Immunology

RNA decay machines: The exosome

(2013) Aleksander Chlebowski et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Exonuclease hDIS3L2 specifies an exosome-independent 3′-5′ degradation pathway of human cytoplasmic mRNA

(2013) Michal Lubas et al.   EMBO JOURNAL

The exoribonuclease Dis3L2 defines a novel eukaryotic RNA degradation pathway

(2013) Michal Malecki et al.   EMBO JOURNAL

Severity of X-linked Dyskeratosis Congenita (DKCX) Cellular Defects Is not Directly Related to Dyskerin (DKC1) Activity in Ribosomal RNA Biogenesis or mRNA Translation

(2013) Naresh R. Thumati et al.   HUMAN MUTATION

The Hbs1-Dom34 Protein Complex Functions in Non-stop mRNA Decay in Mammalian Cells

(2013) Syuhei Saito et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Identification of direct targets and modified bases of RNA cytosine methyltransferases

(2013) Vahid Khoddami et al.   NATURE BIOTECHNOLOGY

The RNA exosome and proteasome: common principles of degradation control

(2013) Debora L. Makino et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Mammalian DIS3L2 exoribonuclease targets the uridylated precursors of let-7 miRNAs

(2013) D. Ustianenko et al.   RNA

Studies of translational misreading in vivo show that the ribosome very efficiently discriminates against most potential errors

(2013) N. Manickam et al.   RNA

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 the cleavage sites on mammalian pre-rRNAs: Where do we stand?

(2012) Sahra-Taylor Mullineux et al.   BIOCHIMIE

Ccr4-Not complex: the control freak of eukaryotic cells

(2012) Jason E. Miller et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

40S subunit dissociation and proteasome-dependent RNA degradation in nonfunctional 25S rRNA decay

(2012) Kotaro Fujii et al.   EMBO JOURNAL

RNA Degradation in Saccharomyces cerevisae

(2012) Roy Parker   GENETICS

An Enhanced H/ACA RNP Assembly Mechanism for Human Telomerase RNA

(2012) E. D. Egan et al.   MOLECULAR AND CELLULAR BIOLOGY

The Human Base Excision Repair Enzyme SMUG1 Directly Interacts with DKC1 and Contributes to RNA Quality Control

(2012) Laure Jobert et al.   MOLECULAR CELL

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

(2012) Dan Dominissini et al.   NATURE

Germline mutations in DIS3L2 cause the Perlman syndrome of overgrowth and Wilms tumor susceptibility

(2012) Dewi Astuti et al.   NATURE GENETICS

NMD: a multifaceted response to premature translational termination

(2012) Stephanie Kervestin et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Yeast Rrp8p, a novel methyltransferase responsible for m1A 645 base modification of 25S rRNA

(2012) Christian Peifer et al.   NUCLEIC ACIDS RESEARCH

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

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

The yeast rapid tRNA decay pathway competes with elongation factor 1A for substrate tRNAs and acts on tRNAs lacking one or more of several modifications

(2012) J. M. Dewe et al.   RNA

Degradation of mRNAs that lack a stop codon: a decade of nonstop progress

(2012) A. Alejandra Klauer et al.   Wiley Interdisciplinary Reviews-RNA

Dissociation by Pelota, Hbs1 and ABCE1 of mammalian vacant 80S ribosomes and stalled elongation complexes

(2011) Vera P Pisareva et al.   EMBO JOURNAL

The yeast rapid tRNA decay pathway primarily monitors the structural integrity of the acceptor and T-stems of mature tRNA

(2011) J. M. Whipple et al.   GENES & DEVELOPMENT

Structure of the no-go mRNA decay complex Dom34–Hbs1 bound to a stalled 80S ribosome

(2011) Thomas Becker et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

UNG-initiated base excision repair is the major repair route for 5-fluorouracil in DNA, but 5-fluorouracil cytotoxicity depends mainly on RNA incorporation

(2011) Henrik Sahlin Pettersen et al.   NUCLEIC ACIDS RESEARCH

The eukaryotic RNA exosome: Same scaffold but variable catalytic subunits

(2011) Søren Lykke-Andersen et al.   RNA Biology

Implication of Ccr4-Not complex function in mRNA quality control in Saccharomyces cerevisiae

(2011) J. Assenholt et al.   RNA

tRNAs Marked with CCACCA Are Targeted for Degradation

(2011) J. E. Wilusz et al.   SCIENCE

Overview of Base Excision Repair Biochemistry

(2011) Yun-Jeong Kim et al.   Current Molecular Pharmacology

Loss of Function of the Tumor Suppressor DKC1 Perturbs p27 Translation Control and Contributes to Pituitary Tumorigenesis

(2010) C. Bellodi et al.   CANCER RESEARCH

Deregulation of oncogene-induced senescence and p53 translational control in X-linked dyskeratosis congenita

(2010) Cristian Bellodi et al.   EMBO JOURNAL

Structure of the Dom34–Hbs1 complex and implications for no-go decay

(2010) Liming Chen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Dissection of Dom34–Hbs1 reveals independent functions in two RNA quality control pathways

(2010) Antonia M G van den Elzen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The RNA modification database, RNAMDB: 2011 update

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

Dom34:Hbs1 Promotes Subunit Dissociation and Peptidyl-tRNA Drop-Off to Initiate No-Go Decay

(2010) C. J. Shoemaker et al.   SCIENCE

No-go decay: a quality control mechanism for RNA in translation

(2010) Yuriko Harigaya et al.   Wiley Interdisciplinary Reviews-RNA

Effect of a quaternary pentamine on RNA stabilization and enzymatic methylation

(2009) Armine Hayrapetyan et al.   BIOLOGICAL CHEMISTRY

APE1/Ref-1 Interacts with NPM1 within Nucleoli and Plays a Role in the rRNA Quality Control Process

(2009) C. Vascotto et al.   MOLECULAR AND CELLULAR BIOLOGY

Analysis of Dom34 and Its Function in No-Go Decay

(2009) Dario O. Passos et al.   MOLECULAR BIOLOGY OF THE CELL

A Convergence of rRNA and mRNA Quality Control Pathways Revealed by Mechanistic Analysis of Nonfunctional rRNA Decay

(2009) Sarah E. Cole et al.   MOLECULAR CELL

The CCR4-NOT Complex Physically and Functionally Interacts with TRAMP and the Nuclear Exosome

(2009) Nowel Azzouz et al.   PLoS One

Specific roles for the Ccr4-Not complex subunits in expression of the genome

(2009) N. Azzouz et al.   RNA

Upf1 Phosphorylation Triggers Translational Repression during Nonsense-Mediated mRNA Decay

(2008) Olaf Isken et al.   CELL

RNA cytosine methylation analysis by bisulfite sequencing

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