Dihydrouridine in the Transcriptome: New Life for This Ancient RNA Chemical Modification

Chemical modifications to mRNA nucleobases impact translation elongation and termination

(2022) Monika K. Franco et al.   BIOPHYSICAL CHEMISTRY

Human transfer RNA modopathies: diseases caused by aberrations in transfer RNA modifications

(2021) Takeshi Chujo et al.   FEBS Journal

The expanding world of tRNA modifications and their disease relevance

(2021) Tsutomu Suzuki   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Dihydrouridine synthesis in tRNAs is under reductive evolution in mollicutes

(2021) Bruno Faivre et al.   RNA Biology

Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing

(2021) Oguzhan Begik et al.   NATURE BIOTECHNOLOGY

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Highly accurate protein structure prediction for the human proteome

(2021) Kathryn Tunyasuvunakool et al.   NATURE

Activity-based RNA-modifying enzyme probing reveals DUS3L-mediated dihydrouridylation

(2021) Wei Dai et al.   Nature Chemical Biology

AlphaFold2 and the future of structural biology

(2021) Patrick Cramer   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Modifications of the human tRNA anticodon loop and their associations with genetic diseases

(2021) Jing-Bo Zhou et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Transcription-wide mapping of dihydrouridine reveals that mRNA dihydrouridylation is required for meiotic chromosome segregation

(2021) Olivier Finet et al.   MOLECULAR CELL

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

(2021) Mihaly Varadi et al.   NUCLEIC ACIDS RESEARCH

RNA nucleotide methylation: 2021 update

(2021) Yuri Motorin et al.   Wiley Interdisciplinary Reviews-RNA

RNA modifications and cancer

(2020) Phensinee Haruehanroengra et al.   RNA Biology

Reductive Evolution and Diversification of C5-Uracil Methylation in the Nucleic Acids of Mollicutes

(2020) Pascal Sirand-Pugnet et al.   Biomolecules

DUS4L Silencing Suppresses Cell Proliferation and Promotes Apoptosis in Human Lung Adenocarcinoma Cell Line A549

(2020) Zheng Li et al.   Cancer Management and Research

The search for a PKR code — Differential regulation of Protein Kinase R activity by diverse RNA and protein regulators

(2019) Charles Bou-Nader et al.   RNA

Conformational Stability Adaptation of a Double-Stranded RNA-Binding Domain to Transfer RNA Ligand

(2019) Charles Bou-Nader et al.   BIOCHEMISTRY

To be or not to be modified: Miscellaneous aspects influencing nucleotide modifications in tRNAs

(2019) Pierre Barraud et al.   IUBMB LIFE

RNA modifications regulating cell fate in cancer

(2019) Sylvain Delaunay et al.   NATURE CELL BIOLOGY

Genome-wide identification of mRNA 5-methylcytosine in mammals

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

Identification and Quantification of Modified Nucleosides in Saccharomyces cerevisiae mRNAs

(2019) Mehmet Tardu et al.   ACS Chemical Biology

AlkB Homologue 1 Demethylates N3-Methylcytidine in mRNA of Mammals

(2019) Cheng-Jie Ma et al.   ACS Chemical Biology

Time-resolved NMR monitoring of tRNA maturation

(2019) Pierre Barraud et al.   Nature Communications

Protein kinase R and its cellular regulators in cancer: An active player or a surveillant?

(2019) Yong Sun Lee et al.   Wiley Interdisciplinary Reviews-RNA

Recognition of RNA N6-methyladenosine by IGF2BP proteins enhances mRNA stability and translation

(2018) Huilin Huang et al.   NATURE CELL BIOLOGY

RNA-modifying proteins as anticancer drug targets

(2018) P. Ann Boriack-Sjodin et al.   NATURE REVIEWS DRUG DISCOVERY

Mapping of ribosomal 23S ribosomal RNA modifications in Clostridium sporogenes.

(2018) Finn Kirpekar et al.   RNA Biology

A rationale for tRNA modification circuits in the anticodon loop

(2018) Lu Han et al.   RNA

Improving RNA modification mapping sequence coverage by LC-MS through a nonspecific RNase U2-E49A mutant

(2018) Beulah Solivio et al.   ANALYTICA CHIMICA ACTA

AlkAniline-Seq: Profiling of m7 G and m3 C RNA Modifications at Single Nucleotide Resolution

(2018) Virginie Marchand et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Acetylation of Cytidine in mRNA Promotes Translation Efficiency

(2018) Daniel Arango et al.   CELL

Molecular basis for transfer RNA recognition by the double-stranded RNA-binding domain of human dihydrouridine synthase 2

(2018) Charles Bou-Nader et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Modi Safra et al.   GENOME RESEARCH

Base-Resolution Mapping Reveals Distinct m 1 A Methylome in Nuclear- and Mitochondrial-Encoded Transcripts

(2017) Xiaoyu Li et al.   MOLECULAR CELL

Editing and methylation at a single site by functionally interdependent activities

(2017) Mary Anne T. Rubio et al.   NATURE

The m1A landscape on cytosolic and mitochondrial mRNA at single-base resolution

(2017) Modi Safra et al.   NATURE

Detecting RNA modifications in the epitranscriptome: predict and validate

(2017) Mark Helm et al.   NATURE REVIEWS GENETICS

Unveiling structural and functional divergences of bacterial tRNA dihydrouridine synthases: perspectives on the evolution scenario

(2017) Charles Bou-Nader et al.   NUCLEIC ACIDS RESEARCH

Recurrent fusion RNA DUS4L-BCAP29 in non-cancer human tissues and cells

(2017) Yue Tang et al.   Oncotarget

Discriminating Self and Non-Self by RNA: Roles for RNA Structure, Misfolding, and Modification in Regulating the Innate Immune Sensor PKR

(2016) Chelsea M. Hull et al.   ACCOUNTS OF CHEMICAL RESEARCH

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

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

(2016) Michaela Frye et al.   NATURE REVIEWS GENETICS

Post-transcriptional gene regulation by mRNA modifications

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

Correlation between the stability of tRNA tertiary structure and the catalytic efficiency of a tRNA-modifying enzyme, archaeal tRNA-guanine transglycosylase

(2015) Yuichiro Nomura et al.   GENES TO CELLS

In vitrodihydrouridine formation by tRNA dihydrouridine synthase fromThermus thermophilus, an extreme-thermophilic eubacterium

(2015) Hiroaki Kusuba et al.   JOURNAL OF BIOCHEMISTRY

Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome

(2015) Xiaoyu Li et al.   Nature Chemical Biology

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

(2015) Aaron E Cozen et al.   NATURE METHODS

An extended dsRBD is required for post-transcriptional modification in human tRNAs

(2015) Charles Bou-Nader et al.   NUCLEIC ACIDS RESEARCH

Contribution of dihydrouridine in folding of the D-arm in tRNA

(2015) N. Dyubankova et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Major reorientation of tRNA substrates defines specificity of dihydrouridine synthases

(2015) Robert T. Byrne et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

From bacterial to human dihydrouridine synthase: automated structure determination

(2015) Fiona Whelan et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

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

(2015) Felix Spenkuch et al.   RNA Biology

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

(2014) Schraga Schwartz et al.   CELL

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

(2014) Thomas M. Carlile et al.   NATURE

Quantitative analysis of ribonucleoside modifications in tRNA by HPLC-coupled mass spectrometry

(2014) Dan Su et al.   Nature Protocols

Dynamics of RNA modification by a multi-site-specific tRNA methyltransferase

(2014) Djemel Hamdane et al.   NUCLEIC ACIDS RESEARCH

A complete landscape of post-transcriptional modifications in mammalian mitochondrial tRNAs

(2014) T. Suzuki 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

A bimodular nuclear localization signal assembled via an extended double-stranded RNA-binding domain acts as an RNA-sensing signal for transportin 1

(2014) P. Barraud et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial noncoding Y RNAs are widespread and mimic tRNAs

(2014) Xinguo Chen et al.   RNA

Structure of dihydrouridine synthase C (DusC) fromEscherichia coli

(2013) Minghao Chen et al.   Acta Crystallographica Section F-Structural Biology and Crystallization Communications

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

(2013) Mark Helm et al.   CHEMISTRY & BIOLOGY

Methylation Modifications in Eukaryotic Messenger RNA

(2013) Jun Liu et al.   Journal of Genetics and Genomics

N6-methyladenosine-dependent regulation of messenger RNA stability

(2013) Xiao Wang et al.   NATURE

Novel fusion transcripts in human gastric cancer revealed by transcriptome analysis

(2013) H-P Kim et al.   ONCOGENE

N6-methyl-adenosine modification in messenger and long non-coding RNA

(2013) Tao Pan   TRENDS IN BIOCHEMICAL SCIENCES

Biosynthesis and Function of Posttranscriptional Modifications of Transfer RNAs

(2012) Basma El Yacoubi et al.   Annual Review of Genetics

Enzymology of tRNA modification in the bacterial MnmEG pathway

(2012) M.-Eugenia Armengod et al.   BIOCHIMIE

Molecular evolution of dihydrouridine synthases

(2012) Joanna M Kasprzak et al.   BMC BIOINFORMATICS

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

(2012) Kate D. Meyer et al.   CELL

RNA recognition by double-stranded RNA binding domains: a matter of shape and sequence

(2012) Grégoire Masliah et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

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

The human tRNA m5C methyltransferase Misu is multisite-specific

(2012) Sylvie Auxilien et al.   RNA Biology

Reversible RNA adenosine methylation in biological regulation

(2012) Guifang Jia et al.   TRENDS IN GENETICS

Transfer RNA modifications: nature's combinatorial chemistry playground

(2012) Jane E. Jackman et al.   Wiley Interdisciplinary Reviews-RNA

A Catalytic Intermediate and Several Flavin Redox States Stabilized by Folate-Dependent tRNA Methyltransferase fromBacillus subtilis

(2011) Djemel Hamdane et al.   BIOCHEMISTRY

An extended dsRBD with a novel zinc-binding motif mediates nuclear retention of fission yeast Dicer

(2011) Pierre Barraud et al.   EMBO JOURNAL

3-(3-amino-3-carboxypropyl)-5,6-Dihydrouridine is one of two novel post-transcriptional modifications in tRNALys(UUU) from Trypanosoma brucei

(2011) Jesper S. Krog et al.   FEBS Journal

Insights into Folate/FAD-dependent tRNA Methyltransferase Mechanism

(2011) Djemel Hamdane et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

N6-Methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO

(2011) Guifang Jia et al.   Nature Chemical Biology

Molecular basis of dihydrouridine formation on tRNA

(2011) F. Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fluorescent labeling of tRNA dihydrouridine residues: Mechanism and distribution

(2011) J. Kaur et al.   RNA

The Solution Structure of the ADAR2 dsRBM-RNA Complex Reveals a Sequence-Specific Readout of the Minor Groove

(2010) Richard Stefl et al.   CELL

Deciphering synonymous codons in the three domains of life: Co-evolution with specific tRNA modification enzymes

(2009) Henri Grosjean et al.   FEBS LETTERS

Mechanism of Dihydrouridine Synthase 2 from Yeast and the Importance of Modifications for Efficient tRNA Reduction

(2009) Lance W. Rider et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Mitochondrial Protein Compendium Elucidates Complex I Disease Biology

(2008) David J. Pagliarini et al.   CELL

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

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

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