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

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

(2014) Schraga Schwartz et al.   CELL

Profiling of RNA modifications by multiplexed stable isotope labelling

(2014) Stefanie Kellner et al.   CHEMICAL COMMUNICATIONS

28S rRNA is inducibly pseudouridylated by the mTOR pathway translational control in CHO cell cultures

(2014) Franck C. Courtes et al.   JOURNAL OF BIOTECHNOLOGY

Quantitative Analysis of rRNA Modifications Using Stable Isotope Labeling and Mass Spectrometry

(2014) Anna M. Popova 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

Crystal structure of a 4-thiouridine synthetase–RNA complex reveals specificity of tRNA U8 modification

(2014) Piotr Neumann et al.   NUCLEIC ACIDS RESEARCH

Partial Methylation at Am100 in 18S rRNA of Baker's Yeast Reveals Ribosome Heterogeneity on the Level of Eukaryotic rRNA Modification

(2014) Markus Buchhaupt et al.   PLoS One

Steroid Receptor RNA Activator (SRA) Modification by the Human Pseudouridine Synthase 1 (hPus1p): RNA Binding, Activity, and Atomic Model

(2014) Tiphaine Huet et al.   PLoS One

A Pseudouridine Residue in the Spliceosome Core Is Part of the Filamentous Growth Program in Yeast

(2014) Anindita Basak et al.   Cell Reports

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

(2013) Mark Helm et al.   CHEMISTRY & BIOLOGY

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

In Human Pseudouridine Synthase 1 (hPus1), a C-Terminal Helical Insert Blocks tRNA from Binding in the Same Orientation as in the Pus1 Bacterial Homologue TruA, Consistent with Their Different Target Selectivities

(2013) Nadine Czudnochowski et al.   JOURNAL OF MOLECULAR BIOLOGY

tRNA Binding, Positioning, and Modification by the Pseudouridine Synthase Pus10

(2013) Rajashekhar Kamalampeta et al.   JOURNAL OF MOLECULAR BIOLOGY

Transfection of pseudouridine-modified mRNA encoding CPD-photolyase leads to repair of DNA damage in human keratinocytes: A new approach with future therapeutic potential

(2013) Gábor Boros et al.   JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY

Unusual base pairing during the decoding of a stop codon by the ribosome

(2013) Israel S. Fernández et al.   NATURE

An arginine-aspartate network in the active site of bacterial TruB is critical for catalyzing pseudouridine formation

(2013) J. Friedt et al.   NUCLEIC ACIDS RESEARCH

The mechanism of pseudouridine synthases from a covalent complex with RNA, and alternate specificity for U2605 versus U2604 between close homologs

(2013) Nadine Czudnochowski et al.   NUCLEIC ACIDS RESEARCH

Structure modulation of helix 69 from Escherichia coli 23S ribosomal RNA by pseudouridylations

(2013) Jun Jiang et al.   NUCLEIC ACIDS RESEARCH

The contribution of pseudouridine to stabilities and structure of RNAs

(2013) Elzbieta Kierzek et al.   NUCLEIC ACIDS RESEARCH

Comparative Study of Two Box H/ACA Ribonucleoprotein Pseudouridine-Synthases: Relation between Conformational Dynamics of the Guide RNA, Enzyme Assembly and Activity

(2013) Jean-Baptiste Fourmann et al.   PLoS One

Structural basis for C-ribosylation in the alnumycin A biosynthetic pathway

(2013) Terhi Oja et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Thermodynamic contribution and nearest-neighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides

(2013) G. A. Hudson et al.   RNA

Role of forefinger and thumb loops in production of  54 and  55 in tRNAs by archaeal Pus10

(2013) A. Joardar et al.   RNA

RNA pseudouridylation: new insights into an old modification

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

Role of Pseudouridine in Structural Rearrangements of Helix 69 During Bacterial Ribosome Assembly

(2012) Yogo Sakakibara et al.   ACS Chemical Biology

Isotope-Based Analysis of Modified tRNA Nucleosides Correlates Modification Density with Translational Efficiency

(2012) Caterina Brandmayr et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Ligand- and pH-Induced Conformational Changes of RNA Domain Helix 69 Revealed by 2-Aminopurine Fluorescence

(2012) Yogo Sakakibara et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Pseudouridine Monophosphate Glycosidase: A New Glycosidase Mechanism

(2012) Siyu Huang et al.   BIOCHEMISTRY

Different sensitivity of H69 modification enzymes RluD and RlmH to mutations in Escherichia coli 23S rRNA

(2012) Margus Leppik et al.   BIOCHIMIE

Increased tRNA modification and gene-specific codon usage regulate cell cycle progression during the DNA damage response

(2012) Ashish Patil et al.   CELL CYCLE

Increased Erythropoiesis in Mice Injected With Submicrogram Quantities of Pseudouridine-containing mRNA Encoding Erythropoietin

(2012) Katalin Karikó et al.   MOLECULAR THERAPY

Kinetic and thermodynamic characterization of the reaction pathway of box H/ACA RNA-guided pseudouridine formation

(2012) X. Yang et al.   NUCLEIC ACIDS RESEARCH

MODOMICS: a database of RNA modification pathways—2013 update

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

Identification of the enzyme responsible for N1-methylation of pseudouridine 54 in archaeal tRNAs

(2012) J. P. Wurm et al.   RNA

Rationalization and prediction of selective decoding of pseudouridine-modified nonsense and sense codons

(2012) M. Parisien et al.   RNA

Archaeal proteins Nop10 and Gar1 increase the catalytic activity of Cbf5 in pseudouridylating tRNA

(2012) Rajashekhar Kamalampeta et al.   Scientific Reports

Human Mitochondrial tRNAs: Biogenesis, Function, Structural Aspects, and Diseases

(2011) Tsutomu Suzuki et al.   Annual Review of Genetics

Uridine Phosphorylase fromTrypanosoma cruzi: Kinetic and Chemical Mechanisms

(2011) Rafael G. Silva et al.   BIOCHEMISTRY

Pseudouridylation of 23S rRNA helix 69 promotes peptide release by release factor RF2 but not by release factor RF1

(2011) Kalle Kipper et al.   BIOCHIMIE

Comparison of solution conformations and stabilities of modified helix 69 rRNA analogs from bacteria and human

(2011) Minako Sumita et al.   BIOPOLYMERS

Single-Molecule FRET Reveals a Cooperative Effect of Two Methyl Group Modifications in the Folding of Human Mitochondrial tRNALys

(2011) Andrei Yu Kobitski et al.   CHEMISTRY & BIOLOGY

Reconstitution and structural analysis of the yeast box H/ACA RNA-guided pseudouridine synthase

(2011) S. Li et al.   GENES & DEVELOPMENT

Conformation Effects of Base Modification on the Anticodon Stem–Loop of Bacillus subtilis tRNATyr

(2011) Andria P. Denmon et al.   JOURNAL OF MOLECULAR BIOLOGY

Human tRNALys3UUU Is Pre-Structured by Natural Modifications for Cognate and Wobble Codon Binding through Keto–Enol Tautomerism

(2011) Franck A.P. Vendeix et al.   JOURNAL OF MOLECULAR BIOLOGY

Probing Conformational States of Modified Helix 69 in 50S Ribosomes

(2011) Yogo Sakakibara et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Products of 5-Fluorouridine by the Action of the Pseudouridine Synthase TruB Disfavor One Mechanism and Suggest Another

(2011) Edward J. Miracco et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Mass Spectrometry-Based Quantification of Pseudouridine in RNA

(2011) Balasubrahmanyam Addepalli et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Pseudouridine synthase 1: a site-specific synthase without strict sequence recognition requirements

(2011) B. S. Sibert et al.   NUCLEIC ACIDS RESEARCH

Nucleoside modifications in RNA limit activation of 2'-5'-oligoadenylate synthetase and increase resistance to cleavage by RNase L

(2011) B. R. Anderson et al.   NUCLEIC ACIDS RESEARCH

Pre-steady-state kinetic analysis of the three Escherichia coli pseudouridine synthases TruB, TruA, and RluA reveals uniformly slow catalysis

(2011) J. R. Wright et al.   RNA

Pseudouridine formation in archaeal RNAs: The case of Haloferax volcanii

(2011) I. K. Blaby et al.   RNA

RNA nucleotide methylation

(2011) Yuri Motorin et al.   Wiley Interdisciplinary Reviews-RNA

Functions and mechanisms of spliceosomal small nuclear RNA pseudouridylation

(2011) Guowei Wu et al.   Wiley Interdisciplinary Reviews-RNA

HDHD1, which is often deleted in X-linked ichthyosis, encodes a pseudouridine-5′-phosphatase

(2010) Alice Preumont et al.   BIOCHEMICAL JOURNAL

tRNA Stabilization by Modified Nucleotides

(2010) Yuri Motorin et al.   BIOCHEMISTRY

Highly Efficient Reprogramming to Pluripotency and Directed Differentiation of Human Cells with Synthetic Modified mRNA

(2010) Luigi Warren et al.   Cell Stem Cell

U2 snRNA is inducibly pseudouridylated at novel sites by Pus7p and snR81 RNP

(2010) Guowei Wu et al.   EMBO JOURNAL

Identification, localization, and relative quantitation of pseudouridine in RNA by tandem mass spectrometry of hydrolysis products

(2010) Monika Taucher et al.   INTERNATIONAL JOURNAL OF MASS SPECTROMETRY

A Flexible RNA Backbone within the Polypyrimidine Tract Is Required for U2AF65 Binding and Pre-mRNA Splicing In Vivo

(2010) C. Chen et al.   MOLECULAR AND CELLULAR 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

Pseudouridine at position 55 in tRNA controls the contents of other modified nucleotides for low-temperature adaptation in the extreme-thermophilic eubacterium Thermus thermophilus

(2010) Kazuo Ishida et al.   NUCLEIC ACIDS RESEARCH

Structural insight into the functional mechanism of Nep1/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis

(2010) Seth R. Thomas et al.   NUCLEIC ACIDS RESEARCH

The ribosome assembly factor Nep1 responsible for Bowen–Conradi syndrome is a pseudouridine-N1-specific methyltransferase

(2010) Jan Philip Wurm et al.   NUCLEIC ACIDS RESEARCH

The Bowen–Conradi syndrome protein Nep1 (Emg1) has a dual role in eukaryotic ribosome biogenesis, as an essential assembly factor and in the methylation of Ψ1191 in yeast 18S rRNA

(2010) Britta Meyer et al.   NUCLEIC ACIDS RESEARCH

Incorporation of pseudouridine into mRNA enhances translation by diminishing PKR activation

(2010) Bart R. Anderson et al.   NUCLEIC ACIDS RESEARCH

Spliceosomal snRNA modifications and their function

(2010) John Karijolich et al.   RNA Biology

Differential effects of nucleotide analogs on scanning-dependent initiation and elongation of mammalian mRNA translation in vitro

(2010) J. L. Aspden et al.   RNA

Specificity and kinetics of 23S rRNA modification enzymes RlmH and RluD

(2010) R. Ero et al.   RNA

Mutation of a Gene Essential for Ribosome Biogenesis, EMG1, Causes Bowen-Conradi Syndrome

(2009) Joy Armistead et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Enzymatic characterization and mutational studies of TruD – the fifth family of pseudouridine synthases

(2009) Chio Mui Chan et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

The Box H/ACA Ribonucleoprotein Complex: Interplay of RNA and Protein Structures in Post-transcriptional RNA Modification

(2009) Tomoko Hamma et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Crystal Structure of an RluF–RNA Complex: A Base-Pair Rearrangement Is the Key to Selectivity of RluF for U2604 of the Ribosome

(2009) Akram Alian et al.   JOURNAL OF MOLECULAR BIOLOGY

Nucleotide modifications in three functionally important regions of the Saccharomyces cerevisiae ribosome affect translation accuracy

(2009) Agnès Baudin-Baillieu et al.   NUCLEIC ACIDS RESEARCH

Deficiency of the tRNA Tyr :Ψ35-synthase aPus7 in Archaea of the Sulfolobales order might be rescued by the H/ACA sRNA-guided machinery

(2009) Sébastien Muller et al.   NUCLEIC ACIDS RESEARCH

Loss of rRNA modifications in the decoding center of the ribosome impairs translation and strongly delays pre-rRNA processing

(2009) X.-h. Liang et al.   RNA

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

(2008) Anita Durairaj et al.   ANALYTICA CHIMICA ACTA

X-ray Structures of U2 snRNA−Branchpoint Duplexes Containing Conserved Pseudouridines†‡

(2008) Yuan Lin et al.   BIOCHEMISTRY

RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes

(2008) Henri Grosjean et al.   BMC GENOMICS

RNA Sequence and Two-dimensional Structure Features Required for Efficient Substrate Modification by theSaccharomyces cerevisiaeRNA:Ψ-Synthase Pus7p

(2008) Alan Urban et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Molecular Identification of Pseudouridine-metabolizing Enzymes

(2008) Alice Preumont et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Different Mechanisms for Pseudouridine Formation in Yeast 5S and 5.8S rRNAs

(2008) W. A. Decatur et al.   MOLECULAR AND CELLULAR BIOLOGY

Incorporation of Pseudouridine Into mRNA Yields Superior Nonimmunogenic Vector With Increased Translational Capacity and Biological Stability

(2008) Katalin Karikó et al.   MOLECULAR THERAPY

Pseudouridines in rRNA helix 69 play a role in loop stacking interactions

(2008) Jean-Paul Desaulniers et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

pH-dependent structural changes of helix 69 from Escherichia coli 23S ribosomal RNA

(2008) S. C. Abeysirigunawardena et al.   RNA

Identification of pseudouridine methyltransferase in Escherichia coli

(2008) R. Ero et al.   RNA

Partial activity is seen with many substitutions of highly conserved active site residues in human Pseudouridine synthase 1

(2008) B. S. Sibert et al.   RNA

Long-distance placement of substrate RNA by H/ACA proteins

(2008) B. Liang et al.   RNA

YbeA is the m3  methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA

(2008) E. Purta et al.   RNA

Archaeal Pus10 proteins can produce both pseudouridine 54 and 55 in tRNA

(2008) P. Gurha et al.   RNA

Functionality and substrate specificity of human box H/ACA guide RNAs

(2008) M. Xiao et al.   RNA